[med-svn] r9492 - in trunk/packages: R/r-cran-bitops/trunk/debian R/r-cran-combinat/trunk/debian R/r-cran-epitools/trunk/debian R/r-cran-g.data/trunk/debian R/r-cran-genabel/trunk/debian R/r-cran-haplo.stats/trunk/debian R/r-cran-qtl/trunk/debian R/r-cran-qvalue/trunk/debian R/r-cran-randomforest/trunk/debian R/r-cran-rocr/trunk/debian R/r-cran-sparsem/trunk/debian R/r-other-bio3d/trunk/debian R/r-other-mott-happy/trunk/debian acedb/trunk/debian adun.app/trunk/debian alien-hunter/trunk/debian altree/trunk/debian autodock-vina/trunk/debian autodocksuite/trunk/debian biomaj/trunk/debian bioperl/trunk/debian blat/trunk/debian cd-hit/trunk/debian circos/trunk/debian clonalframe/trunk/debian clustalo/trunk/debian coils/trunk/debian dialign/trunk/debian dialign-t/trunk/debian dicomscope/trunk/debian elastix/trunk/debian epigrass/trunk/debian exonerate/trunk/debian gassst/trunk/debian glam2/trunk/debian hhsuite/trunk/debian hmmer/trunk/debian infernal/trunk/debian kalign/trunk/debian last-align/trunk/debian libhmsbeagle/trunk/debian libtfbs-perl/trunk/debian mafft/trunk/debian maq/trunk/debian maude/trunk/debian melting/trunk/debian mgltools/autodocktools/trunk/debian mipe/trunk/debian mira/trunk/debian mothur/trunk/debian mummer/trunk/debian mustang/trunk/debian phy-spread/trunk/debian phyml/trunk/debian poa/trunk/debian primer3/trunk/debian probalign/trunk/debian probcons/trunk/debian proda/trunk/debian python-pynast/trunk/debian qiime/trunk/debian raster3d/trunk/debian raxml/trunk/debian rnahybrid/trunk/debian rostlab/disulfinder/trunk/debian rostlab/libzerg/trunk/debian rostlab/libzerg-perl/trunk/debian rostlab/profphd/trunk/debian seaview/trunk/debian seqan/trunk/debian sigma-align/trunk/debian t-coffee/trunk/debian tm-align/trunk/debian transtermhp/trunk/debian treeviewx/trunk/debian velvet/trunk/debian
Charles Plessy
plessy at alioth.debian.org
Sun Jan 29 03:35:59 UTC 2012
Author: plessy
Date: 2012-01-29 03:35:57 +0000 (Sun, 29 Jan 2012)
New Revision: 9492
Added:
trunk/packages/R/r-cran-bitops/trunk/debian/upstream
trunk/packages/R/r-cran-combinat/trunk/debian/upstream
trunk/packages/R/r-cran-epitools/trunk/debian/upstream
trunk/packages/R/r-cran-g.data/trunk/debian/upstream
trunk/packages/R/r-cran-genabel/trunk/debian/upstream
trunk/packages/R/r-cran-haplo.stats/trunk/debian/upstream
trunk/packages/R/r-cran-qtl/trunk/debian/upstream
trunk/packages/R/r-cran-qvalue/trunk/debian/upstream
trunk/packages/R/r-cran-randomforest/trunk/debian/upstream
trunk/packages/R/r-cran-rocr/trunk/debian/upstream
trunk/packages/R/r-cran-sparsem/trunk/debian/upstream
trunk/packages/R/r-other-bio3d/trunk/debian/upstream
trunk/packages/R/r-other-mott-happy/trunk/debian/upstream
trunk/packages/acedb/trunk/debian/upstream
trunk/packages/adun.app/trunk/debian/upstream
trunk/packages/alien-hunter/trunk/debian/upstream
trunk/packages/altree/trunk/debian/upstream
trunk/packages/autodock-vina/trunk/debian/upstream
trunk/packages/autodocksuite/trunk/debian/upstream
trunk/packages/biomaj/trunk/debian/upstream
trunk/packages/bioperl/trunk/debian/upstream
trunk/packages/blat/trunk/debian/upstream
trunk/packages/cd-hit/trunk/debian/upstream
trunk/packages/circos/trunk/debian/upstream
trunk/packages/clonalframe/trunk/debian/upstream
trunk/packages/clustalo/trunk/debian/upstream
trunk/packages/coils/trunk/debian/upstream
trunk/packages/dialign-t/trunk/debian/upstream
trunk/packages/dialign/trunk/debian/upstream
trunk/packages/dicomscope/trunk/debian/upstream
trunk/packages/elastix/trunk/debian/upstream
trunk/packages/epigrass/trunk/debian/upstream
trunk/packages/exonerate/trunk/debian/upstream
trunk/packages/gassst/trunk/debian/upstream
trunk/packages/glam2/trunk/debian/upstream
trunk/packages/hhsuite/trunk/debian/upstream
trunk/packages/hmmer/trunk/debian/upstream
trunk/packages/infernal/trunk/debian/upstream
trunk/packages/kalign/trunk/debian/upstream
trunk/packages/last-align/trunk/debian/upstream
trunk/packages/libhmsbeagle/trunk/debian/upstream
trunk/packages/libtfbs-perl/trunk/debian/upstream
trunk/packages/mafft/trunk/debian/upstream
trunk/packages/maq/trunk/debian/upstream
trunk/packages/maude/trunk/debian/upstream
trunk/packages/melting/trunk/debian/upstream
trunk/packages/mgltools/autodocktools/trunk/debian/upstream
trunk/packages/mipe/trunk/debian/upstream
trunk/packages/mira/trunk/debian/upstream
trunk/packages/mothur/trunk/debian/upstream
trunk/packages/mummer/trunk/debian/upstream
trunk/packages/mustang/trunk/debian/upstream
trunk/packages/phy-spread/trunk/debian/upstream
trunk/packages/phyml/trunk/debian/upstream
trunk/packages/poa/trunk/debian/upstream
trunk/packages/primer3/trunk/debian/upstream
trunk/packages/probalign/trunk/debian/upstream
trunk/packages/probcons/trunk/debian/upstream
trunk/packages/proda/trunk/debian/upstream
trunk/packages/python-pynast/trunk/debian/upstream
trunk/packages/qiime/trunk/debian/upstream
trunk/packages/raster3d/trunk/debian/upstream
trunk/packages/raxml/trunk/debian/upstream
trunk/packages/rnahybrid/trunk/debian/upstream
trunk/packages/rostlab/disulfinder/trunk/debian/upstream
trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream
trunk/packages/rostlab/libzerg/trunk/debian/upstream
trunk/packages/rostlab/profphd/trunk/debian/upstream
trunk/packages/seaview/trunk/debian/upstream
trunk/packages/seqan/trunk/debian/upstream
trunk/packages/sigma-align/trunk/debian/upstream
trunk/packages/t-coffee/trunk/debian/upstream
trunk/packages/tm-align/trunk/debian/upstream
trunk/packages/transtermhp/trunk/debian/upstream
trunk/packages/treeviewx/trunk/debian/upstream
trunk/packages/velvet/trunk/debian/upstream
Removed:
trunk/packages/R/r-cran-bitops/trunk/debian/upstream-metadata.yaml
trunk/packages/R/r-cran-combinat/trunk/debian/upstream-metadata.yaml
trunk/packages/R/r-cran-epitools/trunk/debian/upstream-metadata.yaml
trunk/packages/R/r-cran-g.data/trunk/debian/upstream-metadata.yaml
trunk/packages/R/r-cran-genabel/trunk/debian/upstream-metadata.yaml
trunk/packages/R/r-cran-haplo.stats/trunk/debian/upstream-metadata.yaml
trunk/packages/R/r-cran-qtl/trunk/debian/upstream-metadata.yaml
trunk/packages/R/r-cran-qvalue/trunk/debian/upstream-metadata.yaml
trunk/packages/R/r-cran-randomforest/trunk/debian/upstream-metadata.yaml
trunk/packages/R/r-cran-rocr/trunk/debian/upstream-metadata.yaml
trunk/packages/R/r-cran-sparsem/trunk/debian/upstream-metadata.yaml
trunk/packages/R/r-other-bio3d/trunk/debian/upstream-metadata.yaml
trunk/packages/R/r-other-mott-happy/trunk/debian/upstream-metadata.yaml
trunk/packages/acedb/trunk/debian/upstream-metadata.yaml
trunk/packages/adun.app/trunk/debian/upstream-metadata.yaml
trunk/packages/alien-hunter/trunk/debian/upstream-metadata.yaml
trunk/packages/altree/trunk/debian/upstream-metadata.yaml
trunk/packages/autodock-vina/trunk/debian/upstream-metadata.yaml
trunk/packages/autodocksuite/trunk/debian/upstream-metadata.yaml
trunk/packages/biomaj/trunk/debian/upstream-metadata.yaml
trunk/packages/bioperl/trunk/debian/upstream-metadata.yaml
trunk/packages/blat/trunk/debian/upstream-metadata.yaml
trunk/packages/cd-hit/trunk/debian/upstream-metadata.yaml
trunk/packages/circos/trunk/debian/upstream-metadata.yaml
trunk/packages/clonalframe/trunk/debian/upstream-metadata.yaml
trunk/packages/clustalo/trunk/debian/upstream-metadata.yaml
trunk/packages/coils/trunk/debian/upstream-metadata.yaml
trunk/packages/dialign-t/trunk/debian/upstream-metadata.yaml
trunk/packages/dialign/trunk/debian/upstream-metadata.yaml
trunk/packages/dicomscope/trunk/debian/upstream-metadata.yaml
trunk/packages/elastix/trunk/debian/upstream-metadata.yaml
trunk/packages/epigrass/trunk/debian/upstream-metadata.yaml
trunk/packages/exonerate/trunk/debian/upstream-metadata.yaml
trunk/packages/gassst/trunk/debian/upstream-metadata.yaml
trunk/packages/glam2/trunk/debian/upstream-metadata.yaml
trunk/packages/hhsuite/trunk/debian/upstream-metadata.yaml
trunk/packages/hmmer/trunk/debian/upstream-metadata.yaml
trunk/packages/infernal/trunk/debian/upstream-metadata.yaml
trunk/packages/kalign/trunk/debian/upstream-metadata.yaml
trunk/packages/last-align/trunk/debian/upstream-metadata.yaml
trunk/packages/libhmsbeagle/trunk/debian/upstream-metadata.yaml
trunk/packages/libtfbs-perl/trunk/debian/upstream-metadata.yaml
trunk/packages/mafft/trunk/debian/upstream-metadata.yaml
trunk/packages/maq/trunk/debian/upstream-metadata.yaml
trunk/packages/maude/trunk/debian/upstream-metadata.yaml
trunk/packages/melting/trunk/debian/upstream-metadata.yaml
trunk/packages/mgltools/autodocktools/trunk/debian/upstream-metadata.yaml
trunk/packages/mipe/trunk/debian/upstream-metadata.yaml
trunk/packages/mira/trunk/debian/upstream-metadata.yaml
trunk/packages/mothur/trunk/debian/upstream-metadata.yaml
trunk/packages/mummer/trunk/debian/upstream-metadata.yaml
trunk/packages/mustang/trunk/debian/upstream-metadata.yaml
trunk/packages/phy-spread/trunk/debian/upstream-metadata.yaml
trunk/packages/phyml/trunk/debian/upstream-metadata.yaml
trunk/packages/poa/trunk/debian/upstream-metadata.yaml
trunk/packages/primer3/trunk/debian/upstream-metadata.yaml
trunk/packages/probalign/trunk/debian/upstream-metadata.yaml
trunk/packages/probcons/trunk/debian/upstream-metadata.yaml
trunk/packages/proda/trunk/debian/upstream-metadata.yaml
trunk/packages/python-pynast/trunk/debian/upstream-metadata.yaml
trunk/packages/qiime/trunk/debian/upstream-metadata.yaml
trunk/packages/raster3d/trunk/debian/upstream-metadata.yaml
trunk/packages/raxml/trunk/debian/upstream-metadata.yaml
trunk/packages/rnahybrid/trunk/debian/upstream-metadata.yaml
trunk/packages/rostlab/disulfinder/trunk/debian/upstream-metadata.yaml
trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream-metadata.yaml
trunk/packages/rostlab/libzerg/trunk/debian/upstream-metadata.yaml
trunk/packages/rostlab/profphd/trunk/debian/upstream-metadata.yaml
trunk/packages/seaview/trunk/debian/upstream-metadata.yaml
trunk/packages/seqan/trunk/debian/upstream-metadata.yaml
trunk/packages/sigma-align/trunk/debian/upstream-metadata.yaml
trunk/packages/t-coffee/trunk/debian/upstream-metadata.yaml
trunk/packages/tm-align/trunk/debian/upstream-metadata.yaml
trunk/packages/transtermhp/trunk/debian/upstream-metadata.yaml
trunk/packages/treeviewx/trunk/debian/upstream-metadata.yaml
trunk/packages/velvet/trunk/debian/upstream-metadata.yaml
Log:
Renamed debian/upstream-metadata.yaml to debian/upstream.
Copied: trunk/packages/R/r-cran-bitops/trunk/debian/upstream (from rev 9491, trunk/packages/R/r-cran-bitops/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/R/r-cran-bitops/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-cran-bitops/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,8 @@
+Archive: CRAN
+Contact: Steve Dutky <sdutky at terpalum.umd.edu>
+Download: http://cran.r-project.org/src/contrib/
+Homepage: http://cran.r-project.org/web/packages/bitops/
+Name: bitops
+Watch: |
+ version=3
+ http://cran.r-project.org/src/contrib/bitops_([\d.-]*)\.tar.gz
Deleted: trunk/packages/R/r-cran-bitops/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-cran-bitops/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/R/r-cran-bitops/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,8 +0,0 @@
-Archive: CRAN
-Contact: Steve Dutky <sdutky at terpalum.umd.edu>
-Download: http://cran.r-project.org/src/contrib/
-Homepage: http://cran.r-project.org/web/packages/bitops/
-Name: bitops
-Watch: |
- version=3
- http://cran.r-project.org/src/contrib/bitops_([\d.-]*)\.tar.gz
Copied: trunk/packages/R/r-cran-combinat/trunk/debian/upstream (from rev 9491, trunk/packages/R/r-cran-combinat/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/R/r-cran-combinat/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-cran-combinat/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,6 @@
+Contact: Vince Carey <stvjc at channing.harvard.edu>
+CRAN: combinat
+Download: http://cran.r-project.org/src/contrib/
+Homepage: http://cran.r-project.org/web/packages/combinat/
+Name: combinat
+Watch: http://cran.r-project.org/src/contrib/combinat_([-0-9\.]*)\.tar\.gz
Deleted: trunk/packages/R/r-cran-combinat/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-cran-combinat/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/R/r-cran-combinat/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,6 +0,0 @@
-Contact: Vince Carey <stvjc at channing.harvard.edu>
-CRAN: combinat
-Download: http://cran.r-project.org/src/contrib/
-Homepage: http://cran.r-project.org/web/packages/combinat/
-Name: combinat
-Watch: http://cran.r-project.org/src/contrib/combinat_([-0-9\.]*)\.tar\.gz
Copied: trunk/packages/R/r-cran-epitools/trunk/debian/upstream (from rev 9491, trunk/packages/R/r-cran-epitools/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/R/r-cran-epitools/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-cran-epitools/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,8 @@
+Archive: CRAN
+Contact: Tomas Aragon <aragon at berkeley.edu>
+CRAN: epitools
+Download: http://cran.r-project.org/src/contrib/
+Help: http://groups.yahoo.com/group/epitools/
+Homepage: http://sites.google.com/site/medepi/epitools
+Name: EpiTools
+Watch: http://cran.r-project.org/src/contrib/epitools_([-\d.]*)\.tar\.gz
Deleted: trunk/packages/R/r-cran-epitools/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-cran-epitools/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/R/r-cran-epitools/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,8 +0,0 @@
-Archive: CRAN
-Contact: Tomas Aragon <aragon at berkeley.edu>
-CRAN: epitools
-Download: http://cran.r-project.org/src/contrib/
-Help: http://groups.yahoo.com/group/epitools/
-Homepage: http://sites.google.com/site/medepi/epitools
-Name: EpiTools
-Watch: http://cran.r-project.org/src/contrib/epitools_([-\d.]*)\.tar\.gz
Copied: trunk/packages/R/r-cran-g.data/trunk/debian/upstream (from rev 9491, trunk/packages/R/r-cran-g.data/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/R/r-cran-g.data/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-cran-g.data/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,7 @@
+Archive: http://cran.r-project.org/src/contrib/
+Contact: David Brahm <brahm at alum.mit.edu>
+CRAN: g.data
+Distributor: CRAN
+Homepage: http://cran.r-project.org/web/packages/g.data/
+Name: g.data
+Watch: http://cran.r-project.org/src/contrib/g.data_([-0-9\.]*)\.tar\.gz
Deleted: trunk/packages/R/r-cran-g.data/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-cran-g.data/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/R/r-cran-g.data/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,7 +0,0 @@
-Archive: http://cran.r-project.org/src/contrib/
-Contact: David Brahm <brahm at alum.mit.edu>
-CRAN: g.data
-Distributor: CRAN
-Homepage: http://cran.r-project.org/web/packages/g.data/
-Name: g.data
-Watch: http://cran.r-project.org/src/contrib/g.data_([-0-9\.]*)\.tar\.gz
Copied: trunk/packages/R/r-cran-genabel/trunk/debian/upstream (from rev 9491, trunk/packages/R/r-cran-genabel/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/R/r-cran-genabel/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-cran-genabel/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,21 @@
+Archive: CRAN
+Bug-Database: https://r-forge.r-project.org/tracker/?atid=2058&group_id=505
+Contact: GenABEL developers <genabel.project at gmail.com>
+Name: GenABEL
+Homepage: http://www.genabel.org/
+Reference:
+ author: Aulchenko, Yurii S. and Ripke, Stephan and Isaacs, Aaron and van Duijn, Cornelia M.
