[med-svn] [Git][med-team/community/bio-linux][master] I finally removed what I think is in Debian - may be somebody does a double check

Thu Aug 16 07:08:33 BST 2018

Andreas Tille pushed to branch master at Debian Med / community / bio-linux


Commits:
09087160 by Andreas Tille at 2018-08-16T06:07:53Z
I finally removed what **I** think is in Debian - may be somebody does a double check

- - - - -


1 changed file:

- debian-med_missings.txt


Changes:

=====================================
debian-med_missings.txt
=====================================

--- a/debian-med_missings.txt
+++ b/debian-med_missings.txt
@@ -11,13 +11,7 @@ beam2:
     at  http://sites.stat.psu.edu/~yzz2/software/
   - This article https://academic.oup.com/bioinformatics/article/26/20/2517/194775
     might be related
-bioperl-run:
-  - ??? This is in Debian
-blast:
-  - ??? This is in Debian - may be blast2 or ncbi-blast+-legacy ?
 bldp-files
-bowtie2, bowtie2-examples, bowtie-examples:
-  - ??? This is in Debian
 cap3:
   - http://seq.cs.iastate.edu/cap3.html
   - also used in ugene
@@ -28,21 +22,11 @@ catchall:
   - link to source bounces, ask authors
   - https://www.ncbi.nlm.nih.gov/pubmed/21121040,
    https://www.ncbi.nlm.nih.gov/pubmed/22333246
-chimeraslayer:
-  - ??? This is in Debian (inside microbiomeutil source package)
-clustal:
-  - ??? do you mean clustalo, clustalw or clustalx
-cufflinks:
-  - ??? This is in non-free (thus available as package)
 dendroscope:
   - https://github.com/danielhuson/dendroscope3
   - http://dendroscope.org/
   - Should be packaged since used by beast2
   - Asked for Release tags: https://github.com/danielhuson/dendroscope3/issues/8
-dialign:
-  - ??? Debian has dialign and dialign-tx
-dotter
-  - ??? Just packaged and is available, will be included in next med-bio metapackage
 dust:
   - https://github.com/lh3/mdust
     mdust from DFCI Gene Indices Software Tools (archived for a historical record only)
@@ -53,20 +37,12 @@ estscan2:
 emmax:
   - https://anonscm.debian.org/git/debian-med/emmax.git
   - Asked author for license
-fastqc:
-  - ??? Available in Debian
 galaxy-server-all:
   - https://galaxyproject.org/
 gap2caf:
   - http://www.sanger.ac.uk/science/tools/caf
-glimmer3
-  - ??? Avaliable as tigr-glimmer
 happy:
   - ??? do you mean r-other-mott-happy which is in Debian?
-hyphy:
-  - ??? Available as hyphy-mpi
-jemboss:
-  - ??? in Debian
 jmotu:
   - http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019259
   - It is refering to http://www.nematodes.org/ which seems to be offline but
@@ -76,31 +52,21 @@ jmotu:
 jprofilegrid:
   - http://www.profilegrid.org/
   - Download available, claims to be GPL
-last-align:
-  - ??? Availanle in Debian
 lastz:
   - https://github.com/lastz/lastz
     (might be an easy target)
 libbiojava-java-demos
   - ??? Debian has libbiojava - what files should be provided as demos
 -libio-string-perl
-maq:
-  - ??? Available in Debian
 meme, meme-examples:
   - https://anonscm.debian.org/git/debian-med/meme.git
   - Package in non-free, needs to be finalised
   - Ask authors for free license
-microbiomeutil:
-  - ??? in Debian
 mira, mira-3rdparty, mira-3rd-party, mira-doc, mira-examples
   - What is the difference between mira and mira-assembler
-mira-assembler
-  - ??? in Debian
 mspcrunch:
   - http://sonnhammer.org/MSPcrunch.html
   - Source at http://sonnhammer.sbc.su.se/download/software/MSPcrunch+Blixem/
-ncbi-tools-bin, ncbi-tools-x11:
-  - ??? both are in Debian
 nrdb:
   - Situation unclear.  According to http://seqanswers.com/forums/showthread.php?t=6697
     Seems you can some ask for some private license.  Moreover
@@ -121,34 +87,9 @@ pass2:
     No idea how we can obtain the source from there
