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.

Suggests: conda-package-handling

Recommends: bioperl, bioperl-run, libncbi6-dev

Recommends: mcl
X-Category: Analysis of network structure
X-Importance: Clustering of graphs

Recommends: biosquid

Recommends: cwltool, snakemake, python3-wdlparse

Suggests: cwlformat

Recommends: libvibrant6-dev

Recommends: python3-biopython

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

Recommends: python3-cogent3

Suggests: python3-joypy

Suggests: python3-ncls

Suggests: python3-pycosat

Recommends: python3-screed

Recommends: python3-cutadapt, python3-dnaio

Recommends: python3-tinyalign

Recommends: ruby-bio

Recommends: libbiojava-java, libbiojava4-java, libbiojava5-java

Recommends: libgenome-dev, libmuscle-dev, libmems-dev

Recommends: libhtsjdk-java

Recommends: libai-fann-perl

Recommends: libbio-mage-perl
Why: Useful for the submission of microarray data to public repositories.

Recommends: libnhgri-blastall-perl

Suggests: libtfbs-perl

Suggests: libfreecontact-dev, libfreecontact-perl

Suggests: libfreecontact-doc

Recommends: libhdf5-dev

Suggets: libhnswlib-dev

Recommends: libgo-perl

Recommends: libbio-graphics-perl, libbio-coordinate-perl

Recommends: libbio-primerdesigner-perl

Recommends: libbio-alignio-stockholm-perl, libbio-cluster-perl,
            libbio-db-biofetch-perl, libbio-db-embl-perl, libbio-db-hts-perl, libbio-db-ncbihelper-perl,
            libbio-featureio-perl, libbio-tools-run-remoteblast-perl, libbio-variation-perl

Recommends: libace-perl

Recommends: libbiococoa-dev

Recommends: libcifpp-dev

Recommends: libstaden-read-dev

Recommends: libsrf-dev

Recommends: libzerg0-dev, libzerg-perl

Recommends: librg-reprof-bundle-perl

Recommends: python3-corepywrap

Recommends: librcsb-core-wrapper0-dev

Recommends: libsbml5-dev, sbmltoolbox

Recommends: libseqan2-dev, libseqan3-dev

Recommends: libbio-mage-utils-perl

Recommends: libchado-perl

Recommends: libpal-java

Recommends: libpdb-redo-dev

Recommends: libbioparser-dev, libspoa-dev, libedlib-dev, libthread-pool-dev

Recommends: python3-pyspoa

Recommends: 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: qiime,
          q2-alignment,
          q2-composition,
          q2-cutadapt,
          q2-dada2,
          q2-deblur,
          q2-demux,
          q2-diversity,
          q2-emperor,
          q2-feature-classifier,
          q2-feature-table,
          q2-fragment-insertion,
          q2-gneiss,
          q2-longitudinal,
          q2-metadata,
          q2-phylogeny,
          q2-quality-control,
          q2-quality-filter,
          q2-sample-classifier,
          q2-shogun,
          q2-taxa,
          q2-types,
          q2-vsearch,
          q2cli,
          q2cwl,
          q2lint,
          q2templates

Suggests: r-bioc-affxparser,
          r-bioc-affy,
          r-bioc-affyio,
          r-bioc-altcdfenvs,
          r-bioc-annotate,
          r-bioc-annotationdbi,
          r-bioc-annotationhub,
          r-bioc-aroma.light,
          r-bioc-arrayexpress,
          r-bioc-biocgenerics,
          r-bioc-biocneighbors,
          r-bioc-biomart,
          r-bioc-biomformat,
          r-bioc-biostrings,
          r-bioc-biovizbase,
          r-bioc-bitseq,
          r-bioc-bridgedbr,
          r-bioc-bsgenome,
          r-bioc-cager,
          r-bioc-cner,
          r-bioc-complexheatmap,
          r-bioc-cummerbund,
          r-bioc-ctc,
          r-bioc-dada2,
          r-bioc-deseq,
          r-bioc-deseq2,
          r-bioc-dnacopy,
          r-bioc-ebseq,
          r-bioc-enrichedheatmap,
          r-bioc-ensembldb,
          r-bioc-genefilter,
          r-bioc-geneplotter,
          r-bioc-genomeinfodb,
          r-bioc-genomicalignments,
          r-bioc-genomicfeatures,
          r-bioc-genomicranges,
          r-bioc-geoquery,
          r-bioc-go.db,
          r-bioc-graph,
          r-bioc-gseabase,
          r-bioc-gsva,
          r-bioc-gviz,
          r-bioc-hypergraph,
          r-bioc-impute,
          r-bioc-iranges,
          r-bioc-limma,
          r-bioc-makecdfenv,
          r-bioc-mergeomics,
          r-bioc-metagenomeseq,
          r-bioc-mofa,
          r-bioc-multiassayexperiment,
          r-bioc-nanostringqcpro,
          r-bioc-oligo,
          r-bioc-oligoclasses,
          r-bioc-org.hs.eg.db,
          r-bioc-pcamethods,
          r-bioc-phyloseq,
          r-bioc-preprocesscore,
          r-bioc-purecn,
          r-bioc-qusage,
          r-bioc-rbgl,
          r-bioc-rsamtools,
          r-bioc-rentrez,
          r-bioc-rtracklayer,
          r-bioc-s4vectors,
          r-bioc-savr,
          r-bioc-shortread,
          r-bioc-snpstats,
          r-bioc-structuralvariantannotation,
          r-bioc-titancna,
          r-bioc-tfbstools, 
          r-bioc-tximport,
          r-bioc-variantannotation,
          r-bioc-xvector

