[Blends-commit] [SCM] fun branch, master, updated. 5796d7e776d2b36fc8af55fd5bec307a1ee75cf3

[Andreas Tille]

The following commit has been merged in the master branch:
commit 5796d7e776d2b36fc8af55fd5bec307a1ee75cf3
Author: Andreas Tille <tille at debian.org>
Date:   Sat May 14 08:08:47 2016 +0200

    Try original task from Debian Med since the stripped down version is OK

diff --git a/tasks/bio-dev b/tasks/bio-dev
index 9291d66..f9b10af 100644
--- a/tasks/bio-dev
+++ b/tasks/bio-dev
@@ -3,6 +3,128 @@ Description: Debian Med packages for development of bioinformatics applications
  This metapackage will install Debian packages which might be helpful
  for development of applications for biological research.
 
+Depends: bioperl, bioperl-run, libncbi6-dev
+
+Depends: mcl
+X-Category: Analysis of network structure
+X-Importance: Clustering of graphs
+
+Depends: biosquid
+
+Depends: libvibrant6-dev
+
+Depends: python-biopython | python3-biopython
+
+Suggests: python-biopython-sql | python3-biopython-sql, python-biopython-doc
+
+Depends: python-cogent
+
+Depends: python-screed
+
+Depends: python3-cutadapt | python-cutadapt
+
+Depends: ruby-bio
+
+Depends: libbiojava-java, libbiojava3-java, libbiojava4-java
+
+Depends: libgenome-1.3-dev, libmuscle-3.7-dev, libmems-1.6-dev
+
+Depends: libhtsjdk-java
+
+Depends: libai-fann-perl
+
+Depends: libbio-mage-perl
+Why: Useful for the submission of microarray data to public repositories.
+
+Depends: libnhgri-blastall-perl
+
+Depends: libtfbs-perl
+
+Depends: libfreecontact0-dev, libfreecontact-perl
+
+Suggests: libfreecontact-doc
+
+Depends: libgo-perl
+
+Depends: r-cran-genetics, r-cran-haplo.stats
+
+Depends: r-cran-rncl, r-cran-rnexml
+
+# Depends: octave-bioinfo
+# Not maintained upstream, see ROM: #620648
+# Latest version: http://snapshot.debian.org/archive/debian/20100201T042505Z/pool/main/o/octave-bioinfo/octave-bioinfo_0.1.2-2.dsc
+
+Depends: libbio-graphics-perl
+
+Depends: libbio-primerdesigner-perl
+
+Depends: libace-perl
+
+Depends: libbiococoa-dev
+
+Depends: libstaden-read-dev
+
+Depends: libsrf-dev
+
+Depends: libzerg0-dev, libzerg-perl
+
+Depends: librg-reprof-bundle-perl
+
+Depends: python-corepywrap, librcsb-core-wrapper0-dev
+
+Depends: libsbml5-dev, sbmltoolbox
+
+Suggests: r-cran-rocr
+Why: Even if this package is not directly connected to biology it is maintained by
+     Debian Med team and should be in our focus and it is not wrong to suggest this
+     package for development of biological applications based on R
+
+Depends: seqan-dev
+
+Depends: libbio-mage-utils-perl
+
+Depends: libchado-perl
+
+Depends: libpal-java
+
+Depends: libjebl2-java
+Remark: Fork from jebl
+ This is a branch of the original JEBL on
+ http://sourceforge.net/projects/jebl/ to develop a new API and class
+ library.
+
+Suggests: r-bioc-affy,
+          r-bioc-affyio,
+          r-bioc-altcdfenvs,
+          r-bioc-annotationdbi,
+          r-bioc-biocgenerics,
+          r-bioc-biomart,
+          r-bioc-biovizbase,
+          r-bioc-bsgenome,
+          r-bioc-genomeinfodb,
+          r-bioc-genomicalignments,
+          r-bioc-genomicfeatures,
+          r-bioc-genomicranges,
+          r-bioc-graph,
+          r-bioc-hypergraph,
+          r-bioc-iranges,
+          r-bioc-makecdfenv,
+          r-bioc-preprocesscore,
+          r-bioc-rsamtools,
+          r-bioc-shortread,
+          r-bioc-snpstats,
+          r-bioc-variantannotation,
+          r-bioc-xvector
+
+Depends: r-bioc-biobase
+Remark: This is a part of Bioconductor project
+ A nice overview about all modules of BioDonductor is given at
+ http://www.bioconductor.org/packages/release/bioc/
+
+Depends: libffindex0-dev
+
+Depends: librostlab3-dev
+
 Suggests: librostlab-doc
 
 Depends: librostlab-blast0-dev
@@ -161,3 +283,29 @@ Depends: libqcpp-dev
 
 Depends: libbpp-core-dev, libbpp-phyl-dev, libbpp-phyl-omics-dev, libbpp-popgen-dev, libbpp-qt-dev, libbpp-raa-dev, libbpp-seq-dev, libbpp-seq-omics-dev
 
+Depends: libgbfp-dev
+Homepage: http://code.google.com/p/gbfp/
+License: GPL
+Language: C
+WNPP: 612814
+Responsible: Scott Christley <schristley at mac.com>
+Pkg-Description: GBParsy is a GenBank flatfile parser library
+ GBParsy is a library of functions that parses the GenBank flatfile,
+ which is a representative and popular sequence format. The library is
+ optimized for speed and efficient use of memory so it can rapidly parse
+ large sequence such as Arabidopsis chromosome for genomic analysis.
+
+Depends: octace-bioinfo
+Homepage: http://octave.sourceforge.net/bioinfo/index.html
+License: GPL-2+
+Pkg-Description: Bioinformatics manipulation for Octave
+  aa2int:
+    Convert amino acid characters into integers.
+  aminolookup:
+    Convert between amino acid representations.
+  cleave:
+    Cleave a peptide SEQUENCE using the PATTERN at the POSITION relative to the pattern.
+  int2aa
+    Convert amino acid integers into characters.
+  seqreverse
+    Reverse a nucleotide sequence.

-- 
Debian Fun Blend