[Blends-commit] [SCM] fun branch, master, updated. 2d00869e2e8f2b29f39651d929ff24c981cb8bad

[Andreas Tille]

The following commit has been merged in the master branch:
commit 2d00869e2e8f2b29f39651d929ff24c981cb8bad
Author: Andreas Tille <tille at debian.org>
Date:   Sat May 14 08:06:28 2016 +0200

    Try bisecting bio-dev task which is lacking libbpp libraries in output

diff --git a/tasks/bio-dev b/tasks/bio-dev
new file mode 100644
index 0000000..9291d66
--- /dev/null
+++ b/tasks/bio-dev
@@ -0,0 +1,163 @@
+Task: Biology Development
+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.
+
+Suggests: librostlab-doc
+
+Depends: librostlab-blast0-dev
+
+Suggests: librostlab-blast-doc
+
+Depends: librg-blast-parser-perl
+
+Depends: libsort-key-top-perl
+
+Depends: libhmsbeagle-dev
+
+Depends: libforester-java
+
+X-Mark: Prospective packages are starting here.
+
+X-Mark: Packages in Vcs - Information about these is queried from UDD as well
+
+Depends: libbambamc-dev
+
+Depends: libbamtools-dev
+
+Depends: libpbbam-dev
+
+Depends: libbio-das-lite-perl
+
+Depends: python-mmtk
+Language: C, Python
+
+Depends: libopenms-dev
+
+Depends: libgenometools0-dev
+
+Depends: librdp-taxonomy-tree-java
+
+Depends: python-biom-format
+
+Depends: python-rdkit
+
+Suggests: libswarm2-dev
+
+Depends: libgenome-perl, libgenome-model-tools-music-perl
+
+Depends: pyfai
+
+Depends: libhts-dev
+
+Depends: python-htseq
+
+Depends: python-csb | python3-csb
+
+Depends: python-miso
+
+Depends: python-freecontact
+
+Depends: python3-pymummer
+
+Suggests: libgtextutils-dev
+
+Depends: libkmer-dev
+
+Depends: libsnp-sites1-dev
+
+Depends: libssm-dev
+
+Depends: librelion-dev
+
+Depends: libdivsufsort-dev
+
+Depends: bioclipse
+Homepage: http://www.bioclipse.net/
+License: Eclipse Public License (EPL) + exception
+Pkg-Description: platform for chemo- and bioinformatics based on Eclipse
+ The Bioclipse project is aimed at creating a Java-based, open source,
+ visual platform for chemo- and bioinformatics based on the Eclipse
+ Rich Client Platform (RCP). Bioclipse, as any RCP application, is based
+ on a plugin architecture that inherits basic functionality and visual
+ interfaces from Eclipse, such as help system, software updates,
+ preferences, cross-platform deployment etc.
+ .
+ Bioclipse will provide functionality for chemo- and bioinformatics,
+ and extension points that easily can be extended by plugins to provide
+ added functionality. The first version of Bioclipse includes a
+ CDK-plugin (bc_cdk) to provide a chemoinformatic backend, a Jmol-plugin
+ (bc_jmol) for 3D-visualization and a general logging plugin. To stay
+ updated on upcoming features, releases, new plugins etc, please register
+ for the mailing list bioclipse-announce. The development is best
+ followed on the Bioclipse Wiki where we document the progress and
+ ideas of the development on a daily basis.
+
+Depends: libgff-dev
+
+Depends: libgff-perl
+Homepage: http://www.sanger.ac.uk/Software/formats/GFF/
+Responsible: David Paleino <d.paleino at gmail.com>
+License: GPL-1+
+WNPP: 468826
+Pkg-Description: Perl bindings for GFF Annotation Protocol
+ GFF (Gene Finding Feature) is a format for describing genes and other
+ features associated with DNA, RNA and Protein sequences.
+ .
+ This package provides a Perl module to use GFF objects.
+
+Depends: python-pysam
+
+Depends: python-pbcore, python-pbh5tools
+
+Depends: python-cobra
+
+Depends: libvcflib, libtabixpp-dev
+
+Depends: python3-ruffus | python-ruffus
+
+Depends: python3-hyphy | python-hyphy
+
+Depends: python3-dendropy | python-dendropy
+
+Depends: python3-skbio | python-skbio
+
+Depends: python3-pbconsensuscore | python-pbconsensuscore
+
+Depends: python-pbcommand
+
+Depends: python3-pyvcf | python-pyvcf
+
+Depends: python3-pyfaidx | python-pyfaidx
+
+Depends: python-intervaltree-bio | python3-intervaltree-bio
+
+Depends: python-kineticstools
+
+Depends: python3-pyfasta | python-pyfasta
+Remark: Testsuite uncovers problems and code is not actively maintained
+ The upstream author of python-pyfasta confirmed that he stopped
+ the development and recommends python-pyfaidx instead.  So the
+ packaging code for python-pyfasta in SVN works but there is no
+ intend to really upload the package.
+
+Suggests: libbam-dev
+
+Depends: libqes-dev
+
+Depends: libfast5-dev
+
+Depends: libpbseq-dev, libpbdata-dev, libpbihdf-dev, libblasr-dev
+
+Depends: libbio-das-lite-perl
+
+Depends: libminimap-dev
+
+Depends: libncl-dev
+
+Depends: libngs-sdk-dev, libngs-java, python-ngs, python3-ngs
+
+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
+

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