+ title: GenABEL: an R library for genome-wide association analysis
+ volume: 23
+ number: 10
+ pages: 1294-1296
+ year: 2007
+ doi: 10.1093/bioinformatics/btm108
+ URL: http://bioinformatics.oxfordjournals.org/content/23/10/1294.abstract
+ eprint: http://bioinformatics.oxfordjournals.org/content/23/10/1294.full.pdf+html
+ journal: Bioinformatics
+ PMID: 17384015
+Repostiory: svn://svn.r-forge.r-project.org/svnroot/genabel
+Repository-Browse: https://r-forge.r-project.org/scm/viewvc.php/?root=genabel
+Watch: |
+ http://cran.r-project.org/src/contrib/GenABEL_(.*)\.tar\.gz
Deleted: trunk/packages/R/r-cran-genabel/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-cran-genabel/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/R/r-cran-genabel/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,21 +0,0 @@
-Archive: CRAN
-Bug-Database: https://r-forge.r-project.org/tracker/?atid=2058&group_id=505
-Contact: GenABEL developers <genabel.project at gmail.com>
-Name: GenABEL
-Homepage: http://www.genabel.org/
-Reference:
- author: Aulchenko, Yurii S. and Ripke, Stephan and Isaacs, Aaron and van Duijn, Cornelia M.
- title: GenABEL: an R library for genome-wide association analysis
- volume: 23
- number: 10
- pages: 1294-1296
- year: 2007
- doi: 10.1093/bioinformatics/btm108
- URL: http://bioinformatics.oxfordjournals.org/content/23/10/1294.abstract
- eprint: http://bioinformatics.oxfordjournals.org/content/23/10/1294.full.pdf+html
- journal: Bioinformatics
- PMID: 17384015
-Repostiory: svn://svn.r-forge.r-project.org/svnroot/genabel
-Repository-Browse: https://r-forge.r-project.org/scm/viewvc.php/?root=genabel
-Watch: |
- http://cran.r-project.org/src/contrib/GenABEL_(.*)\.tar\.gz
Copied: trunk/packages/R/r-cran-haplo.stats/trunk/debian/upstream (from rev 9491, trunk/packages/R/r-cran-haplo.stats/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/R/r-cran-haplo.stats/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-cran-haplo.stats/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,2 @@
+Contact: Jason P. Sinnwell <sinnwell.jason at mayo.edu>
+Homepage: http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm
Deleted: trunk/packages/R/r-cran-haplo.stats/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-cran-haplo.stats/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/R/r-cran-haplo.stats/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,2 +0,0 @@
-Contact: Jason P. Sinnwell <sinnwell.jason at mayo.edu>
-Homepage: http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm
Copied: trunk/packages/R/r-cran-qtl/trunk/debian/upstream (from rev 9491, trunk/packages/R/r-cran-qtl/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/R/r-cran-qtl/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-cran-qtl/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,9 @@
+Homepage: http://www.rqtl.org
+Name: R/qtl: A QTL mapping environment
+Reference:
+ Author: K. W. Broman, H. Wu, S. Sen, G. A. Churchill
+ Title: R/qtl: QTL mapping in experimental crosses.
+ Journal: Bioinformatics
+ Number: 19
+ Pages: 889-890
+ Year: 2003
Deleted: trunk/packages/R/r-cran-qtl/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-cran-qtl/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/R/r-cran-qtl/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,9 +0,0 @@
-Homepage: http://www.rqtl.org
-Name: R/qtl: A QTL mapping environment
-Reference:
- Author: K. W. Broman, H. Wu, S. Sen, G. A. Churchill
- Title: R/qtl: QTL mapping in experimental crosses.
- Journal: Bioinformatics
- Number: 19
- Pages: 889-890
- Year: 2003
Copied: trunk/packages/R/r-cran-qvalue/trunk/debian/upstream (from rev 9491, trunk/packages/R/r-cran-qvalue/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/R/r-cran-qvalue/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-cran-qvalue/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,19 @@
+Bioconductor: http://www.bioconductor.org/packages/bioc/html/qvalue.html
+Contact: John D. Storey <jstorey at u.washington.edu>
+CRAN: http://cran.r-project.org/web/packages/qvalue/
+DOI: 10.1073/pnas.1530509100
+Homepage: http://cran.r-project.org/web/packages/qvalue/
+Name: qvalue
+PMID: 12883005
+Reference:
+ article: John D.Storey08052003
+ author: Storey, John D. and Tibshirani, Robert
+ title: Statistical significance for genomewide studies
+ journal: Proceedings of the National Academy of Sciences of the United States of America
+ volume: 100
+ number: 16
+ pages: 9440-9445
+ doi: 10.1073/pnas.1530509100
+ year: 2003
+ URL: http://www.pnas.org/content/100/16/9440.abstract
+ eprint: http://www.pnas.org/content/100/16/9440.full.pdf+html
Deleted: trunk/packages/R/r-cran-qvalue/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-cran-qvalue/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/R/r-cran-qvalue/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,19 +0,0 @@
-Bioconductor: http://www.bioconductor.org/packages/bioc/html/qvalue.html
-Contact: John D. Storey <jstorey at u.washington.edu>
-CRAN: http://cran.r-project.org/web/packages/qvalue/
-DOI: 10.1073/pnas.1530509100
-Homepage: http://cran.r-project.org/web/packages/qvalue/
-Name: qvalue
-PMID: 12883005
-Reference:
- article: John D.Storey08052003
- author: Storey, John D. and Tibshirani, Robert
- title: Statistical significance for genomewide studies
- journal: Proceedings of the National Academy of Sciences of the United States of America
- volume: 100
- number: 16
- pages: 9440-9445
- doi: 10.1073/pnas.1530509100
- year: 2003
- URL: http://www.pnas.org/content/100/16/9440.abstract
- eprint: http://www.pnas.org/content/100/16/9440.full.pdf+html
Copied: trunk/packages/R/r-cran-randomforest/trunk/debian/upstream (from rev 9491, trunk/packages/R/r-cran-randomforest/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/R/r-cran-randomforest/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-cran-randomforest/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,5 @@
+Archive: http://cran.r-project.org/src/contrib/Archive/randomForest/
+Contact: Andy Liaw <andy_liaw at merck.com>
+CRAN: RandomForest
+Homepage: http://cran.r-project.org/web/packages/randomForest/
+Name: RandomForest
Deleted: trunk/packages/R/r-cran-randomforest/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-cran-randomforest/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/R/r-cran-randomforest/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,5 +0,0 @@
-Archive: http://cran.r-project.org/src/contrib/Archive/randomForest/
-Contact: Andy Liaw <andy_liaw at merck.com>
-CRAN: RandomForest
-Homepage: http://cran.r-project.org/web/packages/randomForest/
-Name: RandomForest
Copied: trunk/packages/R/r-cran-rocr/trunk/debian/upstream (from rev 9491, trunk/packages/R/r-cran-rocr/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/R/r-cran-rocr/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-cran-rocr/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,22 @@
+Contact:
+ - Tobias Sing <tobias.sing at mpi-sb.mpg.de>
+ - Oliver Sander <osander at mpi-sb.mpg.de>
+DOI: 10.1093/bioinformatics/bti623
+Gallery: http://rocr.bioinf.mpi-sb.mpg.de/rocr_gallery.html
+Homepage: http://rocr.bioinf.mpi-sb.mpg.de
+Name: ROCR
+PMID: 16096348
+Reference: |
+ author: Sing, Tobias and Sander, Oliver and Beerenwinkel, Niko and Lengauer, Thomas
+ title: ROCR: visualizing classifier performance in R
+ journal: Bioinformatics
+ volume: 21
+ number: 20
+ pages: 3940-3941
+ year: 2005
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/20/3940
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/21/20/3940.pdf
+Screenshot:
+ - http://rocr.bioinf.mpi-sb.mpg.de/plot1.jpg
+ - http://rocr.bioinf.mpi-sb.mpg.de/plot.jpg
+Watch: http://cran.r-project.org/src/contrib/ROCR_([-0-9\.]*)\.tar\.gz
Deleted: trunk/packages/R/r-cran-rocr/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-cran-rocr/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/R/r-cran-rocr/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,22 +0,0 @@
-Contact:
- - Tobias Sing <tobias.sing at mpi-sb.mpg.de>
- - Oliver Sander <osander at mpi-sb.mpg.de>
-DOI: 10.1093/bioinformatics/bti623
-Gallery: http://rocr.bioinf.mpi-sb.mpg.de/rocr_gallery.html
-Homepage: http://rocr.bioinf.mpi-sb.mpg.de
-Name: ROCR
-PMID: 16096348
-Reference: |
- author: Sing, Tobias and Sander, Oliver and Beerenwinkel, Niko and Lengauer, Thomas
- title: ROCR: visualizing classifier performance in R
- journal: Bioinformatics
- volume: 21
- number: 20
- pages: 3940-3941
- year: 2005
- URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/20/3940
- eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/21/20/3940.pdf
-Screenshot:
- - http://rocr.bioinf.mpi-sb.mpg.de/plot1.jpg
- - http://rocr.bioinf.mpi-sb.mpg.de/plot.jpg
-Watch: http://cran.r-project.org/src/contrib/ROCR_([-0-9\.]*)\.tar\.gz
Copied: trunk/packages/R/r-cran-sparsem/trunk/debian/upstream (from rev 9491, trunk/packages/R/r-cran-sparsem/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/R/r-cran-sparsem/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-cran-sparsem/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,7 @@
+Archive: CRAN
+Contact: roger at ysidro.econ.uiuc.edu, Pin.Ng at nau.edu
+CRAN: SparseM
+Download: http://cran.r-project.org/src/contrib/
+Homepage: http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html
+Name: SparseM
+Watch: http://cran.r-project.org/src/contrib/SparseM_([-\d.]*)\.tar\.gz
Deleted: trunk/packages/R/r-cran-sparsem/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-cran-sparsem/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/R/r-cran-sparsem/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,7 +0,0 @@
-Archive: CRAN
-Contact: roger at ysidro.econ.uiuc.edu, Pin.Ng at nau.edu
-CRAN: SparseM
-Download: http://cran.r-project.org/src/contrib/
-Homepage: http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html
-Name: SparseM
-Watch: http://cran.r-project.org/src/contrib/SparseM_([-\d.]*)\.tar\.gz
Copied: trunk/packages/R/r-other-bio3d/trunk/debian/upstream (from rev 9491, trunk/packages/R/r-other-bio3d/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,18 @@
+Contact: Barry Grant <bgrant at mccammon.ucsd.edu>
+DOI: 10.1093/bioinformatics/btl461
+Gallery: http://mccammon.ucsd.edu/~bgrant/bio3d/gallery/gallery.html
+Homepage: http://mccammon.ucsd.edu/~bgrant/bio3d/
+Name: Bio3D
+PMID: 16940322
+Reference:
+ author: Grant, Barry J. and Rodrigues, Ana P. C. and ElSawy, Karim M. and McCammon, J. Andrew and Caves, Leo S. D.
+ title: Bio3d: an R package for the comparative analysis of protein structures
+ journal: Bioinformatics
+ volume: 22
+ number: 21
+ pages: 2695-2696
+ doi: 10.1093/bioinformatics/btl461
+ year: 2006
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/21/2695
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/21/2695.pdf
+Wiki: http://bio3d.pbworks.com/
Deleted: trunk/packages/R/r-other-bio3d/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,18 +0,0 @@
-Contact: Barry Grant <bgrant at mccammon.ucsd.edu>
-DOI: 10.1093/bioinformatics/btl461
-Gallery: http://mccammon.ucsd.edu/~bgrant/bio3d/gallery/gallery.html
-Homepage: http://mccammon.ucsd.edu/~bgrant/bio3d/
-Name: Bio3D
-PMID: 16940322
-Reference:
- author: Grant, Barry J. and Rodrigues, Ana P. C. and ElSawy, Karim M. and McCammon, J. Andrew and Caves, Leo S. D.
- title: Bio3d: an R package for the comparative analysis of protein structures
- journal: Bioinformatics
- volume: 22
- number: 21
- pages: 2695-2696
- doi: 10.1093/bioinformatics/btl461
- year: 2006
- URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/21/2695
- eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/21/2695.pdf
-Wiki: http://bio3d.pbworks.com/
Copied: trunk/packages/R/r-other-mott-happy/trunk/debian/upstream (from rev 9491, trunk/packages/R/r-other-mott-happy/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,15 @@
+Contact: Richard Mott <Richard.Mott at well.ox.ac.uk>
+DOI: 10.1073/pnas.230304397
+Homepage: http://www.well.ox.ac.uk/happy/happyR
+Name: HAPPY
+PMID: 11050180
+Reference:
+ author: Mott, Richard and Talbot, Christopher J. and Turri, Maria G. and Collins, Allan C. and Flint, Jonathan
+ title: A method for fine mapping quantitative trait loci in outbred animal stocks
+ journal: Proc Natl Acad Sci U S A
+ volume: 97
+ number: 23
+ pages: 12649-12654
+ year: 2000
+ URL: http://www.pnas.org/content/97/23/12649.abstract
+ eprint: http://www.pnas.org/content/97/23/12649.full.pdf+html
Deleted: trunk/packages/R/r-other-mott-happy/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,15 +0,0 @@
-Contact: Richard Mott <Richard.Mott at well.ox.ac.uk>
-DOI: 10.1073/pnas.230304397
-Homepage: http://www.well.ox.ac.uk/happy/happyR
-Name: HAPPY
-PMID: 11050180
-Reference:
- author: Mott, Richard and Talbot, Christopher J. and Turri, Maria G. and Collins, Allan C. and Flint, Jonathan
- title: A method for fine mapping quantitative trait loci in outbred animal stocks
- journal: Proc Natl Acad Sci U S A
- volume: 97
- number: 23
- pages: 12649-12654
- year: 2000
- URL: http://www.pnas.org/content/97/23/12649.abstract
- eprint: http://www.pnas.org/content/97/23/12649.full.pdf+html
Copied: trunk/packages/acedb/trunk/debian/upstream (from rev 9491, trunk/packages/acedb/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/acedb/trunk/debian/upstream (rev 0)
+++ trunk/packages/acedb/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,10 @@
+Homepage: http://www.acedb.org/
+Name: dotter
+Reference:
+ Author: E.L.L. Sonnhammer, R. Durbin
+ Title: A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.
+ Journal: Gene
+ Volume: 167
+ Number: 2
+ Pages: GC1-10
+ Year: 1995
Deleted: trunk/packages/acedb/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/acedb/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/acedb/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,10 +0,0 @@
-Homepage: http://www.acedb.org/
-Name: dotter
-Reference:
- Author: E.L.L. Sonnhammer, R. Durbin
- Title: A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.
- Journal: Gene
- Volume: 167
- Number: 2
- Pages: GC1-10
- Year: 1995
Copied: trunk/packages/adun.app/trunk/debian/upstream (from rev 9491, trunk/packages/adun.app/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/adun.app/trunk/debian/upstream (rev 0)
+++ trunk/packages/adun.app/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,23 @@
+Archive: Gna
+DOI: 10.1002/jcc.20312
+Homepage: http://diana.imim.es/Adun
+Name: Adun
+PMID: 16175583
+Reference:
+ Author: Michael A. Johnston, Ignacio Fdez. Galván and Jordi Villà-Freixa
+ Title: Framework-based design of a new all-purpose molecular simulation application: The Adun simulator
+ Journal: J. Comp. Chem.
+ Volume: 26
+ Number: 15
+ Pages: 1647-1659
+ Year: 2005
+ URL: http://www3.interscience.wiley.com/journal/112094040/abstract
+Screenshots: http://cbbl.imim.es:8080/Adun/screenshots
+Watch: |
+ version=3
+ # Upstream used a broken versioning scheme where a major release is
+ # 0.7 and point releases are 0.71, 0.72, etc. Hopefully this is no
+ # longer a concern, but if it turns out it is, uncommenting and
+ # amending the line below should "fix" the watchfile accordingly.
+ #opts=uversionmangle=s/^0\.([78])(\d)/0.$1.$2/, \
+ http://download.gna.org/adun/Adun-([\d.]+)\.tar\.gz
Deleted: trunk/packages/adun.app/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/adun.app/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/adun.app/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,23 +0,0 @@
-Archive: Gna
-DOI: 10.1002/jcc.20312
-Homepage: http://diana.imim.es/Adun
-Name: Adun
-PMID: 16175583
-Reference:
- Author: Michael A. Johnston, Ignacio Fdez. Galván and Jordi Villà-Freixa
- Title: Framework-based design of a new all-purpose molecular simulation application: The Adun simulator
- Journal: J. Comp. Chem.
