Task: Biology Development
Install: true
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: python3-biopython | python-biopython

Suggests: python3-biopython-sql | python-biopython-sql, python-biopython-doc

Depends: python-cogent

Depends: python-screed

Depends: python3-cutadapt | python-cutadapt

Depends: ruby-bio

Depends: libbiojava-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: libfreecontact-dev, libfreecontact-perl

Suggests: libfreecontact-doc

Depends: libgo-perl

Depends: r-cran-genetics, r-cran-haplo.stats, r-cran-phylobase

Depends: r-cran-rncl, r-cran-rnexml

Depends: octave-bioinfo
Homepage: http://octave.sourceforge.net/bioinfo/
Vcs-Git: git://git.debian.org/git/pkg-octave/octave-bioinfo.git
Vcs-Browser: http://git.debian.org/?p=pkg-octave/octave-bioinfo.git
License: GPL-3+
Pkg-Description: bioinformatic functions for Octave
 This package provides functions to do work in bioinformatics in
 Octave, a numerical computation software. It contains functions to
 convert amino acid characters into integers (aa2int), convert between
 amino acid representations (aminolookup), cleave peptides (cleave),
 convert integers into amino acid characters (int2aa) and reverse a
 nucleotide sequence (seqreverse).
 .
 This Octave add-on package is part of the Octave-Forge project.
Remark: Not maintained upstream, see ROM: #620648
Pkg-URL: http://snapshot.debian.org/archive/debian/20100201T042505Z/pool/main/o/octave-bioinfo/octave-bioinfo_0.1.2-2.dsc

Depends: libbio-graphics-perl, libbio-coordinate-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-biomformat,
          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-rbgl,
          r-bioc-rsamtools,
          r-bioc-shortread,
          r-bioc-snpstats,
          r-bioc-variantannotation,
          r-bioc-xvector

Suggests: r-cran-rentrez

Suggests: ruby-rgfa

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: python3-intervaltree-bio | python-intervaltree-bio

Depends: python3-csb | python-csb

Depends: python3-misopy | python-misopy

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@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: libtabixpp-dev

Depends: python3-ruffus | python-ruffus

Depends: python3-hyphy | python-hyphy

Depends: python3-dendropy | python-dendropy

Depends: python3-skbio

Depends: python3-pbconsensuscore | python-pbconsensuscore

Depends: python3-consensuscore2 | python-consensuscore2, libconsensuscore-dev

Depends: python-pbcommand

Depends: python3-pyvcf | python-pyvcf

Depends: python3-pyfaidx | python-pyfaidx

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, python3-fast5 | python-fast5

Depends: libpbseq-dev, libpbdata-dev, libpbihdf-dev, libblasr-dev

Suggests: libpbcopper-dev

Depends: libminimap-dev

Depends: libncl-dev

Depends: libngs-sdk-dev, libngs-java, python3-ngs | python-ngs, libncbi-vdb-dev

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: 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.

Depends: ruby-crb-blast

Depends: libsmithwaterman-dev

Depends: libfastahack-dev

Depends: mgltools-networkeditor, mgltools-vision, mgltools-pybabel

Suggests: libdisorder-dev

Depends: libssw-dev, libssw-java

Depends: libfml-dev

Depends: libgkarrays-dev

Depends: libjloda-java

Depends: libvcflib-dev

Depends: libswiss-perl

Depends: python3-pybedtools

Depends: python3-gffutils
WNPP: 851488

Depends: python3-bx | python-bx
WNPP: 851242

Depends: python3-bd2k | python-bd2k
WNPP: 851341

Depends: libbio-eutilities-perl

Depends: libseqlib-dev

Depends: libroadrunner-dev, python-roadrunner

Depends: python3-biotools | python-biotools

Depends: bio-tradis

Depends: python3-biomaj3 | python-biomaj3

Suggests: python-pyflow

Suggests: r-cran-natserv

Depends: libbiod-dev