 priam:
   - http://priam.prabi.fr/
-probcons:
-  - ??? in Debian
 qiime:
   - Debian has an old version of qiime but the new version
     is not installable due to non-buildable python-burrito-fillings
-r-bioc-affy:
-r-bioc-affyio:
-r-bioc-annotate:
-r-bioc-annotationdbi:
-r-bioc-biocgenerics:
-r-bioc-biocinstaller:
-r-bioc-biomart:
-r-bioc-biostrings:
-r-bioc-genefilter:
-r-bioc-geneplotter:
-r-bioc-genomicranges:
-r-bioc-impute:
-r-bioc-iranges:
-r-bioc-limma:
-r-bioc-multtest:
-r-bioc-preprocesscore:
-r-bioc-qvalue:
-r-bioc-rsamtools:
-  - All these are available in Debian but not explicitly specified
-    in med-bio task since these are implicitly installed due to
-    dependencies
-r-bioc-zlibbioc:
-  - That's not needed - Debian uses plain zlib
 -r-bioc-edger:
   - Used to be in Debian in an old version.  edger now depends from
     locfit which is non-distributable
@@ -161,82 +102,15 @@ r-cran-samr: (ITP #892498)
   - All missing R packages in new queue
 r-cran-locfit:
   - can not be packaged due to license issues -> http://bugs.debian.org/731599
-r-cran-abind:
-r-cran-ade4:
-r-cran-bitops:
-r-cran-catools:
-r-cran-cluster:
-r-cran-dbi:
-r-cran-dichromat:
-r-cran-digest:
-r-cran-evaluate:
-r-cran-gdata:
-r-cran-gee:
-r-cran-getopt:
-r-cran-ggplot2:
-r-cran-gplots:
-r-cran-gtable:
-r-cran-gtools:
-r-cran-labeling:
-r-cran-lattice:
-r-cran-leaps:
-r-cran-lme4:
-r-cran-matrix:
-r-cran-matrixstats:
-r-cran-munsell:
-r-cran-nlme:
-r-cran-optparse:
-r-cran-permute:
-r-cran-plotrix:
-r-cran-plyr:
-r-cran-prettyr:
-r-cran-proto:
-r-cran-rcolorbrewer:
-r-cran-rcpp:
-r-cran-rcurl:
-r-cran-relimp:
-r-cran-reshape2:
-r-cran-rggobi:
-r-cran-rgl:
-r-cran-rgtk2:
-r-cran-r.methodss3:
-r-cran-rmpi:
-r-cran-rserve:
-r-cran-rsqlite:
-r-cran-scales:
-r-cran-scatterplot3d:
-r-cran-snow:
-r-cran-sp:
-r-cran-stringr:
-r-cran-tcltk2:
-r-cran-testthat:
-r-cran-xml:
-r-cran-xtable:
-r-doc-html:
-r-doc-info:
-r-doc-pdf:
-r-mathlib:
-r-recommended:
-  - All these are available in Debian but not explicitly specified
-    in med-bio task since these are implicitly installed due to
-    dependencies
-rdp-classifier:
-  - ??? in Debian
 runurl:
   - Please explain - are you refering to https://shiny.rstudio.com/reference/shiny/0.11/runUrl.html ?
 sampledata:
   - Sounds pretty BioLinux specific.  Let us know if we should include something into Debian.
-seaview:
-  - ??? in Debian
 sputnik-mononucleotide
   - https://bitbucket.org/natefoo/sputnik-mononucleotide
 squint:
   - http://www.bioinformatics.org.nz/en/about/tools-and-resources/software-tools/squint.html
   - https://www.ncbi.nlm.nih.gov/pubmed/17485434
-ssake:
-  - ??? in Debian
-stacks:
-  - ??? in Debian
 stars:
   - https://sourceforge.net/projects/stars/
     Latest version of 2004 accessing very old staden version - is this of any use?
@@ -244,17 +118,7 @@ tablet:
   - https://ics.hutton.ac.uk/tablet/
 themes-v8:
   - BioLinux specific but it could be packaged in principle
-treeview:
-treeviewx:
-  - ??? both are in Debian
 tutorials:
   - BioLinux specific but it could be packaged in principle
-velvet:
-velvet-example:
-velvet-long:
-velvetoptimiser:
-  - ??? all in Debian
 weblogo:
   - http://weblogo.threeplusone.com/
-wise:
-  - ??? in Debian



View it on GitLab: https://salsa.debian.org/med-team/community/bio-linux/commit/090871600b1f72a532a449d88af9f118b0d95868

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[med-svn] [Git][med-team/community/bio-linux][master] I finally removed what **I** think is in Debian - may be somebody does a double check

[med-svn] [Git][med-team/community/bio-linux][master] I finally removed what I think is in Debian - may be somebody does a double check