- Volume: 26
- Number: 15
- Pages: 1647-1659
- Year: 2005
- URL: http://www3.interscience.wiley.com/journal/112094040/abstract
-Screenshots: http://cbbl.imim.es:8080/Adun/screenshots
-Watch: |
- version=3
- # Upstream used a broken versioning scheme where a major release is
- # 0.7 and point releases are 0.71, 0.72, etc. Hopefully this is no
- # longer a concern, but if it turns out it is, uncommenting and
- # amending the line below should "fix" the watchfile accordingly.
- #opts=uversionmangle=s/^0\.([78])(\d)/0.$1.$2/, \
- http://download.gna.org/adun/Adun-([\d.]+)\.tar\.gz
Copied: trunk/packages/alien-hunter/trunk/debian/upstream (from rev 9491, trunk/packages/alien-hunter/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/upstream (rev 0)
+++ trunk/packages/alien-hunter/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,17 @@
+Contact : George Vernikos <gsv at sanger.ac.uk>
+DOI: 10.1093/bioinformatics/btl369
+Homepage: http://www.sanger.ac.uk/resources/software/alien_hunter.html
+Name: Alien_hunter
+PMID: 16837528
+Reference:
+ author: Vernikos, Georgios S. and Parkhill, Julian
+ title: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands
+ journal: Bioinformatics
+ volume: 22
+ number: 18
+ pages: 2196-2203
+ doi: 10.1093/bioinformatics/btl369
+ year: 2006
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/18/2196
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/18/2196.pdf
+Watch: http://www.sanger.ac.uk/Software/analysis/alien_hunter/alien_hunter-([.\d]+)\.tar\.gz
Deleted: trunk/packages/alien-hunter/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/alien-hunter/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,17 +0,0 @@
-Contact : George Vernikos <gsv at sanger.ac.uk>
-DOI: 10.1093/bioinformatics/btl369
-Homepage: http://www.sanger.ac.uk/resources/software/alien_hunter.html
-Name: Alien_hunter
-PMID: 16837528
-Reference:
- author: Vernikos, Georgios S. and Parkhill, Julian
- title: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands
- journal: Bioinformatics
- volume: 22
- number: 18
- pages: 2196-2203
- doi: 10.1093/bioinformatics/btl369
- year: 2006
- URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/18/2196
- eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/18/2196.pdf
-Watch: http://www.sanger.ac.uk/Software/analysis/alien_hunter/alien_hunter-([.\d]+)\.tar\.gz
Copied: trunk/packages/altree/trunk/debian/upstream (from rev 9491, trunk/packages/altree/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/altree/trunk/debian/upstream (rev 0)
+++ trunk/packages/altree/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,14 @@
+Contact: Claire Bardel <Claire.Bardel at univ-lyon1.fr>
+DOI: 10.1093/bioinformatics/btl131
+Homepage: http://claire.bardel.free.fr/software.html
+Name: ALTree
+PMID: 16595555
+Reference-Author: Bardel, Claire and Danjean, Vincent and Genin, Emmanuelle
+Reference-Journal: Bioinformatics
+Reference-Number: 11
+Reference-Pages: 1402-1403
+Reference-Title: ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees
+Reference-URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/11/1402
+Reference-Volume: 22
+Reference-Year: 2006
+Watch: http://claire.bardel.free.fr/files/altree-([[:digit:]].*)\.tar\.gz
Deleted: trunk/packages/altree/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/altree/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/altree/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,14 +0,0 @@
-Contact: Claire Bardel <Claire.Bardel at univ-lyon1.fr>
-DOI: 10.1093/bioinformatics/btl131
-Homepage: http://claire.bardel.free.fr/software.html
-Name: ALTree
-PMID: 16595555
-Reference-Author: Bardel, Claire and Danjean, Vincent and Genin, Emmanuelle
-Reference-Journal: Bioinformatics
-Reference-Number: 11
-Reference-Pages: 1402-1403
-Reference-Title: ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees
-Reference-URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/11/1402
-Reference-Volume: 22
-Reference-Year: 2006
-Watch: http://claire.bardel.free.fr/files/altree-([[:digit:]].*)\.tar\.gz
Copied: trunk/packages/autodock-vina/trunk/debian/upstream (from rev 9491, trunk/packages/autodock-vina/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/upstream (rev 0)
+++ trunk/packages/autodock-vina/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,14 @@
+Contact: Oleg Trott <ot14 at columbia.edu>
+DOI: 10.1002/jcc.21334
+Homepage: http://vina.scripps.edu
+Name: AutoDock Vina
+Reference:
+ author: Oleg Trott, Arthur J. Olson
+ title: AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
+ journal: Journal of Computational Chemistry
+ volume: 31
+ number: 2
+ pages: 455-461
+ year: 2010
+ URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21334/abstract
+ eprint: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21334/full
Deleted: trunk/packages/autodock-vina/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/autodock-vina/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,14 +0,0 @@
-Contact: Oleg Trott <ot14 at columbia.edu>
-DOI: 10.1002/jcc.21334
-Homepage: http://vina.scripps.edu
-Name: AutoDock Vina
-Reference:
- author: Oleg Trott, Arthur J. Olson
- title: AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
- journal: Journal of Computational Chemistry
- volume: 31
- number: 2
- pages: 455-461
- year: 2010
- URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21334/abstract
- eprint: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21334/full
Copied: trunk/packages/autodocksuite/trunk/debian/upstream (from rev 9491, trunk/packages/autodocksuite/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/upstream (rev 0)
+++ trunk/packages/autodocksuite/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,18 @@
+Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
+DOI: 10.1002/jcc.21256
+Homepage: http://autodock.scripps.edu/
+Name: AutoDock
+PMID: 19399780
+Reference:
+ Author: Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell and Arthur J. Olson.
+ Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
+ Journal: Journal of Computational Chemistry
+ Volume: 30
+ Number: 16
+ Pages: 2785-2791
+ Year: 2009
+ URL: http://www3.interscience.wiley.com/journal/122365050/abstract
+Registration: http://autodock.scripps.edu/downloads/autodock-registration
+Watch: |
+ opts="dversionmangle=s/\+rc/~rc/" \
+ http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ \.\./autodock-registration/tars/.*/autodocksuite-(.*)-src\.tar\.gz
Deleted: trunk/packages/autodocksuite/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/autodocksuite/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,18 +0,0 @@
-Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
-DOI: 10.1002/jcc.21256
-Homepage: http://autodock.scripps.edu/
-Name: AutoDock
-PMID: 19399780
-Reference:
- Author: Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell and Arthur J. Olson.
- Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
- Journal: Journal of Computational Chemistry
- Volume: 30
- Number: 16
- Pages: 2785-2791
- Year: 2009
- URL: http://www3.interscience.wiley.com/journal/122365050/abstract
-Registration: http://autodock.scripps.edu/downloads/autodock-registration
-Watch: |
- opts="dversionmangle=s/\+rc/~rc/" \
- http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ \.\./autodock-registration/tars/.*/autodocksuite-(.*)-src\.tar\.gz
Copied: trunk/packages/biomaj/trunk/debian/upstream (from rev 9491, trunk/packages/biomaj/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/biomaj/trunk/debian/upstream (rev 0)
+++ trunk/packages/biomaj/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,10 @@
+DOI: 10.1093/bioinformatics/btn325
+Homepage: http://biomaj.genouest.org
+Reference:
+ Author: Olivier Filangi, Yoann Beausse, Anthony Assi, Ludovic Legrand, Jean-Marc Larré, Véronique Martin, Olivier Collin, Christophe Caron, Hugues Leroy and David Allouche
+ Title: BioMAJ: a flexible framework for databanks synchronization and processing
+ Journal: Oxford Journals Bioinformatics
+ Year: 2008
+ URL: http://bioinformatics.oxfordjournals.org/content/24/16/1823.abstract
+Repository: https://gforge.inria.fr/scm/?group_id=369
+Screenshots: http://biomaj.genouest.org/?page_id=449
Deleted: trunk/packages/biomaj/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/biomaj/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/biomaj/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,10 +0,0 @@
-DOI: 10.1093/bioinformatics/btn325
-Homepage: http://biomaj.genouest.org
-Reference:
- Author: Olivier Filangi, Yoann Beausse, Anthony Assi, Ludovic Legrand, Jean-Marc Larré, Véronique Martin, Olivier Collin, Christophe Caron, Hugues Leroy and David Allouche
- Title: BioMAJ: a flexible framework for databanks synchronization and processing
- Journal: Oxford Journals Bioinformatics
- Year: 2008
- URL: http://bioinformatics.oxfordjournals.org/content/24/16/1823.abstract
-Repository: https://gforge.inria.fr/scm/?group_id=369
-Screenshots: http://biomaj.genouest.org/?page_id=449
Copied: trunk/packages/bioperl/trunk/debian/upstream (from rev 9491, trunk/packages/bioperl/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/bioperl/trunk/debian/upstream (rev 0)
+++ trunk/packages/bioperl/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,20 @@
+Bug-Database: https://redmine.open-bio.org/projects/bioperl
+Contact: Bioperl developers <bioperl-l at bioperl.org>
+DOI: 10.1101/gr.361602
+Homepage: http://www.bioperl.org/
+Name: BioPerl
+PMID: 12368254
+Reference:
+ author: >
+ J.E. Stajich and D. Block and K. Boulez and S.E. Brenner
+ and S.A. Chervitz and C. Dagdigian and G. Fuellen and J.G. Gilbert
+ and I. Korf and H. Lapp and H. Lehvaslaiho and C. Matsalla and
+ C.J. Mungall and B.I. Osborne and M.R. Pocock and P. Schattner and
+ M. Senger and L.D. Stein and E. Stupka and M.D. Wilkinson and E. Birney
+ title: "The Bioperl toolkit: Perl modules for the life sciences."
+ journal: Genome Res.
+ year: 2002
+ volume: 12
+ number: 10
+ pages: 1611-1618
+Repository: https://github.com/bioperl/bioperl-live
Deleted: trunk/packages/bioperl/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/bioperl/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/bioperl/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,20 +0,0 @@
-Bug-Database: https://redmine.open-bio.org/projects/bioperl
-Contact: Bioperl developers <bioperl-l at bioperl.org>
-DOI: 10.1101/gr.361602
-Homepage: http://www.bioperl.org/
-Name: BioPerl
-PMID: 12368254
-Reference:
- author: >
- J.E. Stajich and D. Block and K. Boulez and S.E. Brenner
- and S.A. Chervitz and C. Dagdigian and G. Fuellen and J.G. Gilbert
- and I. Korf and H. Lapp and H. Lehvaslaiho and C. Matsalla and
- C.J. Mungall and B.I. Osborne and M.R. Pocock and P. Schattner and
- M. Senger and L.D. Stein and E. Stupka and M.D. Wilkinson and E. Birney
- title: "The Bioperl toolkit: Perl modules for the life sciences."
- journal: Genome Res.
- year: 2002
- volume: 12
- number: 10
- pages: 1611-1618
-Repository: https://github.com/bioperl/bioperl-live
Copied: trunk/packages/blat/trunk/debian/upstream (from rev 9491, trunk/packages/blat/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/blat/trunk/debian/upstream (rev 0)
+++ trunk/packages/blat/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,12 @@
+NAME: BLAT
+Reference:
+ author = Kent, W. James
+ title = BLAT—The BLAST-Like Alignment Tool
+ journal = Genome Research
+ volume = 12
+ number = 4
+ pages = 656-664
+ doi = 10.1101/gr.229202
+ year = 2002
+ URL = http://genome.cshlp.org/content/12/4/656.abstract
+ eprint = http://genome.cshlp.org/content/12/4/656.full.pdf+html
Deleted: trunk/packages/blat/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/blat/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/blat/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,12 +0,0 @@
-NAME: BLAT
-Reference:
- author = Kent, W. James
- title = BLAT—The BLAST-Like Alignment Tool
- journal = Genome Research
- volume = 12
- number = 4
- pages = 656-664
- doi = 10.1101/gr.229202
- year = 2002
- URL = http://genome.cshlp.org/content/12/4/656.abstract
- eprint = http://genome.cshlp.org/content/12/4/656.full.pdf+html
Copied: trunk/packages/cd-hit/trunk/debian/upstream (from rev 9491, trunk/packages/cd-hit/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/cd-hit/trunk/debian/upstream (rev 0)
+++ trunk/packages/cd-hit/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,12 @@
+Contact: Weizhong Li <liwz at sdsc.edu>
+DOI: 10.1093/bioinformatics/btl158
+Homepage: http://weizhong-lab.ucsd.edu/cd-hit/
+Name: CD-HIT
+PMID: 16731699
+Reference:
+ author: Weizhong Li, Adam Godzik
+ title: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.
+ journal: Bioinformatics
+ volume: 22
+ year: 2006
+ URL: http://bioinformatics.oxfordjournals.org/content/22/13/1658.full.pdf+html
Deleted: trunk/packages/cd-hit/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/cd-hit/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/cd-hit/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,12 +0,0 @@
-Contact: Weizhong Li <liwz at sdsc.edu>
-DOI: 10.1093/bioinformatics/btl158
-Homepage: http://weizhong-lab.ucsd.edu/cd-hit/
-Name: CD-HIT
-PMID: 16731699
-Reference:
- author: Weizhong Li, Adam Godzik
- title: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.