Suggests: r-cran-adegenet, r-cran-adephylo

Suggests: r-cran-amap

Suggests: r-cran-biwt

Recommends: r-cran-boolnet

Recommends: r-cran-corrplot

Recommends: r-cran-distory

Recommends: r-cran-drinsight

Suggests: r-cran-dt

Suggests: r-cran-dynamictreecut

Suggests: r-cran-fastcluster,

Recommends: r-cran-forecast

Recommends: r-cran-fitdistrplus

Suggests: r-cran-future.apply

Suggests: r-cran-future.batchtools

Recommends: r-cran-genetics

Recommends: r-cran-gprofiler2

Recommends: r-cran-haplo.stats

Suggests: r-cran-ica

Suggests: r-cran-itertools

Suggests: r-cran-kaos

Recommends: r-cran-metamix

Suggests: r-cran-metap

Suggests: r-cran-minerva

Suggests: r-cran-natserv

Suggests: r-cran-nmf

Suggests: r-cran-optimalcutpoints

Suggests: r-cran-parmigene

Suggests: r-cran-pcapp

Recommends: r-cran-phangorn

Recommends: r-cran-pheatmap

Recommends: r-cran-phylobase

Suggests: r-cran-proc

Recommends: r-cran-pscbs

Recommends: r-cran-qqman

Suggests: r-cran-rann

Suggests: r-cran-rcpphnsw

Recommends: r-cran-rentrez

Recommends: r-cran-rncl, r-cran-rnexml

Suggests: r-cran-robustrankaggreg

Suggests: r-cran-rocr

Suggests: r-cran-rook

Suggests: r-cran-rsvd

Recommends: r-cran-rotl

Recommends: r-cran-samr

Recommends: r-cran-sctransform

Recommends: r-cran-seurat

Recommends: r-cran-seqinr

Suggests: r-cran-shazam

Suggests: r-cran-sitmo

Recommends: r-cran-tsne

Recommends: r-cran-vegan

Suggests: r-cran-venndiagram

Recommends: r-cran-webgestaltr

Recommends: r-other-apmswapp

Suggests: ruby-rgfa

Recommends: 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/

Recommends: libffindex0-dev

Recommends: libpwiz-dev

Recommends: librostlab3-dev

Suggests: librostlab-doc

Recommends: librostlab-blast0-dev

Suggests: librostlab-blast-doc

Recommends: librg-blast-parser-perl

Recommends: libsort-key-top-perl

Recommends: libhmsbeagle-dev

Recommends: libforester-java

X-Mark: Prospective packages are starting here.

X-Mark: Packages in Vcs - Information about these is queried from UDD as well

Recommends: libbambamc-dev

Recommends: libbamtools-dev

Recommends: libpbbam-dev

Recommends: libbigwig-dev

Recommends: libbio-das-lite-perl

Recommends: libopenms-dev

Recommends: libgenometools0-dev

Recommends: librdp-taxonomy-tree-java

Recommends: python3-biom-format

Recommends: python3-rdkit

Suggests: libswarm2-dev

Recommends: libgenome-perl, libgenome-model-tools-music-perl

Recommends: pyfai

Recommends: libhts-dev

Recommends: python3-htseq

Recommends: python3-intervaltree-bio

Recommends: python3-csb

Recommends: python3-misopy

Recommends: python3-freecontact

Recommends: python3-pymummer

Recommends: libkmer-dev

Recommends: libsnp-sites1-dev

Recommends: libssm-dev

Recommends: librelion-dev

Recommends: libdivsufsort-dev

Recommends: nim-hts-dev, nim-kexpr-dev, nim-lapper-dev

Recommends: 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.

