[Blends-commit] r3260 - in /projects/med/trunk/debian-med/tasks: bio bio-ngs bio-phylogeny

Wed Apr 4 07:40:45 UTC 2012

Author: tille
Date: Wed Apr  4 07:40:44 2012
New Revision: 3260

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3260
Log:
Good to see duplicated data in different tasks vanishing because of the new debian/upstream file usage

Modified:
    projects/med/trunk/debian-med/tasks/bio
    projects/med/trunk/debian-med/tasks/bio-ngs
    projects/med/trunk/debian-med/tasks/bio-phylogeny

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=3260&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Wed Apr  4 07:40:44 2012
@@ -318,12 +318,6 @@
 Depends: ballview
 
 Depends: pynast
-X-References_in_debian_upstream: yes
-Published-Title: PyNAST: a flexible tool for aligning sequences to a template alignment
-Published-Authors: J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight
-Published-In: Bioinformatics 26: 266-267
-Published-Year: 2010
-Published-DOI: 10.1093/bioinformatics/btp636
 
 Depends: raxml
 
@@ -334,8 +328,6 @@
 Depends: cd-hit
 
 Depends: cufflinks
-X-References_in_debian_upstream: yes
-Published-In: Nature Biotechnology
 
 Depends: r-bioc-cummerbund
 

Modified: projects/med/trunk/debian-med/tasks/bio-ngs
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-ngs?rev=3260&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-ngs (original)
+++ projects/med/trunk/debian-med/tasks/bio-ngs Wed Apr  4 07:40:44 2012
@@ -33,10 +33,6 @@
 Depends: cufflinks
 
 Depends: mira-assembler
-X-References_in_debian_upstream: yes
-Published-Authors: Chevreux B, Pfisterer T, Drescher B, Driesel AJ, MÃ¼ller WE, Wetter T, Suhai S.
-Published-In: Genome Res. Jun;14(6):1147-59.
-Published-URL: http://pubmed.org/15140833
 
 Depends: ssaha2
 Homepage: http://www.sanger.ac.uk/resources/software/ssaha2/

Modified: projects/med/trunk/debian-med/tasks/bio-phylogeny
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-phylogeny?rev=3260&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-phylogeny (original)
+++ projects/med/trunk/debian-med/tasks/bio-phylogeny Wed Apr  4 07:40:44 2012
@@ -43,83 +43,35 @@
 Depends:     muscle
 
 Depends: t-coffee
-Published-Title: T-Coffee: A novel method for multiple sequence alignments
-Published-Authors: C. Notredame, D. Higgins, J. Heringa
-Published-In: Journal of Molecular Biology 302(1):205-217
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10964570
 
 Depends: kalign
-Published-Title: Kalign--an accurate and fast multiple sequence alignment algorithm
-Published-Authors: Lassmann T, Sonnhammer EL.
-Published-In: BMC Bioinformatics, 6:298
-Published-Year: 2005
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16343337
-Published-PubMed: 16343337
 
 Depends: hmmer
-Published-Title: Multiple Alignment Using Hidden Markov Models.
-Published-Authors: S. R. Eddy.
-Published-In: Proc. Third Int. Conf. Intelligent Systems for Molecular Biology, 114-120.
-Published-Year: 1995
-Published-URL: ftp://selab.janelia.org/pub/publications/Eddy95b/Eddy95b-preprint.pdf
 
 Depends: exonerate
-Published-Authors: G.C. Slater, E. Birney
-Published-In: BMC Bioinformatics 6:31
-Published-URL: http://www.biomedcentral.com/1471-2105/6/31/abstract
 
 Depends: dialign
-Published-Authors: Burkhard Morgenstern
-Published-Title: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
-Published-In: Bioinformatics 15(3):211-218
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10222408
 
 Depends: dialign-tx
-Published-Authors: Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern
-Published-Title: Improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies
-Published-In: Algorithms for Molecular Biology 3:6
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/18505568
 
 Depends: poa
-Published-Authors: C. Grasso, C. Lee
-Published-In: Bioinformatics 20(10):1546-1556.
 
 Depends: probcons
-Published-Authors: C. B. Do, M. S. P. Mahabhashyam, M. Brudno, S. Batzoglou
-Published-In: Genome Research 15: 330-340
 
 Depends: proda
-Published-Authors: T. M. Phuong, C. B. Do, R. C. Edgar, S. Batzoglou
-Published-In: Nucleic Acids Research 34(20), 5932-5942
 
 Depends: seaview
-Published-Authors: N. Galtier, M. Gouy, C. Gautier
-Published-Title: SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny
-Published-In: Comput. Applic. Biosci. 12:543-548
-Published-Year: 1996
 
 Depends: sigma-align
 
 Depends: gmap
-Published-Authors: Thomas D. Wu, Colin K. Watanabe
-Published-In: Bioinformatics
-Published-URL: http://bioinformatics.oupjournals.org/cgi/content/full/21/9/1859
 
 Depends:     clustalx
 Why:         Sequence alignments and related programs (Non-free, thus only suggested).
 
-Depends: clustalw
-Published-Authors: M. Larkin, et al.
-Published-In: Bioinformatics 23(21):2947-2948
-
-Depends: clustalw-mpi
-Comment: Originally the dependency was clustalw | clustalw-mpi but currently it is
- not possible to specify an "OR relation" and tag the Published-* fields to only one
- of them.
+Depends: clustalw | clustalw-mpi
 
 Depends: mustang
-Published-Authors: A. S. Konagurthu, J. C. Whisstock, P. J. Stuckey, A. M. Lesk
-Published-In: Proteins: Structure, Function, and Bioinformatics. 64(3):559-574
 
 X-End-Category: Sequence alignments and related programs.
 