- journal: Bioinformatics
- volume: 22
- year: 2006
- URL: http://bioinformatics.oxfordjournals.org/content/22/13/1658.full.pdf+html
Copied: trunk/packages/circos/trunk/debian/upstream (from rev 9491, trunk/packages/circos/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/circos/trunk/debian/upstream (rev 0)
+++ trunk/packages/circos/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,10 @@
+DOI: 10.1101/gr.092759.109
+Homepage: http://circos.ca/
+Reference:
+ Author: Martin I Krzywinski, Jacqueline E Schein, Inanc Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, and Marco A Marra
+ Title: Circos: An information aesthetic for comparative genomics
+ Journal: Genome Research
+ Year: 2009
+ URL: http://genome.cshlp.org/content/early/2009/06/15/gr.092759.109.full.pdf+html
+Repository: http://circos.ca/software/download/
+Screenshots: http://circos.ca/tutorials/images/small/
Deleted: trunk/packages/circos/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/circos/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/circos/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,10 +0,0 @@
-DOI: 10.1101/gr.092759.109
-Homepage: http://circos.ca/
-Reference:
- Author: Martin I Krzywinski, Jacqueline E Schein, Inanc Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, and Marco A Marra
- Title: Circos: An information aesthetic for comparative genomics
- Journal: Genome Research
- Year: 2009
- URL: http://genome.cshlp.org/content/early/2009/06/15/gr.092759.109.full.pdf+html
-Repository: http://circos.ca/software/download/
-Screenshots: http://circos.ca/tutorials/images/small/
Copied: trunk/packages/clonalframe/trunk/debian/upstream (from rev 9491, trunk/packages/clonalframe/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/clonalframe/trunk/debian/upstream (rev 0)
+++ trunk/packages/clonalframe/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,12 @@
+Contact: Xavier Didelot <xavier.didelot at gmail.com>
+DOI: 10.1534/genetics.106.063305
+Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
+Name: ClonalFrame
+Reference:
+ author: Xavier Didelot, Daniel Falush
+ title: Inference of Bacterial Microevolution Using Multilocus Sequence Data
+ journal: Genetics Advance
+ volume: 175
+ pages: 1251-1266
+ year: 2006
+ URL: http://www.genetics.org/cgi/content/abstract/175/3/1251
Deleted: trunk/packages/clonalframe/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/clonalframe/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/clonalframe/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,12 +0,0 @@
-Contact: Xavier Didelot <xavier.didelot at gmail.com>
-DOI: 10.1534/genetics.106.063305
-Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
-Name: ClonalFrame
-Reference:
- author: Xavier Didelot, Daniel Falush
- title: Inference of Bacterial Microevolution Using Multilocus Sequence Data
- journal: Genetics Advance
- volume: 175
- pages: 1251-1266
- year: 2006
- URL: http://www.genetics.org/cgi/content/abstract/175/3/1251
Copied: trunk/packages/clustalo/trunk/debian/upstream (from rev 9491, trunk/packages/clustalo/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/clustalo/trunk/debian/upstream (rev 0)
+++ trunk/packages/clustalo/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,13 @@
+Contact: Fabian Sievers (UCD Dublin, Ireland)
+DOI: 10.1038/msb.2011.75
+Homepage: http://www.clustal.org/omega/
+Name: Clustal Omega
+PMID: 21988835
+Reference:
+ author: Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D Thompson and Desmond G Higgins
+ title: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
+ journal: Molecular Systems Biology
+ volume: 7
+ number: 539
+ year: 2011
+ URL: http://www.nature.com/msb/journal/v7/n1/full/msb201175.html
Deleted: trunk/packages/clustalo/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/clustalo/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/clustalo/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,13 +0,0 @@
-Contact: Fabian Sievers (UCD Dublin, Ireland)
-DOI: 10.1038/msb.2011.75
-Homepage: http://www.clustal.org/omega/
-Name: Clustal Omega
-PMID: 21988835
-Reference:
- author: Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D Thompson and Desmond G Higgins
- title: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
- journal: Molecular Systems Biology
- volume: 7
- number: 539
- year: 2011
- URL: http://www.nature.com/msb/journal/v7/n1/full/msb201175.html
Copied: trunk/packages/coils/trunk/debian/upstream (from rev 9491, trunk/packages/coils/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/coils/trunk/debian/upstream (rev 0)
+++ trunk/packages/coils/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,10 @@
+Homepage: http://www.russelllab.org/cgi-bin/coils/coils-svr.pl
+Name: Coils
+PMID: 2031185
+Reference:
+ Author: A. Lupas, M. Van Dyke, and J. Stock
+ Title: Predicting coiled coils from protein sequences
+ Journal: Science
+ Volume: 252
+ Pages: 1162-1164
+ Year: 1991
Deleted: trunk/packages/coils/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/coils/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/coils/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,10 +0,0 @@
-Homepage: http://www.russelllab.org/cgi-bin/coils/coils-svr.pl
-Name: Coils
-PMID: 2031185
-Reference:
- Author: A. Lupas, M. Van Dyke, and J. Stock
- Title: Predicting coiled coils from protein sequences
- Journal: Science
- Volume: 252
- Pages: 1162-1164
- Year: 1991
Copied: trunk/packages/dialign/trunk/debian/upstream (from rev 9491, trunk/packages/dialign/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/dialign/trunk/debian/upstream (rev 0)
+++ trunk/packages/dialign/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,15 @@
+DOI: 10.1093/bioinformatics/15.3.211
+Name: DIALIGN
+Homepage: http://dialign.gobics.de/
+PMID: 10222408
+Reference:
+ Author: Morgenstern, B
+ Title: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment
+ Journal: Bioinformatics
+ Volume: 15
+ Number: 3
+ Pages: 211-218
+ Year: 1999
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/15/3/211
+ Eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/15/3/211.pdf
+Watch: http://dialign.gobics.de/download/dialign-(.*)-linux\.i586\.tar\.gz
Deleted: trunk/packages/dialign/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/dialign/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/dialign/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,15 +0,0 @@
-DOI: 10.1093/bioinformatics/15.3.211
-Name: DIALIGN
-Homepage: http://dialign.gobics.de/
-PMID: 10222408
-Reference:
- Author: Morgenstern, B
- Title: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment
- Journal: Bioinformatics
- Volume: 15
- Number: 3
- Pages: 211-218
- Year: 1999
- URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/15/3/211
- Eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/15/3/211.pdf
-Watch: http://dialign.gobics.de/download/dialign-(.*)-linux\.i586\.tar\.gz
Copied: trunk/packages/dialign-t/trunk/debian/upstream (from rev 9491, trunk/packages/dialign-t/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/dialign-t/trunk/debian/upstream (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,17 @@
+Contact: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
+DOI: 10.1186/1748-7188-3-6
+Homepage: http://dialign-tx.gobics.de/
+PMID: 18505568
+Name: DIALIGN-T
+Reference:
+ AUTHOR: Subramanian, Amarendran and Kaufmann, Michael and Morgenstern, Burkhard
+ TITLE: DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment
+ JOURNAL: Algorithms for Molecular Biology
+ VOLUME: 3
+ YEAR: 2008
+ NUMBER: 1
+ PAGES: 6
+ URL: http://www.almob.org/content/3/1/6
+ DOI: 10.1186/1748-7188-3-6
+ ISSN: 1748-7188
+Watch: http://dialign-tx.gobics.de/download http://dialign-tx.gobics.de/DIALIGN-TX_(.*)\.tar\.gz
Deleted: trunk/packages/dialign-t/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/dialign-t/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/dialign-t/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,17 +0,0 @@
-Contact: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
-DOI: 10.1186/1748-7188-3-6
-Homepage: http://dialign-tx.gobics.de/
-PMID: 18505568
-Name: DIALIGN-T
-Reference:
- AUTHOR: Subramanian, Amarendran and Kaufmann, Michael and Morgenstern, Burkhard
- TITLE: DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment
- JOURNAL: Algorithms for Molecular Biology
- VOLUME: 3
- YEAR: 2008
- NUMBER: 1
- PAGES: 6
- URL: http://www.almob.org/content/3/1/6
- DOI: 10.1186/1748-7188-3-6
- ISSN: 1748-7188
-Watch: http://dialign-tx.gobics.de/download http://dialign-tx.gobics.de/DIALIGN-TX_(.*)\.tar\.gz
Copied: trunk/packages/dicomscope/trunk/debian/upstream (from rev 9491, trunk/packages/dicomscope/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/dicomscope/trunk/debian/upstream (rev 0)
+++ trunk/packages/dicomscope/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,2 @@
+Donation: http://dicom.offis.de/donation.php.en
+Homepage: http://dicom.offis.de/dscope.php.en
Deleted: trunk/packages/dicomscope/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/dicomscope/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/dicomscope/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,2 +0,0 @@
-Donation: http://dicom.offis.de/donation.php.en
-Homepage: http://dicom.offis.de/dscope.php.en
Copied: trunk/packages/elastix/trunk/debian/upstream (from rev 9491, trunk/packages/elastix/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/elastix/trunk/debian/upstream (rev 0)
+++ trunk/packages/elastix/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,12 @@
+Contact: Stefan Klein and Marius Staring
+Homepage: http://elastix.isi.uu.nl/
+Name: Elastix
+Reference:
+ author: S. Klein, M. Staring, K. Murphy, M. A. Viergever, J. Pluim
+ title: elastix: A Toolbox for Intensity-Based Medical Image Registration
+ journal: IEEE Transactions on Medical Imaging
+ volume: 29
+ number: 1
+ pages: 196 - 205
+ year: 2010
+ URL: http://ieeexplore.ieee.org/xpls/abs_all.jsp?tp=&arnumber=5338015&isnumber=5371922
Deleted: trunk/packages/elastix/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/elastix/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/elastix/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,12 +0,0 @@
-Contact: Stefan Klein and Marius Staring
-Homepage: http://elastix.isi.uu.nl/
-Name: Elastix
-Reference:
- author: S. Klein, M. Staring, K. Murphy, M. A. Viergever, J. Pluim
- title: elastix: A Toolbox for Intensity-Based Medical Image Registration
- journal: IEEE Transactions on Medical Imaging
- volume: 29
- number: 1
- pages: 196 - 205
- year: 2010
- URL: http://ieeexplore.ieee.org/xpls/abs_all.jsp?tp=&arnumber=5338015&isnumber=5371922
Copied: trunk/packages/epigrass/trunk/debian/upstream (from rev 9491, trunk/packages/epigrass/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/epigrass/trunk/debian/upstream (rev 0)
+++ trunk/packages/epigrass/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,18 @@
+Contact: Flavio Codeco Coelho <fccoelho at gmail.com>
+DOI: 10.1186/1751-0473-3-3
+Homepage: http://epigrass.sourceforge.net/
+Name: EpiGrass
+Watch: http://pypi.python.org/packages/source/e/epigrass/epigrass-(.*).tar.gz
+PMID: 18302744
+Reference:
+ author: Coelho, Flavio and Cruz, Oswaldo and Codeco, Claudia
+ title: Epigrass: a tool to study disease spread in complex networks
+ journal: Source Code for Biology and Medicine
+ volume: 3
+ year: 2008
+ number: 1
+ pages: 3
+ URL: http://www.scfbm.org/content/3/1/3
+ ISSN: 1751-0473
+}
+
Deleted: trunk/packages/epigrass/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/epigrass/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/epigrass/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,18 +0,0 @@
-Contact: Flavio Codeco Coelho <fccoelho at gmail.com>
-DOI: 10.1186/1751-0473-3-3
-Homepage: http://epigrass.sourceforge.net/
-Name: EpiGrass
-Watch: http://pypi.python.org/packages/source/e/epigrass/epigrass-(.*).tar.gz
-PMID: 18302744
-Reference:
- author: Coelho, Flavio and Cruz, Oswaldo and Codeco, Claudia
- title: Epigrass: a tool to study disease spread in complex networks
- journal: Source Code for Biology and Medicine
- volume: 3
- year: 2008
- number: 1
- pages: 3
- URL: http://www.scfbm.org/content/3/1/3
- ISSN: 1751-0473
-}
-
Copied: trunk/packages/exonerate/trunk/debian/upstream (from rev 9491, trunk/packages/exonerate/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/exonerate/trunk/debian/upstream (rev 0)
+++ trunk/packages/exonerate/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,16 @@
+Contact: Guy St.C. Slater <guy AT ebi.ac.uk>
+DOI: 10.1186/1471-2105-6-31
+Name: Exonerate
+Homepage: http://www.ebi.ac.uk/~guy/exonerate/
+PMID: 15713233
+Reference:
+ Author: Slater, Guy and Birney, Ewan
+ Title: Automated generation of heuristics for biological sequence comparison
+ Journal: BMC Bioinformatics
+ Volume: 6
+ Year: 2005
+ Number: 1
+ Pages: 31
+ URL: http://www.biomedcentral.com/1471-2105/6/31
+ ISSN: 1471-2105
+Watch: http://www.ebi.ac.uk/~guy/exonerate/exonerate-([0-9.]*)\.tar\.gz
Deleted: trunk/packages/exonerate/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/exonerate/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/exonerate/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,16 +0,0 @@
-Contact: Guy St.C. Slater <guy AT ebi.ac.uk>
-DOI: 10.1186/1471-2105-6-31
-Name: Exonerate
-Homepage: http://www.ebi.ac.uk/~guy/exonerate/
-PMID: 15713233
-Reference:
- Author: Slater, Guy and Birney, Ewan
- Title: Automated generation of heuristics for biological sequence comparison
- Journal: BMC Bioinformatics
- Volume: 6
- Year: 2005
- Number: 1
- Pages: 31
- URL: http://www.biomedcentral.com/1471-2105/6/31
- ISSN: 1471-2105
-Watch: http://www.ebi.ac.uk/~guy/exonerate/exonerate-([0-9.]*)\.tar\.gz
Copied: trunk/packages/gassst/trunk/debian/upstream (from rev 9491, trunk/packages/gassst/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/gassst/trunk/debian/upstream (rev 0)
+++ trunk/packages/gassst/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,12 @@
+Contact: Dominique Lavanier <dominique.lavanier at irisa.fr>
+DOI: 10.1093/bioinformatics/btq485
+Homepage: http://www.irisa.fr/symbiose/projects/gassst/
+Name: GASSST
+Reference:
+ author: Guillaume Rizk and Dominique Lavanier
+ title: GASSST: global alignment short sequence search tool
+ journal: Bioinformatics
+ volume: 20
+ number: 36
+ year: 2010
+ URL: http://bioinformatics.oxfordjournals.org/content/26/20/2534.abstract?keytype=ref&ijkey=f5zH80QsuCqixRH
Deleted: trunk/packages/gassst/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/gassst/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/gassst/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,12 +0,0 @@
-Contact: Dominique Lavanier <dominique.lavanier at irisa.fr>
-DOI: 10.1093/bioinformatics/btq485
-Homepage: http://www.irisa.fr/symbiose/projects/gassst/
-Name: GASSST
-Reference:
- author: Guillaume Rizk and Dominique Lavanier
- title: GASSST: global alignment short sequence search tool
- journal: Bioinformatics
- volume: 20
- number: 36
- year: 2010
- URL: http://bioinformatics.oxfordjournals.org/content/26/20/2534.abstract?keytype=ref&ijkey=f5zH80QsuCqixRH
Copied: trunk/packages/glam2/trunk/debian/upstream (from rev 9491, trunk/packages/glam2/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/glam2/trunk/debian/upstream (rev 0)
+++ trunk/packages/glam2/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,17 @@
+Contact: Martin C Frith <martin at cbrc.jp> and Timothy L Bailey <t.bailey at imb.uq.edu.au>
+DOI: 10.1371/journal.pcbi.1000071
+Homepage: http://bioinformatics.org.au/glam2/
+Name: GLAM2
+PMID: 18437229
+Reference:
+ author: Frith, Martin C. AND Saunders, Neil F. W. AND Kobe, Bostjan AND Bailey, Timothy L.
+ journal: PLoS Comput Biol
+ publisher: Public Library of Science
+ title: Discovering Sequence Motifs with Arbitrary Insertions and Deletions
+ year: 2008
+ month: 05
+ volume: 4
+ url: http://dx.plos.org/10.1371/journal.pcbi.1000071
+ pages: e1000071
+ number: 5
+Watch: http://bioinformatics.org.au/glam2/archive/glam2-(\d+)\.zip
Deleted: trunk/packages/glam2/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/glam2/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/glam2/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,17 +0,0 @@
-Contact: Martin C Frith <martin at cbrc.jp> and Timothy L Bailey <t.bailey at imb.uq.edu.au>
-DOI: 10.1371/journal.pcbi.1000071
-Homepage: http://bioinformatics.org.au/glam2/
-Name: GLAM2
-PMID: 18437229
-Reference:
- author: Frith, Martin C. AND Saunders, Neil F. W. AND Kobe, Bostjan AND Bailey, Timothy L.
- journal: PLoS Comput Biol
- publisher: Public Library of Science
- title: Discovering Sequence Motifs with Arbitrary Insertions and Deletions
- year: 2008
- month: 05
- volume: 4
- url: http://dx.plos.org/10.1371/journal.pcbi.1000071
- pages: e1000071
- number: 5
-Watch: http://bioinformatics.org.au/glam2/archive/glam2-(\d+)\.zip
Copied: trunk/packages/hhsuite/trunk/debian/upstream (from rev 9491, trunk/packages/hhsuite/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/hhsuite/trunk/debian/upstream (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,19 @@
+Name: hhsuite
+Contact: Andreas Hauser <hauser at genzentrum.lmu.de>
+Homepage: http://toolkit.genzentrum.lmu.de/hhblits
+Reference:
+ - Author: Remmert M., Biegert A., Hauser A., and Soding J.
+ Title: 'HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. '
+ Journal: Nat. Methods
+ DOI: 10.1038/NMETH.1818.
+ year: 2011
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/22198341
+ PMID: 22198341
+ - Author: Soding J.
+ Title: Protein homology detection by HMM-HMM comparison.
+ Journal: Bioinformatics
+ Volume: 21
+ Pages: 951-960
+ Year: 2005
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/15531603
+ PMID: 15531603
Deleted: trunk/packages/hhsuite/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/hhsuite/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/hhsuite/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,19 +0,0 @@
-Name: hhsuite
-Contact: Andreas Hauser <hauser at genzentrum.lmu.de>
-Homepage: http://toolkit.genzentrum.lmu.de/hhblits
-Reference:
- - Author: Remmert M., Biegert A., Hauser A., and Soding J.
- Title: 'HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. '
- Journal: Nat. Methods
- DOI: 10.1038/NMETH.1818.
- year: 2011
- URL: http://www.ncbi.nlm.nih.gov/pubmed/22198341
- PMID: 22198341
- - Author: Soding J.
- Title: Protein homology detection by HMM-HMM comparison.
- Journal: Bioinformatics
- Volume: 21
- Pages: 951-960
- Year: 2005
- URL: http://www.ncbi.nlm.nih.gov/pubmed/15531603
- PMID: 15531603
Copied: trunk/packages/hmmer/trunk/debian/upstream (from rev 9491, trunk/packages/hmmer/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/hmmer/trunk/debian/upstream (rev 0)
+++ trunk/packages/hmmer/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,15 @@
+Contact: http://selab.janelia.org/people/eddys/contact.html
+DOI: 10.1093/bioinformatics/14.9.755
+Name: HMMER
+Homepage: http://hmmer.janelia.org
+PMID: 9918945
+Reference:
+ Author: Eddy, SR
+ Title: Profile hidden Markov models
+ Journal: Bioinformatics
+ Volume: 14
+ Number: 9
+ Pages: 755-763
+ Year: 1998
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/14/9/755
+Watch: ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz
Deleted: trunk/packages/hmmer/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/hmmer/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/hmmer/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,15 +0,0 @@
-Contact: http://selab.janelia.org/people/eddys/contact.html
-DOI: 10.1093/bioinformatics/14.9.755
-Name: HMMER
-Homepage: http://hmmer.janelia.org
-PMID: 9918945
-Reference:
- Author: Eddy, SR
- Title: Profile hidden Markov models
- Journal: Bioinformatics
- Volume: 14
- Number: 9
- Pages: 755-763
- Year: 1998
- URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/14/9/755
-Watch: ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz
Copied: trunk/packages/infernal/trunk/debian/upstream (from rev 9491, trunk/packages/infernal/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/infernal/trunk/debian/upstream (rev 0)
+++ trunk/packages/infernal/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,14 @@
+DOI: 10.1093/bioinformatics/btp157
+Homepage: http://infernal.janelia.org/
+PMID: 19307242
+Reference:
+ author: Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R.