Recommends: libgff-dev

Recommends: python3-pysam

Recommends: python3-pbcore

Recommends: python3-cobra

Recommends: python3-pybigwig

Recommends: python3-bcbio-gff

Recommends: libtabixpp-dev

Suggests: python3-networkx

Recommends: python3-ruffus

Recommends: python3-dendropy

Recommends: python3-skbio

Recommends: libparasail-dev, python3-parasail

Recommends: python3-pbconsensuscore

Recommends: python3-consensuscore2, libconsensuscore-dev

Recommends: python3-pbcommand

Recommends: python3-pyvcf

Recommends: python3-pyfaidx

Recommends: python3-shasta

Recommends: python3-sqt

Recommends: python3-kineticstools

Suggests: libbam-dev

Recommends: libqes-dev

Suggests: libfast-perl

Recommends: libfast5-dev, python3-fast5

Recommends: ont-fast5-api

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

Suggests: libpbcopper-dev

Suggests: libminimap-dev

Recommends: libminimap2-dev

Recommends: libncl-dev

Recommends: libngs-sdk-dev, libngs-java, python3-ngs, libncbi-vdb-dev

Recommends: libqcpp-dev

Recommends: 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

Recommends: 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.

Recommends: ruby-crb-blast

Recommends: libsmithwaterman-dev

Recommends: libfastahack-dev

Suggests: libdisorder-dev

Recommends: libssw-dev, libssw-java

Recommends: libfml-dev

Recommends: libgkarrays-dev

Recommends: libjloda-java

Recommends: libvcflib-dev

Recommends: libswiss-perl

Recommends: python3-pybedtools

Recommends: python3-gffutils

Recommends: python3-bx

Recommends: toil, python3-galaxy-lib

Suggests: cthreadpool-dev

Recommends: libbio-eutilities-perl

Recommends: libseqlib-dev

Recommends: libroadrunner-dev, python3-roadrunner

Recommends: python3-biotools

Recommends: bio-tradis

Recommends: python3-biomaj3

Suggests: python3-pyflow

Recommends: python3-ete3

Recommends: python3-gfapy

Recommends: goby-java

Recommends: python3-seqcluster

Recommends: python3-cyvcf2

Recommends: libgatbcore-dev

Recommends: python3-airr, python3-presto

Suggests: libmilib-java, vdjtools

Suggests: python3-alignlib

Recommends: python3-bcbio

Suggests: python3-ctdopts, ctdconverter

Recommends: libpll-dev

Suggests: libmodhmm-dev, libsvmloc-dev

Recommends: libstatgen-dev

Recommends: python3-pyani

Recommends: python3-treetime

Recommends: libbio-tools-run-alignment-tcoffee-perl, libbio-asn1-entrezgene-perl, libbio-chado-schema-perl, libbio-samtools-perl, libbio-scf-perl, libbio-tools-phylo-paml-perl, libbio-tools-run-alignment-clustalw-perl

Recommends: python3-pybel

Suggests: python3-bel-resources

Recommends: python3-mirtop

Recommends: libnexml-java

Recommends: python3-cgecore

Recommends: python3-deeptools, python3-deeptoolsintervals, python3-py2bit

Recommends: python3-loompy

Recommends: gffread, libgclib-dev

Ignore: golang-github-biogo-hts-dev
Comment: As explained on the Debian Med mailing list
         https://lists.debian.org/debian-med/2019/04/msg00036.html
         there is no point to recommend this package to users

Suggests: libmaus2-dev

Recommends: biobambam2

Recommends: libcdk-java

Recommends: libhtscodecs-dev

Recommends: python3-torch

Recommends: python3-pyabpoa

Recommends: python3-anndata

Recommends: python3-bx

Suggests: libbbhash-dev

Recommends: python3-cooler, python3-pairix

Recommends: python3-pangolearn

Recommends: python3-pyranges

Recommends: python3-streamz

Recommends: libssu-dev, python3-unifrac

Suggests:  python3-intake

Recommends:  python3-nanoget

Recommends: python3-peptidebuilder

Recommends: libopenmm-dev, libmmblib-dev

Suggests: libconcurrentqueue-dev, libxxsds-dynamic-dev, libatomicqueue-dev, libargs-dev

Suggests: libsuma-dev

Recommends: python3-scanpy

Recommends: python3-propka

Recommends: python3-cigar

Recommends: python3-compclust
X-Category: Genomics; Clustering analysis (+GUI)

Suggests: capsule-nextflow, libcapsule-maven-nextflow-java

Suggests: libgatk-bwamem-java, libgatk-bwamem-jni, libgatk-fermilite-java, libgatk-fermilite-jni, libgenomicsdb-java, libgenomicsdb-dev

Suggests: libicb-utils-java

Suggests: libbiosoup-dev

Recommends: libslow5-dev, python3-slow5

Suggests: libvbz-hdf-plugin-dev

Suggests: python3-bioblend

Recommends: python3-gtfparse

Suggests: libterraces-dev
