[Blends-commit] [SCM] fun branch, master, updated. e85809a1f70068d65cd93f9035c77b0e7751779a

Fri Sep 22 13:08:19 UTC 2017

The following commit has been merged in the master branch:
commit e85809a1f70068d65cd93f9035c77b0e7751779a
Author: Andreas Tille <tille at debian.org>
Date:   Fri Sep 22 15:07:39 2017 +0200

    Minimal set of Dependencies to test registry entries

diff --git a/tasks/bio b/tasks/bio
new file mode 100644
index 0000000..bf209b0
--- /dev/null
+++ b/tasks/bio
@@ -0,0 +1,6 @@
+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.
+
+Depends: bwa, bowtie, snpomatic, dindel, phyml, idba, fastqc
diff --git a/tasks/bio-dev b/tasks/bio-dev
deleted file mode 100644
index 10833c2..0000000
--- a/tasks/bio-dev
+++ /dev/null
@@ -1,307 +0,0 @@
-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.
-
-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: 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
-
-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
-
-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