+ title: Infernal 1.0: inference of RNA alignments
+ journal: Bioinformatics
+ volume: 25
+ number: 10
+ pages: 1335-1337
+ doi: 10.1093/bioinformatics/btp157
+ year: 2009
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/10/1335
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/25/10/1335.pdf
Deleted: trunk/packages/infernal/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/infernal/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/infernal/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,14 +0,0 @@
-DOI: 10.1093/bioinformatics/btp157
-Homepage: http://infernal.janelia.org/
-PMID: 19307242
-Reference:
- author: Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R.
- title: Infernal 1.0: inference of RNA alignments
- journal: Bioinformatics
- volume: 25
- number: 10
- pages: 1335-1337
- doi: 10.1093/bioinformatics/btp157
- year: 2009
- URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/10/1335
- eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/25/10/1335.pdf
Copied: trunk/packages/kalign/trunk/debian/upstream (from rev 9491, trunk/packages/kalign/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/kalign/trunk/debian/upstream (rev 0)
+++ trunk/packages/kalign/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,15 @@
+Contact: Timo Lassmann <timolassmann at gmail.com>
+DOI: 10.1093/nar/gkn1006
+Name: Kalign
+Homepage: http://msa.cgb.ki.se
+PMID: 19103665
+Reference:
+ Author: Lassmann, Timo and Frings, Oliver and Sonnhammer, Erik L. L.
+ Journal: Nucl. Acids Res.
+ Number: 3
+ Pages: 858-865
+ Title: Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features
+ URL: http://nar.oxfordjournals.org/cgi/content/abstract/37/3/858
+ Volume: 37
+ Year: 2009
+Watch: NA
Deleted: trunk/packages/kalign/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/kalign/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/kalign/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,15 +0,0 @@
-Contact: Timo Lassmann <timolassmann at gmail.com>
-DOI: 10.1093/nar/gkn1006
-Name: Kalign
-Homepage: http://msa.cgb.ki.se
-PMID: 19103665
-Reference:
- Author: Lassmann, Timo and Frings, Oliver and Sonnhammer, Erik L. L.
- Journal: Nucl. Acids Res.
- Number: 3
- Pages: 858-865
- Title: Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features
- URL: http://nar.oxfordjournals.org/cgi/content/abstract/37/3/858
- Volume: 37
- Year: 2009
-Watch: NA
Copied: trunk/packages/last-align/trunk/debian/upstream (from rev 9491, trunk/packages/last-align/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/last-align/trunk/debian/upstream (rev 0)
+++ trunk/packages/last-align/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,22 @@
+Contact: last (ATmark) cbrc (dot) jp
+DOI: 10.1093/nar/gkq010
+Name: LAST
+Homepage: http://last.cbrc.jp/
+PMID: 20110255
+Reference:
+ author: Frith, Martin C. and Wan, Raymond and Horton, Paul
+ title: Incorporating sequence quality data into alignment improves DNA read mapping
+ journal: Nucl. Acids Res.
+ volume: 38
+ number: 7
+ pages: e100
+ doi: 10.1093/nar/gkq010
+ year: 2010
+ URL: http://nar.oxfordjournals.org/cgi/content/abstract/38/7/e100
+ eprint: http://nar.oxfordjournals.org/cgi/reprint/38/7/e100.pdf
+ PMID: 20110255
+Repository:
+ Browse: http://last.cbrc.jp/last/
+ Checkout: svn co http://last.cbrc.jp/last
+Watch:
+Webservice: http://lastweb.cbrc.jp/
Deleted: trunk/packages/last-align/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/last-align/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/last-align/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,22 +0,0 @@
-Contact: last (ATmark) cbrc (dot) jp
-DOI: 10.1093/nar/gkq010
-Name: LAST
-Homepage: http://last.cbrc.jp/
-PMID: 20110255
-Reference:
- author: Frith, Martin C. and Wan, Raymond and Horton, Paul
- title: Incorporating sequence quality data into alignment improves DNA read mapping
- journal: Nucl. Acids Res.
- volume: 38
- number: 7
- pages: e100
- doi: 10.1093/nar/gkq010
- year: 2010
- URL: http://nar.oxfordjournals.org/cgi/content/abstract/38/7/e100
- eprint: http://nar.oxfordjournals.org/cgi/reprint/38/7/e100.pdf
- PMID: 20110255
-Repository:
- Browse: http://last.cbrc.jp/last/
- Checkout: svn co http://last.cbrc.jp/last
-Watch:
-Webservice: http://lastweb.cbrc.jp/
Copied: trunk/packages/libhmsbeagle/trunk/debian/upstream (from rev 9491, trunk/packages/libhmsbeagle/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/upstream (rev 0)
+++ trunk/packages/libhmsbeagle/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,12 @@
+Contact: Andrew Rambaut <rambaut at gmail.com>
+DOI: 10.1093/sysbio/syr100
+Homepage: http://code.google.com/p/beagle-lib
+Name: beagle-lib
+PMID: 21963610
+Reference:
+ author: Daniel L. Ayres, Aaron Darling, Derrick J. Zwickl, Peter Beerli, Mark T. Holder, Paul O. Lewis, John P. Huelsenbeck, Fredrik Ronquist, David L. Swofford, Michael P. Cummings, Andrew Rambaut and Marc A. Suchard
+ title: BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
+ journal: Systematic Biology
+ year: 2011
+ URL: http://sysbio.oxfordjournals.org/content/early/2011/09/29/sysbio.syr100.abstract
+ eprint: http://sysbio.oxfordjournals.org/content/early/2011/09/29/sysbio.syr100.full.pdf+html
Deleted: trunk/packages/libhmsbeagle/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/libhmsbeagle/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,12 +0,0 @@
-Contact: Andrew Rambaut <rambaut at gmail.com>
-DOI: 10.1093/sysbio/syr100
-Homepage: http://code.google.com/p/beagle-lib
-Name: beagle-lib
-PMID: 21963610
-Reference:
- author: Daniel L. Ayres, Aaron Darling, Derrick J. Zwickl, Peter Beerli, Mark T. Holder, Paul O. Lewis, John P. Huelsenbeck, Fredrik Ronquist, David L. Swofford, Michael P. Cummings, Andrew Rambaut and Marc A. Suchard
- title: BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
- journal: Systematic Biology
- year: 2011
- URL: http://sysbio.oxfordjournals.org/content/early/2011/09/29/sysbio.syr100.abstract
- eprint: http://sysbio.oxfordjournals.org/content/early/2011/09/29/sysbio.syr100.full.pdf+html
Copied: trunk/packages/libtfbs-perl/trunk/debian/upstream (from rev 9491, trunk/packages/libtfbs-perl/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/upstream (rev 0)
+++ trunk/packages/libtfbs-perl/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,15 @@
+Contact: Boris.Lenhard at bccs.uib.no
+DOI: 10.1093/bioinformatics/18.8.1135
+Homepage: http://tfbs.genereg.net/
+Name: TFBS
+PMID: 12176838
+Reference-Journal: Bioinformatics
+Reference-Title: TFBS: Computational framework for transcription factor binding site analysis
+Reference-Authors: Lenhard, Boris and Wasserman, Wyeth W.
+Reference-Volume: 18
+Reference-Number: 8
+Reference-Pages: 1135-1136
+Reference-Year: 2002
+Reference-URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1135
+Repository: http://www.ii.uib.no/svn/lenhard/TFBS/
+Watch: http://tfbs.genereg.net/TFBS-(.*)\.tar\.gz
Deleted: trunk/packages/libtfbs-perl/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/libtfbs-perl/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,15 +0,0 @@
-Contact: Boris.Lenhard at bccs.uib.no
-DOI: 10.1093/bioinformatics/18.8.1135
-Homepage: http://tfbs.genereg.net/
-Name: TFBS
-PMID: 12176838
-Reference-Journal: Bioinformatics
-Reference-Title: TFBS: Computational framework for transcription factor binding site analysis
-Reference-Authors: Lenhard, Boris and Wasserman, Wyeth W.
-Reference-Volume: 18
-Reference-Number: 8
-Reference-Pages: 1135-1136
-Reference-Year: 2002
-Reference-URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1135
-Repository: http://www.ii.uib.no/svn/lenhard/TFBS/
-Watch: http://tfbs.genereg.net/TFBS-(.*)\.tar\.gz
Copied: trunk/packages/mafft/trunk/debian/upstream (from rev 9491, trunk/packages/mafft/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/mafft/trunk/debian/upstream (rev 0)
+++ trunk/packages/mafft/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,15 @@
+Contact: Kazutaka Katoh <katoh at bioreg.kyushu-u.ac.jp>
+DOI: 10.1093/bib/bbn013
+Name: MAFFT
+Homepage: http://mafft.cbrc.jp/alignment/software/
+PMID: 18372315
+Reference-Author: Katoh, Kazutaka and Toh, Hiroyuki
+Reference-Journal: Brief Bioinform
+Reference-Number: 4
+Reference-Pages: 286-298
+Reference-Title: Recent developments in the MAFFT multiple sequence alignment program
+Reference-URL: http://bib.oxfordjournals.org/cgi/content/abstract/9/4/286
+Reference-Volume: 9
+Reference-Year: 2008
+Watch: |
+ http://mafft.cbrc.jp/alignment/software/source.html mafft-(.*)-with-extensions-src.tgz
Deleted: trunk/packages/mafft/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/mafft/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/mafft/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,15 +0,0 @@
-Contact: Kazutaka Katoh <katoh at bioreg.kyushu-u.ac.jp>
-DOI: 10.1093/bib/bbn013
-Name: MAFFT
-Homepage: http://mafft.cbrc.jp/alignment/software/
-PMID: 18372315
-Reference-Author: Katoh, Kazutaka and Toh, Hiroyuki
-Reference-Journal: Brief Bioinform
-Reference-Number: 4
-Reference-Pages: 286-298
-Reference-Title: Recent developments in the MAFFT multiple sequence alignment program
-Reference-URL: http://bib.oxfordjournals.org/cgi/content/abstract/9/4/286
-Reference-Volume: 9
-Reference-Year: 2008
-Watch: |
- http://mafft.cbrc.jp/alignment/software/source.html mafft-(.*)-with-extensions-src.tgz
Copied: trunk/packages/maq/trunk/debian/upstream (from rev 9491, trunk/packages/maq/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/maq/trunk/debian/upstream (rev 0)
+++ trunk/packages/maq/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,20 @@
+Archive: SourceForge
+Contact: Heng Li <lh3 at sanger.ac.uk>
+DOI: 10.1101/gr.078212.108
+FAQ: http://maq.sourceforge.net/faq.shtml
+Name: Maq
+Homepage: http://maq.sourceforge.net/
+PMID: 18714091
+Reference:
+ author: Li, Heng and Ruan, Jue and Durbin, Richard
+ title: Mapping short DNA sequencing reads and calling variants using mapping quality scores
+ journal: Genome Research
+ volume: 18
+ number: 11
+ pages: 1851-1858
+ doi: 10.1101/gr.078212.108
+ year: 2008
+ URL: http://genome.cshlp.org/content/18/11/1851.abstract
+ eprint: http://genome.cshlp.org/content/18/11/1851.full.pdf+html
+Watch: |
+ http://sf.net/maq/maq-([\d\.]+)\.tar\.bz2
Deleted: trunk/packages/maq/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/maq/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/maq/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,20 +0,0 @@
-Archive: SourceForge
-Contact: Heng Li <lh3 at sanger.ac.uk>
-DOI: 10.1101/gr.078212.108
-FAQ: http://maq.sourceforge.net/faq.shtml
-Name: Maq
-Homepage: http://maq.sourceforge.net/
-PMID: 18714091
-Reference:
- author: Li, Heng and Ruan, Jue and Durbin, Richard
- title: Mapping short DNA sequencing reads and calling variants using mapping quality scores
- journal: Genome Research
- volume: 18
- number: 11
- pages: 1851-1858
- doi: 10.1101/gr.078212.108
- year: 2008
- URL: http://genome.cshlp.org/content/18/11/1851.abstract
- eprint: http://genome.cshlp.org/content/18/11/1851.full.pdf+html
-Watch: |
- http://sf.net/maq/maq-([\d\.]+)\.tar\.bz2
Copied: trunk/packages/maude/trunk/debian/upstream (from rev 9491, trunk/packages/maude/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/maude/trunk/debian/upstream (rev 0)
+++ trunk/packages/maude/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,13 @@
+Contact: Richard J. Wagner
+DOI: 10.1145/272991.272995
+Homepage: http://www-personal.umich.edu/~wagnerr/MersenneTwister.html
+Name: Mersenne Twister Random Number Generator
+Reference:
+ author: M. Matsumoto and T. Nishimura
+ title: Mersenne Twister: A 623-Dimensionally Equidistributed Uniform Pseudo-Random Number Generator
+ journal: ACM Transactions on Modeling and Computer Simulation
+ volume: 8
+ number: 1
+ year: 1998
+ pages: 3-30
+ URL: http://dl.acm.org/citation.cfm?id=272995
Deleted: trunk/packages/maude/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/maude/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/maude/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,13 +0,0 @@
-Contact: Richard J. Wagner
-DOI: 10.1145/272991.272995
-Homepage: http://www-personal.umich.edu/~wagnerr/MersenneTwister.html
-Name: Mersenne Twister Random Number Generator
-Reference:
- author: M. Matsumoto and T. Nishimura
- title: Mersenne Twister: A 623-Dimensionally Equidistributed Uniform Pseudo-Random Number Generator
- journal: ACM Transactions on Modeling and Computer Simulation
- volume: 8
- number: 1
- year: 1998
- pages: 3-30
- URL: http://dl.acm.org/citation.cfm?id=272995
Copied: trunk/packages/melting/trunk/debian/upstream (from rev 9491, trunk/packages/melting/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/melting/trunk/debian/upstream (rev 0)
+++ trunk/packages/melting/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,17 @@
+Contact: Nicolas Le Novère <lenov at ebi.ac.uk>
+DOI: 10.1093/bioinformatics/17.12.1226
+Homepage: http://www.ebi.ac.uk/compneur-srv/melting/
+Name: MELTING
+PMID: 11751232
+Reference:
+ author: Le Novère, Nicolas
+ title: MELTING, computing the melting temperature of nucleic acid duplex
+ journal: Bioinformatics
+ volume: 17
+ number: 12
+ pages: 1226-1227
+ year: 2001
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1226
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/17/12/1226.pdf
+Screenshot: http://www.ebi.ac.uk/compneur-srv/melting/melting.jpg
+Webservice: http://www.ebi.ac.uk/compneur-srv/melting/melt.php
Deleted: trunk/packages/melting/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/melting/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/melting/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,17 +0,0 @@
-Contact: Nicolas Le Novère <lenov at ebi.ac.uk>
-DOI: 10.1093/bioinformatics/17.12.1226
-Homepage: http://www.ebi.ac.uk/compneur-srv/melting/
-Name: MELTING
-PMID: 11751232
-Reference:
- author: Le Novère, Nicolas
- title: MELTING, computing the melting temperature of nucleic acid duplex
- journal: Bioinformatics
- volume: 17
- number: 12
- pages: 1226-1227
- year: 2001
- URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1226
- eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/17/12/1226.pdf
-Screenshot: http://www.ebi.ac.uk/compneur-srv/melting/melting.jpg
-Webservice: http://www.ebi.ac.uk/compneur-srv/melting/melt.php
Copied: trunk/packages/mgltools/autodocktools/trunk/debian/upstream (from rev 9491, trunk/packages/mgltools/autodocktools/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/mgltools/autodocktools/trunk/debian/upstream (rev 0)
+++ trunk/packages/mgltools/autodocktools/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,24 @@
+Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
+DOI: 10.1002/jcc.21256
+Homepage: http://autodock.scripps.edu/
+Name: AutoDockTools
+PMID: 19399780
+Reference:
+ Author: Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell and Arthur J. Olson.
+ Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
+ Journal: Journal of Computational Chemistry
+ Volume: 30
+ Number: 16
+ Pages: 2785-2791
+ Year: 2009
+ URL: http://www3.interscience.wiley.com/journal/122365050/abstract
+Reference:
+ Author: Harris R, Olson AJ, Goodsell DS.
+ Title: Automated prediction of ligand-binding sites in proteins.
+ Journal: Proteins
+ Year: 2008
+ Volume: 70
+ Number: 4
+ Pages: 1506-1517
+Registration: http://autodock.scripps.edu/downloads/autodock-registration
+Watch: http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz
Deleted: trunk/packages/mgltools/autodocktools/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/mgltools/autodocktools/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/mgltools/autodocktools/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,24 +0,0 @@
-Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
-DOI: 10.1002/jcc.21256
-Homepage: http://autodock.scripps.edu/
-Name: AutoDockTools
-PMID: 19399780
-Reference:
- Author: Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell and Arthur J. Olson.
- Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
- Journal: Journal of Computational Chemistry
- Volume: 30
- Number: 16
- Pages: 2785-2791
- Year: 2009
- URL: http://www3.interscience.wiley.com/journal/122365050/abstract
-Reference:
- Author: Harris R, Olson AJ, Goodsell DS.
- Title: Automated prediction of ligand-binding sites in proteins.
- Journal: Proteins
- Year: 2008
- Volume: 70
- Number: 4
- Pages: 1506-1517
-Registration: http://autodock.scripps.edu/downloads/autodock-registration
-Watch: http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz
Copied: trunk/packages/mipe/trunk/debian/upstream (from rev 9491, trunk/packages/mipe/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/mipe/trunk/debian/upstream (rev 0)
+++ trunk/packages/mipe/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,12 @@
+Archive: SourceForge
+Contact: Jan Aerts (aerts at users.sourceforge.net)
+Homepage: http://mipe.sourceforge.net
+Reference:
+ Author: Aerts J & Veenendaal T.
+ Title: MIPE - a XML-format to facilitate the storage and exchange of PCR-related data
+ Journal: Online Journal of Bioinformatics
+ Number: 2
+ Volume: 6
+ Pages: 114-120
+ Year: 2005
+Watch: http://sf.net/mipe/ mipe-(.*)\.tar.gz
Deleted: trunk/packages/mipe/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/mipe/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/mipe/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,12 +0,0 @@
-Archive: SourceForge
-Contact: Jan Aerts (aerts at users.sourceforge.net)
-Homepage: http://mipe.sourceforge.net
-Reference:
- Author: Aerts J & Veenendaal T.
- Title: MIPE - a XML-format to facilitate the storage and exchange of PCR-related data
- Journal: Online Journal of Bioinformatics
- Number: 2
- Volume: 6
- Pages: 114-120
- Year: 2005
-Watch: http://sf.net/mipe/ mipe-(.*)\.tar.gz
Copied: trunk/packages/mira/trunk/debian/upstream (from rev 9491, trunk/packages/mira/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/mira/trunk/debian/upstream (rev 0)
+++ trunk/packages/mira/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,18 @@
+Bugs: http://sourceforge.net/apps/trac/mira-assembler/newticket
+DOI: 10.1101/gr.1917404
+Homepage: http://www.chevreux.org/projects_mira.html
+Homepage: http://sourceforge.net/apps/trac/mira-assembler
+PubMed: 15140833
+Reference: |
+ @article{BastienChevreux062004,
+ author = {Chevreux, Bastien and Pfisterer, Thomas and Drescher, Bernd and Driesel, Albert J. and Müller, Werner E.G. and Wetter, Thomas and Suhai, Sándor},
+ title={{Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs}},
+ journal = {Genome Research},
+ volume = {14},
+ number = {6},
+ pages = {1147-1159},
+ doi = {10.1101/gr.1917404},
+ year = {2004},
+ URL = {http://genome.cshlp.org/content/14/6/1147.abstract},
+ eprint = {http://genome.cshlp.org/content/14/6/1147.full.pdf+html}
+ }
Deleted: trunk/packages/mira/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/mira/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/mira/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,18 +0,0 @@
-Bugs: http://sourceforge.net/apps/trac/mira-assembler/newticket
-DOI: 10.1101/gr.1917404
-Homepage: http://www.chevreux.org/projects_mira.html
-Homepage: http://sourceforge.net/apps/trac/mira-assembler
-PubMed: 15140833
-Reference: |
- @article{BastienChevreux062004,
- author = {Chevreux, Bastien and Pfisterer, Thomas and Drescher, Bernd and Driesel, Albert J. and Müller, Werner E.G. and Wetter, Thomas and Suhai, Sándor},
- title={{Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs}},
- journal = {Genome Research},
- volume = {14},
- number = {6},
- pages = {1147-1159},
- doi = {10.1101/gr.1917404},
- year = {2004},
- URL = {http://genome.cshlp.org/content/14/6/1147.abstract},
- eprint = {http://genome.cshlp.org/content/14/6/1147.full.pdf+html}
- }
Copied: trunk/packages/mothur/trunk/debian/upstream (from rev 9491, trunk/packages/mothur/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/mothur/trunk/debian/upstream (rev 0)
+++ trunk/packages/mothur/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,15 @@
+Contact: Patrick D. Schloss <pschloss at umich.edu>
+DOI: 10.1128/AEM.01541-09
+Homepage: http://www.mothur.org
+PMID: 19801464
+Name: Mothur
+Reference:
+ AUTHOR: Schloss, P.D., et al.
+ TITILE: Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
+ JOURNAL: Appl Environ Microbiol
+ YEAR: 2009
+ PAGES: 7537-7541
+ VOLUME: 75
+ NUMBER: 23
+ URL: http://aem.asm.org/cgi/content/full/75/23/7537
+ ISSN: 1098-5336
Deleted: trunk/packages/mothur/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/mothur/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/mothur/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,15 +0,0 @@
-Contact: Patrick D. Schloss <pschloss at umich.edu>
-DOI: 10.1128/AEM.01541-09
-Homepage: http://www.mothur.org
-PMID: 19801464
-Name: Mothur
-Reference:
- AUTHOR: Schloss, P.D., et al.
- TITILE: Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
- JOURNAL: Appl Environ Microbiol
- YEAR: 2009
- PAGES: 7537-7541
- VOLUME: 75
- NUMBER: 23
- URL: http://aem.asm.org/cgi/content/full/75/23/7537
- ISSN: 1098-5336
Copied: trunk/packages/mummer/trunk/debian/upstream (from rev 9491, trunk/packages/mummer/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/mummer/trunk/debian/upstream (rev 0)
+++ trunk/packages/mummer/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,16 @@
+Archive: SourceForge
+DOI: 10.1186/gb-2004-5-2-r12
+Homepage: http://mummer.sourceforge.net/
+PMID: 14759262
+Reference:
+ Author: Kurtz, Stefan and Phillippy, Adam and Delcher, Arthur and Smoot, Michael and Shumway, Martin and Antonescu, Corina and Salzberg, Steven
+ Title: Versatile and open software for comparing large genomes
+ Journal: Genome Biology
+ Volume: 5
+ Year: 2004
+ Number: 2
+ Pages: R12
+ URL: http://genomebiology.com/2004/5/2/R12
+ ISSN: 1465-6906
+Repository: http://mummer.cvs.sourceforge.net/mummer/
+Screenshots: http://sourceforge.net/project/screenshots.php?group_id=133157
Deleted: trunk/packages/mummer/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/mummer/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/mummer/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,16 +0,0 @@
-Archive: SourceForge
-DOI: 10.1186/gb-2004-5-2-r12
-Homepage: http://mummer.sourceforge.net/
-PMID: 14759262
-Reference:
- Author: Kurtz, Stefan and Phillippy, Adam and Delcher, Arthur and Smoot, Michael and Shumway, Martin and Antonescu, Corina and Salzberg, Steven
- Title: Versatile and open software for comparing large genomes
- Journal: Genome Biology
- Volume: 5
- Year: 2004
- Number: 2
- Pages: R12
- URL: http://genomebiology.com/2004/5/2/R12
- ISSN: 1465-6906
-Repository: http://mummer.cvs.sourceforge.net/mummer/
-Screenshots: http://sourceforge.net/project/screenshots.php?group_id=133157
Copied: trunk/packages/mustang/trunk/debian/upstream (from rev 9491, trunk/packages/mustang/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/mustang/trunk/debian/upstream (rev 0)
+++ trunk/packages/mustang/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,15 @@
+Contact: Arun S. Konagurthu (http://www.csse.unimelb.edu.au/~arun)
+DOI: 10.1002/prot.20921
+Homepage: http://www.cs.mu.oz.au/~arun/mustang/
+Name: MUSTANG
+PMID: 16736488
+Reference:
+ Author: Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey and Arthur M. Lesk
+ Title: MUSTANG: A multiple structural alignment algorithm
+ Journal: Proteins: Structure, Function, and Bioinformatics
+ Volume: 64
+ Number: 3
+ Pages: 559-574
+ Year: 2006
+ URL: http://www3.interscience.wiley.com/journal/112638073/abstract
+Watch: http://www.cs.mu.oz.au/~arun/mustang/ ./mustang_v([.\d]*)\.tgz
Deleted: trunk/packages/mustang/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/mustang/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/mustang/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,15 +0,0 @@
-Contact: Arun S. Konagurthu (http://www.csse.unimelb.edu.au/~arun)
-DOI: 10.1002/prot.20921
-Homepage: http://www.cs.mu.oz.au/~arun/mustang/
-Name: MUSTANG
-PMID: 16736488
-Reference:
- Author: Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey and Arthur M. Lesk
- Title: MUSTANG: A multiple structural alignment algorithm
- Journal: Proteins: Structure, Function, and Bioinformatics
- Volume: 64
- Number: 3
- Pages: 559-574
- Year: 2006
- URL: http://www3.interscience.wiley.com/journal/112638073/abstract
-Watch: http://www.cs.mu.oz.au/~arun/mustang/ ./mustang_v([.\d]*)\.tgz
Copied: trunk/packages/phy-spread/trunk/debian/upstream (from rev 9491, trunk/packages/phy-spread/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/phy-spread/trunk/debian/upstream (rev 0)
+++ trunk/packages/phy-spread/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,15 @@
+Contact: Filip Bielejec <filip.bielejec at rega.kuleuven.be>
+DOI: 10.1093/bioinformatics/btr481
+Homepage: http://www.kuleuven.be/aidslab/phylogeography/SPREAD.html
+Name: SPREAD
+PMID: 21911333
+Reference:
+ author: Filip Bielejec, Andrew Rambaut, Marc A. Suchard and Philippe Lemey
+ title: SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics
+ journal: Bioinformatics
+ volume: 27
+ number: 20
+ pages: 2910-2912
+ year: 2011
+ URL: http://bioinformatics.oxfordjournals.org/content/27/20/2910.full
+ eprint: http://bioinformatics.oxfordjournals.org/content/early/2011/09/11/bioinformatics.btr481.full.pdf+html
Deleted: trunk/packages/phy-spread/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/phy-spread/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/phy-spread/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,15 +0,0 @@
-Contact: Filip Bielejec <filip.bielejec at rega.kuleuven.be>
-DOI: 10.1093/bioinformatics/btr481
-Homepage: http://www.kuleuven.be/aidslab/phylogeography/SPREAD.html
-Name: SPREAD
-PMID: 21911333
-Reference:
- author: Filip Bielejec, Andrew Rambaut, Marc A. Suchard and Philippe Lemey
- title: SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics
- journal: Bioinformatics
- volume: 27
- number: 20
- pages: 2910-2912
- year: 2011
- URL: http://bioinformatics.oxfordjournals.org/content/27/20/2910.full
- eprint: http://bioinformatics.oxfordjournals.org/content/early/2011/09/11/bioinformatics.btr481.full.pdf+html
Copied: trunk/packages/phyml/trunk/debian/upstream (from rev 9491, trunk/packages/phyml/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/phyml/trunk/debian/upstream (rev 0)
+++ trunk/packages/phyml/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,23 @@
+Archive: Google code
+Contact: Stephane Guindon <guindon at stat.auckland.ac.nz>
+Name: PhyML
+Homepage: http://www.atgc-montpellier.fr/phyml
+Reference:
+ author: Guindon, Stephane and Gascuel, Olivier
+ title: A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
+ journal: Syst Biol
+ volume: 52
+ number: 5
+ pages: 696-704
+ doi: 10.1080/10635150390235520
+ year: 2003
+ URL: http://sysbio.oxfordjournals.org/cgi/content/abstract/52/5/696
+ eprint: http://sysbio.oxfordjournals.org/cgi/reprint/52/5/696.pdf
+ PMID: 14530136
+Repository: http://phyml.googlecode.com/svn/trunk/
+Repository-Browse: http://code.google.com/p/phyml/source/browse/
+Watch: |
+ version=3
+ http://code.google.com/p/phyml/downloads/list \
+ http://phyml[.]googlecode[.]com/files/phyml_(20.*)[.]tar[.]gz
+Webservice: http://www.atgc-montpellier.fr/phyml
Deleted: trunk/packages/phyml/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/phyml/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/phyml/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,23 +0,0 @@
-Archive: Google code
-Contact: Stephane Guindon <guindon at stat.auckland.ac.nz>
-Name: PhyML
-Homepage: http://www.atgc-montpellier.fr/phyml
-Reference:
- author: Guindon, Stephane and Gascuel, Olivier
- title: A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
- journal: Syst Biol
- volume: 52
- number: 5
- pages: 696-704
- doi: 10.1080/10635150390235520
- year: 2003
- URL: http://sysbio.oxfordjournals.org/cgi/content/abstract/52/5/696
- eprint: http://sysbio.oxfordjournals.org/cgi/reprint/52/5/696.pdf
- PMID: 14530136
-Repository: http://phyml.googlecode.com/svn/trunk/
-Repository-Browse: http://code.google.com/p/phyml/source/browse/
-Watch: |
- version=3
- http://code.google.com/p/phyml/downloads/list \
- http://phyml[.]googlecode[.]com/files/phyml_(20.*)[.]tar[.]gz
-Webservice: http://www.atgc-montpellier.fr/phyml
Copied: trunk/packages/poa/trunk/debian/upstream (from rev 9491, trunk/packages/poa/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/poa/trunk/debian/upstream (rev 0)
+++ trunk/packages/poa/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,18 @@
+Contact: Christopher Lee <leec at mbi.ucla.edu>
+DOI: 10.1093/bioinformatics/bth126
+Homepage: http://www.bioinformatics.ucla.edu/poa
+Name: POA
+PMID: 14962922
+Reference:
+ author: Grasso, Catherine and Lee, Christopher
+ title: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
+ journal: Bioinformatics
+ volume: 20
+ number: 10
+ pages: 1546-1556
+ year: 2004
+ URL: http:°bioinformatics.oxfordjournals.org¢gi¢ontentåbstract½0/10/1546
+ eprint: http:°bioinformatics.oxfordjournals.org¢gi/reprint½0/10/1546.pdf
+Watch: |
+ opts="uversionmangle=s/$/.0/,dversionmangle=s/\+.*$//" \
+ http://sf.net/poamsa/ poaV(.*)\.tar\.gz
Deleted: trunk/packages/poa/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/poa/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/poa/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,18 +0,0 @@
-Contact: Christopher Lee <leec at mbi.ucla.edu>
-DOI: 10.1093/bioinformatics/bth126
-Homepage: http://www.bioinformatics.ucla.edu/poa
-Name: POA
-PMID: 14962922
-Reference:
- author: Grasso, Catherine and Lee, Christopher
- title: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
- journal: Bioinformatics
- volume: 20
- number: 10
- pages: 1546-1556
- year: 2004
- URL: http:°bioinformatics.oxfordjournals.org¢gi¢ontentåbstract½0/10/1546
- eprint: http:°bioinformatics.oxfordjournals.org¢gi/reprint½0/10/1546.pdf
-Watch: |
- opts="uversionmangle=s/$/.0/,dversionmangle=s/\+.*$//" \
- http://sf.net/poamsa/ poaV(.*)\.tar\.gz
Copied: trunk/packages/primer3/trunk/debian/upstream (from rev 9491, trunk/packages/primer3/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/primer3/trunk/debian/upstream (rev 0)
+++ trunk/packages/primer3/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,18 @@
+Contact: Steve Rozen (http://purl.com/STEVEROZEN/)
+Homepage: http://primer3.sourceforge.net
+Name: Primer3
+PMID: 10547847
+Reference:
+ Author: Steve Rozen and Helen J. Skaletsky
+ Year: 2000
+ Title: Primer3 on the WWW for general users and for biologist programmers
+ Booktitle: Bioinformatics Methods and Protocols: Methods in Molecular Biology
+ Journal: Methods Mol Biol.
+ Pages: 365-86
+ Number: 132
+ Publisher: Humana Press
+ Editor: Krawetz S, Misener S
+Watch: http://sf.net/primer3/primer3-([\d.]*)\.tar\.gz
+Webservice:
+ - http://frodo.wi.mit.edu/primer3/
+ - http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
Deleted: trunk/packages/primer3/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/primer3/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/primer3/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,18 +0,0 @@
-Contact: Steve Rozen (http://purl.com/STEVEROZEN/)
-Homepage: http://primer3.sourceforge.net
-Name: Primer3
-PMID: 10547847
-Reference:
- Author: Steve Rozen and Helen J. Skaletsky
- Year: 2000
- Title: Primer3 on the WWW for general users and for biologist programmers
- Booktitle: Bioinformatics Methods and Protocols: Methods in Molecular Biology
- Journal: Methods Mol Biol.
- Pages: 365-86
- Number: 132
- Publisher: Humana Press
- Editor: Krawetz S, Misener S
-Watch: http://sf.net/primer3/primer3-([\d.]*)\.tar\.gz
-Webservice:
- - http://frodo.wi.mit.edu/primer3/
- - http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
Copied: trunk/packages/probalign/trunk/debian/upstream (from rev 9491, trunk/packages/probalign/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/probalign/trunk/debian/upstream (rev 0)
+++ trunk/packages/probalign/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,15 @@
+Contact: Usman Roshan <usman at cs.njit.edu>
+DOI: 10.1093/bioinformatics/btl472
+Homepage: http://cs.njit.edu/usman/probalign/
+PMID: 16954142
+Name: Probalign
+Reference:
+ AUTHOR: Usman Roshan, Dennis R. Livesay
+ TITILE: Probalign: multiple sequence alignment using partition function posterior probabilities
+ JOURNAL: Bioinformatics
+ YEAR: 2006
+ PAGES: 2715-21
+ VOLUME: 22
+ NUMBER: 22
+ URL: http://bioinformatics.oxfordjournals.org/content/22/22/2715.short
+ ISSN: 1460-2059
Deleted: trunk/packages/probalign/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/probalign/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/probalign/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,15 +0,0 @@
-Contact: Usman Roshan <usman at cs.njit.edu>
-DOI: 10.1093/bioinformatics/btl472
-Homepage: http://cs.njit.edu/usman/probalign/
-PMID: 16954142
-Name: Probalign
-Reference:
- AUTHOR: Usman Roshan, Dennis R. Livesay
- TITILE: Probalign: multiple sequence alignment using partition function posterior probabilities
- JOURNAL: Bioinformatics
- YEAR: 2006
- PAGES: 2715-21
- VOLUME: 22
- NUMBER: 22
- URL: http://bioinformatics.oxfordjournals.org/content/22/22/2715.short
- ISSN: 1460-2059
Copied: trunk/packages/probcons/trunk/debian/upstream (from rev 9491, trunk/packages/probcons/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/probcons/trunk/debian/upstream (rev 0)
+++ trunk/packages/probcons/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,16 @@
+Contact: Chuong Do <chuongdo at cs.stanford.edu>
+DOI: 10.1101/gr.2821705
+Homepage: http://probcons.stanford.edu/
+Name: ProbCons
+PMID: 15687296
+Reference:
+ author: Do, Chuong B. and Mahabhashyam, Mahathi S.P. and Brudno, Michael and Batzoglou, Serafim
+ title: ProbCons: Probabilistic consistency-based multiple sequence alignment
+ journal: Genome Research
+ volume: 15
+ number: 2
+ pages: 330-340
+ year: 2005
+ URL: http://genome.cshlp.org/content/15/2/330.abstract
+ eprint: http://genome.cshlp.org/content/15/2/330.full.pdf+html
+Watch: http://probcons.stanford.edu/download.html probcons_v(\d+)_(\d+)\.tar\.gz
Deleted: trunk/packages/probcons/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/probcons/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/probcons/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,16 +0,0 @@
-Contact: Chuong Do <chuongdo at cs.stanford.edu>
-DOI: 10.1101/gr.2821705
-Homepage: http://probcons.stanford.edu/
-Name: ProbCons
-PMID: 15687296
-Reference:
- author: Do, Chuong B. and Mahabhashyam, Mahathi S.P. and Brudno, Michael and Batzoglou, Serafim
- title: ProbCons: Probabilistic consistency-based multiple sequence alignment
- journal: Genome Research
- volume: 15
- number: 2
- pages: 330-340
- year: 2005
- URL: http://genome.cshlp.org/content/15/2/330.abstract
- eprint: http://genome.cshlp.org/content/15/2/330.full.pdf+html
-Watch: http://probcons.stanford.edu/download.html probcons_v(\d+)_(\d+)\.tar\.gz
Copied: trunk/packages/proda/trunk/debian/upstream (from rev 9491, trunk/packages/proda/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/proda/trunk/debian/upstream (rev 0)
+++ trunk/packages/proda/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,17 @@
+DOI: 10.1093/nar/gkl511
+Name: ProDA
+Homepage: http://proda.stanford.edu/
+PMID: 17068081
+Reference:
+ author: Phuong, Tu Minh and Do, Chuong B. and Edgar, Robert C. and Batzoglou, Serafim
+ title: Multiple alignment of protein sequences with repeats and rearrangements
+ journal: Nucl. Acids Res.
+ volume: 34
+ number: 20
+ pages: 5932-5942
+ year: 2006
+ URL: http://nar.oxfordjournals.org/cgi/content/abstract/34/20/5932
+ eprint: http://nar.oxfordjournals.org/cgi/reprint/34/20/5932.pdf
+Watch: |
+ opts="uversionmangle=s/_/\./" \
+ http://proda.stanford.edu/proda_(.*)\.tar\.gz
Deleted: trunk/packages/proda/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/proda/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/proda/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,17 +0,0 @@
-DOI: 10.1093/nar/gkl511
-Name: ProDA
-Homepage: http://proda.stanford.edu/
-PMID: 17068081
-Reference:
- author: Phuong, Tu Minh and Do, Chuong B. and Edgar, Robert C. and Batzoglou, Serafim
- title: Multiple alignment of protein sequences with repeats and rearrangements
- journal: Nucl. Acids Res.
- volume: 34
- number: 20
- pages: 5932-5942
- year: 2006
- URL: http://nar.oxfordjournals.org/cgi/content/abstract/34/20/5932
- eprint: http://nar.oxfordjournals.org/cgi/reprint/34/20/5932.pdf
-Watch: |
- opts="uversionmangle=s/_/\./" \
- http://proda.stanford.edu/proda_(.*)\.tar\.gz
Copied: trunk/packages/python-pynast/trunk/debian/upstream (from rev 9491, trunk/packages/python-pynast/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/python-pynast/trunk/debian/upstream (rev 0)
+++ trunk/packages/python-pynast/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,12 @@
+Name: PyNAST
+Homepage: http://pynast.sourceforge.net/
+DOI: 10.1093/bioinformatics/btp636
+PMID: 19914921
+Reference:
+ Author: J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight
+ Title: PyNAST: a flexible tool for aligning sequences to a template alignment
+ Journal: Bioinformatics
+ Volume: 26
+ Pages: 266-267.
+ Year: 2010
+ URL: http://bioinformatics.oxfordjournals.org/content/26/2/266.long
Deleted: trunk/packages/python-pynast/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/python-pynast/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/python-pynast/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,12 +0,0 @@
-Name: PyNAST
-Homepage: http://pynast.sourceforge.net/
-DOI: 10.1093/bioinformatics/btp636
-PMID: 19914921
-Reference:
- Author: J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight
- Title: PyNAST: a flexible tool for aligning sequences to a template alignment
- Journal: Bioinformatics
- Volume: 26
- Pages: 266-267.
- Year: 2010
- URL: http://bioinformatics.oxfordjournals.org/content/26/2/266.long
Copied: trunk/packages/qiime/trunk/debian/upstream (from rev 9491, trunk/packages/qiime/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/qiime/trunk/debian/upstream (rev 0)
+++ trunk/packages/qiime/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,12 @@
+Name: QIIME
+Homepage: http://www.qiime.org/
+DOI: 10.1038/nmeth.f.303
+PMID: 20383131
+Reference:
+ Author: Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R.
+ Title: QIIME allows analysis of high-throughput community sequencing data
+ Journal: Nature Methods
+ Volume: 7
+ Pages: 335 - 336
+ Year: 2010
+ URL: http://www.nature.com/nmeth/journal/v7/n5/full/nmeth.f.303.html
Deleted: trunk/packages/qiime/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/qiime/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/qiime/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,12 +0,0 @@
-Name: QIIME
-Homepage: http://www.qiime.org/
-DOI: 10.1038/nmeth.f.303
-PMID: 20383131
-Reference:
- Author: Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R.
- Title: QIIME allows analysis of high-throughput community sequencing data
- Journal: Nature Methods
- Volume: 7
- Pages: 335 - 336
- Year: 2010
- URL: http://www.nature.com/nmeth/journal/v7/n5/full/nmeth.f.303.html
Copied: trunk/packages/raster3d/trunk/debian/upstream (from rev 9491, trunk/packages/raster3d/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/raster3d/trunk/debian/upstream (rev 0)
+++ trunk/packages/raster3d/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,11 @@
+Homepage: http://skuld.bmsc.washington.edu/raster3d/
+Name: Raster3D
+PMID: 18488322
+Reference:
+ Article: MerrittBacon1997
+ Author: Merritt, E.A. and Bacon, D.J.
+ Title: Raster3D Photorealistic Molecular Graphics
+ Journal: Methods in Enzymology
+ Volume: 277
+ Pages: 505-524
+ Year: 1997
Deleted: trunk/packages/raster3d/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/raster3d/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/raster3d/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,11 +0,0 @@
-Homepage: http://skuld.bmsc.washington.edu/raster3d/
-Name: Raster3D
-PMID: 18488322
-Reference:
- Article: MerrittBacon1997
- Author: Merritt, E.A. and Bacon, D.J.
- Title: Raster3D Photorealistic Molecular Graphics
- Journal: Methods in Enzymology
- Volume: 277
- Pages: 505-524
- Year: 1997
Copied: trunk/packages/raxml/trunk/debian/upstream (from rev 9491, trunk/packages/raxml/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/raxml/trunk/debian/upstream (rev 0)
+++ trunk/packages/raxml/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,11 @@
+Contact: Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch>
+DOI: 10.1093/bioinformatics/btl446
+Homepage: http://wwwkramer.in.tum.de/exelixis/software.html
+Name: RAxML
+PMID: 16928733
+Reference:
+ author: 16928733
+ title: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
+ journal: Bioinformatics
+ year: 2006
+ URL: http://bioinformatics.oxfordjournals.org/content/22/21/2688.full
Deleted: trunk/packages/raxml/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/raxml/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/raxml/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,11 +0,0 @@
-Contact: Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch>
-DOI: 10.1093/bioinformatics/btl446
-Homepage: http://wwwkramer.in.tum.de/exelixis/software.html
-Name: RAxML
-PMID: 16928733
-Reference:
- author: 16928733
- title: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
- journal: Bioinformatics
- year: 2006
- URL: http://bioinformatics.oxfordjournals.org/content/22/21/2688.full
Copied: trunk/packages/rnahybrid/trunk/debian/upstream (from rev 9491, trunk/packages/rnahybrid/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/rnahybrid/trunk/debian/upstream (rev 0)
+++ trunk/packages/rnahybrid/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,16 @@
+DOI: 10.1261/rna.5248604
+Homepage: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid
+Name: RNAhybrid
+PMID: 15383676
+Reference:
+ author: REHMSMEIER, MARC and STEFFEN, PETER and HÖCHSMANN, MATTHIAS and GIEGERICH, ROBERT
+ title: Fast and effective prediction of microRNA/target duplexes
+ journal: RNA
+ volume: 10
+ number: 10
+ pages: 1507-1517
+ doi: 10.1261/rna.5248604
+ year: 2004
+ URL: http://rnajournal.cshlp.org/content/10/10/1507.abstract
+ eprint: http://rnajournal.cshlp.org/content/10/10/1507.full.pdf+html
+Webservice: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html
Deleted: trunk/packages/rnahybrid/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/rnahybrid/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/rnahybrid/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,16 +0,0 @@
-DOI: 10.1261/rna.5248604
-Homepage: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid
-Name: RNAhybrid
-PMID: 15383676
-Reference:
- author: REHMSMEIER, MARC and STEFFEN, PETER and HÖCHSMANN, MATTHIAS and GIEGERICH, ROBERT
- title: Fast and effective prediction of microRNA/target duplexes
- journal: RNA
- volume: 10
- number: 10
- pages: 1507-1517
- doi: 10.1261/rna.5248604
- year: 2004
- URL: http://rnajournal.cshlp.org/content/10/10/1507.abstract
- eprint: http://rnajournal.cshlp.org/content/10/10/1507.full.pdf+html
-Webservice: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html
Copied: trunk/packages/rostlab/disulfinder/trunk/debian/upstream (from rev 9491, trunk/packages/rostlab/disulfinder/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/upstream (rev 0)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,34 @@
+Name: disulfinder
+Reference:
+ - Author: A. Ceroni and A. Passerini and A. Vullo and P. Frasconi
+ Title: 'DISULFIND: a disulfide bonding state and cysteine connectivity prediction server.'
+ Journal: Nucleic Acids Res
+ Volume: 34
+ Number: Web Server issue
+ Pages: W177-81
+ Year: 2006
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/16844986
+ PMID: 16844986
+ - Comment: For the disulphide connectivity predictor
+ Author: Vullo, Alessandro, and Frasconi, Paolo
+ Title: Disulfide connectivity prediction using recursive neural networks and evolutionary information.
+ Journal: Bioinformatics
+ Volume: 20
+ Number: 5
+ Pages: 653-9
+ Year: 2004
+ Month: March
+ PMID: 15033872
+ - Comment: For the cystein bonding state predictor
+ Author: A. Ceroni, P. Frasconi, A. Passerini and A. Vullo
+ Title: Predicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines
+ Journal: Journal of VLSI Signal Processing
+ Volume: 35
+ Pages: 287-295
+ Year: 2003
+ - Comment: For the cystein bonding state predictor
+ Author: P. Frasconi, A. Passerini and A. Vullo
+ Title: A Two-Stage SVM Architecture for Predicting the Disulfide Bonding State of Cysteines
+ Journal: Proc. IEEE Workshop on Neural Networks for Signal Processing
+ Pages: 25-34
+ Year: 2002
Deleted: trunk/packages/rostlab/disulfinder/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,34 +0,0 @@
-Name: disulfinder
-Reference:
- - Author: A. Ceroni and A. Passerini and A. Vullo and P. Frasconi
- Title: 'DISULFIND: a disulfide bonding state and cysteine connectivity prediction server.'
- Journal: Nucleic Acids Res
- Volume: 34
- Number: Web Server issue
- Pages: W177-81
- Year: 2006
- URL: http://www.ncbi.nlm.nih.gov/pubmed/16844986
- PMID: 16844986
- - Comment: For the disulphide connectivity predictor
- Author: Vullo, Alessandro, and Frasconi, Paolo
- Title: Disulfide connectivity prediction using recursive neural networks and evolutionary information.
- Journal: Bioinformatics
- Volume: 20
- Number: 5
- Pages: 653-9
- Year: 2004
- Month: March
- PMID: 15033872
- - Comment: For the cystein bonding state predictor
- Author: A. Ceroni, P. Frasconi, A. Passerini and A. Vullo
- Title: Predicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines
- Journal: Journal of VLSI Signal Processing
- Volume: 35
- Pages: 287-295
- Year: 2003
- - Comment: For the cystein bonding state predictor
- Author: P. Frasconi, A. Passerini and A. Vullo
- Title: A Two-Stage SVM Architecture for Predicting the Disulfide Bonding State of Cysteines
- Journal: Proc. IEEE Workshop on Neural Networks for Signal Processing
- Pages: 25-34
- Year: 2002
Copied: trunk/packages/rostlab/libzerg/trunk/debian/upstream (from rev 9491, trunk/packages/rostlab/libzerg/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/rostlab/libzerg/trunk/debian/upstream (rev 0)
+++ trunk/packages/rostlab/libzerg/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,14 @@
+Contact: Apuã Paquola <apuapaquola at gmail.com>
+DOI: 10.1093/bioinformatics/btg122
+Homepage: http://code.google.com/p/libzerg/
+Name: libzerg
+Reference:
+ author: Paquola, Apuã C M, Machado, Abimael A, Reis, Eduardo M, Da Silva, Aline M, and Verjovski-Almeida, Sergio
+ title: Zerg: a very fast BLAST parser library.
+ journal: Bioinformatics
+ volume: 19
+ number: 8
+ pages: 1035-6
+ year: 2003
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/12761068
+ PMID: 12761068
Deleted: trunk/packages/rostlab/libzerg/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/rostlab/libzerg/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/rostlab/libzerg/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,14 +0,0 @@
-Contact: Apuã Paquola <apuapaquola at gmail.com>
-DOI: 10.1093/bioinformatics/btg122
-Homepage: http://code.google.com/p/libzerg/
-Name: libzerg
-Reference:
- author: Paquola, Apuã C M, Machado, Abimael A, Reis, Eduardo M, Da Silva, Aline M, and Verjovski-Almeida, Sergio
- title: Zerg: a very fast BLAST parser library.
- journal: Bioinformatics
- volume: 19
- number: 8
- pages: 1035-6
- year: 2003
- URL: http://www.ncbi.nlm.nih.gov/pubmed/12761068
- PMID: 12761068
Copied: trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream (from rev 9491, trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream (rev 0)
+++ trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,14 @@
+Contact: Apuã Paquola <apuapaquola at gmail.com>
+DOI: 10.1093/bioinformatics/btg122
+Homepage: http://code.google.com/p/libzerg/
+Name: libzerg-perl
+Reference:
+ author: Paquola, Apuã C M, Machado, Abimael A, Reis, Eduardo M, Da Silva, Aline M, and Verjovski-Almeida, Sergio
+ title: Zerg: a very fast BLAST parser library.
+ journal: Bioinformatics
+ volume: 19
+ number: 8
+ pages: 1035-6
+ year: 2003
+ URL: http://code.google.com/p/libzerg/
+ PMID: 12761068
Deleted: trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,14 +0,0 @@
-Contact: Apuã Paquola <apuapaquola at gmail.com>
-DOI: 10.1093/bioinformatics/btg122
-Homepage: http://code.google.com/p/libzerg/
-Name: libzerg-perl
-Reference:
- author: Paquola, Apuã C M, Machado, Abimael A, Reis, Eduardo M, Da Silva, Aline M, and Verjovski-Almeida, Sergio
- title: Zerg: a very fast BLAST parser library.
- journal: Bioinformatics
- volume: 19
- number: 8
- pages: 1035-6
- year: 2003
- URL: http://code.google.com/p/libzerg/
- PMID: 12761068
Copied: trunk/packages/rostlab/profphd/trunk/debian/upstream (from rev 9491, trunk/packages/rostlab/profphd/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/upstream (rev 0)
+++ trunk/packages/rostlab/profphd/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,29 @@
+Name: profphd
+Reference:
+ - Author: Rost, B. and Sander, C.
+ Title: 'Combining evolutionary information and neural networks to predict protein secondary structure.'
+ Journal: Proteins
+ Volume: 19
+ Number: 1
+ Pages: 55-72
+ Year: 1994
+ URL: http://rostlab.org/
+ PMID: 8066087
+ - Author: Rost, B. and Sander, C.
+ Title: 'Conservation and prediction of solvent accessibility in protein families.'
+ Journal: Proteins
+ Volume: 20
+ Number: 3
+ Pages: 216-26
+ Year: 1994
+ URL: http://rostlab.org/
+ PMID: 7892171
+ - Author: Rost, B., Casadio, R., Fariselli, P., and Sander, C.
+ Title: 'Transmembrane helices predicted at 95% accuracy.'
+ Journal: Protein Sci
+ Volume: 4
+ Number: 3
+ Pages: 521-33
+ Year: 1995
+ URL: http://rostlab.org/
+ PMID: 7795533
Deleted: trunk/packages/rostlab/profphd/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/rostlab/profphd/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/rostlab/profphd/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,29 +0,0 @@
-Name: profphd
-Reference:
- - Author: Rost, B. and Sander, C.
- Title: 'Combining evolutionary information and neural networks to predict protein secondary structure.'
- Journal: Proteins
- Volume: 19
- Number: 1
- Pages: 55-72
- Year: 1994
- URL: http://rostlab.org/
- PMID: 8066087
- - Author: Rost, B. and Sander, C.
- Title: 'Conservation and prediction of solvent accessibility in protein families.'
- Journal: Proteins
- Volume: 20
- Number: 3
- Pages: 216-26
- Year: 1994
- URL: http://rostlab.org/
- PMID: 7892171
- - Author: Rost, B., Casadio, R., Fariselli, P., and Sander, C.
- Title: 'Transmembrane helices predicted at 95% accuracy.'
- Journal: Protein Sci
- Volume: 4
- Number: 3
- Pages: 521-33
- Year: 1995
- URL: http://rostlab.org/
- PMID: 7795533
Copied: trunk/packages/seaview/trunk/debian/upstream (from rev 9491, trunk/packages/seaview/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/seaview/trunk/debian/upstream (rev 0)
+++ trunk/packages/seaview/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,20 @@
+Contact: Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
+Documentation: http://pbil.univ-lyon1.fr/software/seaview_data/seaview
+Downloads: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/
+Homepage: http://pbil.univ-lyon1.fr/software/seaview
+Name: SeaView
+Reference:
+ author: Gouy, Manolo and Guindon, Stephane and Gascuel, Olivier
+ title: SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building
+ journal: Mol Biol Evol
+ volume: 27
+ number: 2
+ pages: 221-224
+ year: 2010
+ PMID: 19854763
+ DOI: 10.1093/molbev/msp259
+ URL: http://mbe.oxfordjournals.org/cgi/content/abstract/27/2/221
+ eprint: http://mbe.oxfordjournals.org/cgi/reprint/27/2/221.pdf
+Screenshots:
+ - http://pbil.univ-lyon1.fr/binaries/seaview4.png
+ - http://pbil.univ-lyon1.fr/binaries/seaview-tree.png
Deleted: trunk/packages/seaview/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/seaview/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/seaview/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,20 +0,0 @@
-Contact: Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
-Documentation: http://pbil.univ-lyon1.fr/software/seaview_data/seaview
-Downloads: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/
-Homepage: http://pbil.univ-lyon1.fr/software/seaview
-Name: SeaView
-Reference:
- author: Gouy, Manolo and Guindon, Stephane and Gascuel, Olivier
- title: SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building
- journal: Mol Biol Evol
- volume: 27
- number: 2
- pages: 221-224
- year: 2010
- PMID: 19854763
- DOI: 10.1093/molbev/msp259
- URL: http://mbe.oxfordjournals.org/cgi/content/abstract/27/2/221
- eprint: http://mbe.oxfordjournals.org/cgi/reprint/27/2/221.pdf
-Screenshots:
- - http://pbil.univ-lyon1.fr/binaries/seaview4.png
- - http://pbil.univ-lyon1.fr/binaries/seaview-tree.png
Copied: trunk/packages/seqan/trunk/debian/upstream (from rev 9491, trunk/packages/seqan/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/seqan/trunk/debian/upstream (rev 0)
+++ trunk/packages/seqan/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,20 @@
+Contact: SeqAn Team (http://www.seqan.de/contact-us.html)
+DOI: 10.1186/1471-2105-9-11
+Donate: http://www.seqan.de/
+Homepage: http://www.seqan.de/
+Name: SeqAn
+PMID: 18184432
+Reference:
+ AUTHOR: Doring, Andreas and Weese, David and Rausch, Tobias and Reinert, Knut
+ TITLE: SeqAn An efficient, generic C++ library for sequence analysis
+ JOURNAL: BMC Bioinformatics
+ VOLUME: 9
+ YEAR: 2008
+ NUMBER: 1
+ PAGES: 11
+ URL: http://www.biomedcentral.com/1471-2105/9/11
+ ISSN: 1471-2105
+Watch: |
+ http://www.seqan.de/downloads/releases.html \
+ .*/Seqan_Release_([\d\.]+).zip \
+ debian debian/orig-tar.sh
Deleted: trunk/packages/seqan/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/seqan/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/seqan/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,20 +0,0 @@
-Contact: SeqAn Team (http://www.seqan.de/contact-us.html)
-DOI: 10.1186/1471-2105-9-11
-Donate: http://www.seqan.de/
-Homepage: http://www.seqan.de/
-Name: SeqAn
-PMID: 18184432
-Reference:
- AUTHOR: Doring, Andreas and Weese, David and Rausch, Tobias and Reinert, Knut
- TITLE: SeqAn An efficient, generic C++ library for sequence analysis
- JOURNAL: BMC Bioinformatics
- VOLUME: 9
- YEAR: 2008
- NUMBER: 1
- PAGES: 11
- URL: http://www.biomedcentral.com/1471-2105/9/11
- ISSN: 1471-2105
-Watch: |
- http://www.seqan.de/downloads/releases.html \
- .*/Seqan_Release_([\d\.]+).zip \
- debian debian/orig-tar.sh
Copied: trunk/packages/sigma-align/trunk/debian/upstream (from rev 9491, trunk/packages/sigma-align/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/sigma-align/trunk/debian/upstream (rev 0)
+++ trunk/packages/sigma-align/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,16 @@
+Contact: Rahul Siddharthan <rsidd AT imsc.res.in>
+DOI: 10.1186/1471-2105-7-143
+Homepage: http://www.imsc.res.in/~rsidd/sigma/
+PMID: 16542424
+Name: Sigma
+Reference:
+ AUTHOR: Siddharthan, Rahul
+ TITLE: Sigma: multiple alignment of weakly-conserved non-coding DNA sequence
+ JOURNAL: BMC Bioinformatics
+ VOLUME: 7
+ YEAR: 2006
+ NUMBER: 1
+ PAGES: 143
+ URL: http://www.biomedcentral.com/1471-2105/7/143
+ ISSN: 1471-2105
+Watch: http://www.imsc.res.in/~rsidd/sigma/ source/sigma-(.*)\.tar\.gz
Deleted: trunk/packages/sigma-align/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/sigma-align/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/sigma-align/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,16 +0,0 @@
-Contact: Rahul Siddharthan <rsidd AT imsc.res.in>
-DOI: 10.1186/1471-2105-7-143
-Homepage: http://www.imsc.res.in/~rsidd/sigma/
-PMID: 16542424
-Name: Sigma
-Reference:
- AUTHOR: Siddharthan, Rahul
- TITLE: Sigma: multiple alignment of weakly-conserved non-coding DNA sequence
- JOURNAL: BMC Bioinformatics
- VOLUME: 7
- YEAR: 2006
- NUMBER: 1
- PAGES: 143
- URL: http://www.biomedcentral.com/1471-2105/7/143
- ISSN: 1471-2105
-Watch: http://www.imsc.res.in/~rsidd/sigma/ source/sigma-(.*)\.tar\.gz
Copied: trunk/packages/t-coffee/trunk/debian/upstream (from rev 9491, trunk/packages/t-coffee/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/t-coffee/trunk/debian/upstream (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,14 @@
+Contact: Cédric Notredame <cedric.notredame at europe.com>
+DOI: 10.1006/jmbi.2000.4042
+Name: T-Coffee
+Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
+PMID: 10964570
+Reference-Author: Cédric Notredame and Desmond G. Higgins and Jaap Heringa
+Reference-Journal: Journal of Molecular Biology
+Reference-Number: 1
+Reference-Pages: 205-217
+Reference-Title: T-coffee: a novel method for fast and accurate multiple sequence alignment
+Reference-URL: http://www.sciencedirect.com/science/article/B6WK7-45F5150-7S/2/9c2fd0f2a43f877fd801b3245fe0beed
+Reference-Volume: 302
+Reference-Year: 2000
+Watch: http://www.tcoffee.org/Packages/ T-COFFEE_distribution_Version_(.*)\.tar\.gz
Deleted: trunk/packages/t-coffee/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/t-coffee/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/t-coffee/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,14 +0,0 @@
-Contact: Cédric Notredame <cedric.notredame at europe.com>
-DOI: 10.1006/jmbi.2000.4042
-Name: T-Coffee
-Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
-PMID: 10964570
-Reference-Author: Cédric Notredame and Desmond G. Higgins and Jaap Heringa
-Reference-Journal: Journal of Molecular Biology
-Reference-Number: 1
-Reference-Pages: 205-217
-Reference-Title: T-coffee: a novel method for fast and accurate multiple sequence alignment
-Reference-URL: http://www.sciencedirect.com/science/article/B6WK7-45F5150-7S/2/9c2fd0f2a43f877fd801b3245fe0beed
-Reference-Volume: 302
-Reference-Year: 2000
-Watch: http://www.tcoffee.org/Packages/ T-COFFEE_distribution_Version_(.*)\.tar\.gz
Copied: trunk/packages/tm-align/trunk/debian/upstream (from rev 9491, trunk/packages/tm-align/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/tm-align/trunk/debian/upstream (rev 0)
+++ trunk/packages/tm-align/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,15 @@
+Contact: Yang Zhang <zhng at umich.edu>
+DOI: 10.1093/nar/gki524
+Homepage: http://zhanglab.ccmb.med.umich.edu/TM-align/
+PMID: 15849316
+Name: TM-align & TM-score
+Reference:
+ AUTHOR: Y. Zhang, J. Skolnick
+ TITILE: TM-align: A protein structure alignment algorithm based on TM-score
+ JOURNAL: Nucleic Acids Research
+ YEAR: 2005
+ PAGES: 2302-2309
+ VOLUME: 33
+ NUMBER: 7
+ URL: http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.pdf
+ ISSN: 1362-4962
Deleted: trunk/packages/tm-align/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/tm-align/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/tm-align/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,15 +0,0 @@
-Contact: Yang Zhang <zhng at umich.edu>
-DOI: 10.1093/nar/gki524
-Homepage: http://zhanglab.ccmb.med.umich.edu/TM-align/
-PMID: 15849316
-Name: TM-align & TM-score
-Reference:
- AUTHOR: Y. Zhang, J. Skolnick
- TITILE: TM-align: A protein structure alignment algorithm based on TM-score
- JOURNAL: Nucleic Acids Research
- YEAR: 2005
- PAGES: 2302-2309
- VOLUME: 33
- NUMBER: 7
- URL: http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.pdf
- ISSN: 1362-4962
Copied: trunk/packages/transtermhp/trunk/debian/upstream (from rev 9491, trunk/packages/transtermhp/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/transtermhp/trunk/debian/upstream (rev 0)
+++ trunk/packages/transtermhp/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,11 @@
+Contact: Carl Kingsford <carlk at umiacs.umd.edu>
+DOI: 10.1186/gb-2007-8-2-r22
+Homepage: http://transterm.cbcb.umd.edu/
+PMID: 17313685
+Name: TransTermHP
+Reference:
+ AUTHOR: C. Kingsford, K. Ayanbule, S.L. Salzberg
+ TITILE: Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
+ JOURNAL: Genome Biology
+ YEAR: 2007
+ URL: http://genomebiology.com/2007/8/2/R22/abstract
Deleted: trunk/packages/transtermhp/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/transtermhp/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/transtermhp/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,11 +0,0 @@
-Contact: Carl Kingsford <carlk at umiacs.umd.edu>
-DOI: 10.1186/gb-2007-8-2-r22
-Homepage: http://transterm.cbcb.umd.edu/
-PMID: 17313685
-Name: TransTermHP
-Reference:
- AUTHOR: C. Kingsford, K. Ayanbule, S.L. Salzberg
- TITILE: Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
- JOURNAL: Genome Biology
- YEAR: 2007
- URL: http://genomebiology.com/2007/8/2/R22/abstract
Copied: trunk/packages/treeviewx/trunk/debian/upstream (from rev 9491, trunk/packages/treeviewx/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/treeviewx/trunk/debian/upstream (rev 0)
+++ trunk/packages/treeviewx/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,19 @@
+Archive: Google Code
+Contact: Roderic D. M. Page <r.page at bio.gla.ac.uk>
+Download: http://code.google.com/p/treeviewx/downloads/
+Homepage: http://code.google.com/p/treeviewx/
+Name: Treeview X
+Reference:
+ Author: Page, Roderic D. M.
+ Journal: Comput. Appl. Biosci.
+ Number: 4
+ Page: 357-8
+ Title: TreeView: an application to display phylogenetic trees on personal computers
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/citation/12/4/357
+ Volume: 12
+ Year: 1996
+ PMID: 8902363
+ DOI: 10.1093/bioinformatics/12.4.357
+Repository: http://treeviewx.googlecode.com/svn/
+Repository-Browse: http://code.google.com/p/treeviewx/source/browse/
+Watch: http://googlecode.debian.net/p/treeviewx/tv.(\d+.*)\.tar\.gz
Deleted: trunk/packages/treeviewx/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/treeviewx/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/treeviewx/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,19 +0,0 @@
-Archive: Google Code
-Contact: Roderic D. M. Page <r.page at bio.gla.ac.uk>
-Download: http://code.google.com/p/treeviewx/downloads/
-Homepage: http://code.google.com/p/treeviewx/
-Name: Treeview X
-Reference:
- Author: Page, Roderic D. M.
- Journal: Comput. Appl. Biosci.
- Number: 4
- Page: 357-8
- Title: TreeView: an application to display phylogenetic trees on personal computers
- URL: http://bioinformatics.oxfordjournals.org/cgi/content/citation/12/4/357
- Volume: 12
- Year: 1996
- PMID: 8902363
- DOI: 10.1093/bioinformatics/12.4.357
-Repository: http://treeviewx.googlecode.com/svn/
-Repository-Browse: http://code.google.com/p/treeviewx/source/browse/
-Watch: http://googlecode.debian.net/p/treeviewx/tv.(\d+.*)\.tar\.gz
Copied: trunk/packages/velvet/trunk/debian/upstream (from rev 9491, trunk/packages/velvet/trunk/debian/upstream-metadata.yaml)
===================================================================
--- trunk/packages/velvet/trunk/debian/upstream (rev 0)
+++ trunk/packages/velvet/trunk/debian/upstream 2012-01-29 03:35:57 UTC (rev 9492)
@@ -0,0 +1,17 @@
+Contact: Daniel Zerbino <zerbino at ebi.ac.uk>
+DOI: 10.1101/gr.074492.107
+Homepage: http://www.ebi.ac.uk/~zerbino/velvet/
+Name: Velvet
+PMID: 18349386
+Reference:
+ author: Zerbino, Daniel R. and Birney, Ewan
+ title: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
+ journal: Genome Research
+ volume: 18
+ number: 5
+ pages: 821-829
+ year: 2008
+ URL: http://genome.cshlp.org/content/18/5/821.abstract
+ eprint: http://genome.cshlp.org/content/18/5/821.full.pdf+html
+Repository: http://github.com/dzerbino/velvet
+Watch: http://www.ebi.ac.uk/~zerbino/velvet/velvet_([.\d]*).tgz
Deleted: trunk/packages/velvet/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/velvet/trunk/debian/upstream-metadata.yaml 2012-01-28 23:59:25 UTC (rev 9491)
+++ trunk/packages/velvet/trunk/debian/upstream-metadata.yaml 2012-01-29 03:35:57 UTC (rev 9492)
@@ -1,17 +0,0 @@
-Contact: Daniel Zerbino <zerbino at ebi.ac.uk>
-DOI: 10.1101/gr.074492.107
-Homepage: http://www.ebi.ac.uk/~zerbino/velvet/
-Name: Velvet
-PMID: 18349386
-Reference:
- author: Zerbino, Daniel R. and Birney, Ewan
- title: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
- journal: Genome Research
- volume: 18
- number: 5
- pages: 821-829
- year: 2008
- URL: http://genome.cshlp.org/content/18/5/821.abstract
- eprint: http://genome.cshlp.org/content/18/5/821.full.pdf+html
-Repository: http://github.com/dzerbino/velvet
-Watch: http://www.ebi.ac.uk/~zerbino/velvet/velvet_([.\d]*).tgz
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