[Blends-commit] [SCM] med branch, master, updated. 251eda07708f86b03df9afebb8ec3d93c47400b3
Andreas Tille
tille at debian.org
Sun Aug 13 02:05:39 UTC 2017
The following commit has been merged in the master branch:
commit 34fd255d51c69636d2999ff62e3fcad067b8a217
Author: Andreas Tille <tille at debian.org>
Date: Sat Aug 5 13:10:03 2017 +0200
s/Depends/Recommends/
diff --git a/tasks/bio b/tasks/bio
index 2dfc645..232fb8b 100644
--- a/tasks/bio
+++ b/tasks/bio
@@ -6,136 +6,136 @@ Description: Debian Med bioinformatics packages
X-Begin-Category: Phylogenetic analysis
-Depends: altree
+Recommends: altree
-Depends: beast-mcmc, beast2-mcmc
+Recommends: beast-mcmc, beast2-mcmc
-Depends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle
+Recommends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle
-Depends: probalign
+Recommends: probalign
-Depends: treeviewx
+Recommends: treeviewx
-Depends: figtree
+Recommends: figtree
-Depends: hyphygui, hyphy-mpi | hyphy-pt
+Recommends: hyphygui, hyphy-mpi | hyphy-pt
-Depends: spread-phy
+Recommends: spread-phy
X-End-Category: Phylogenetic analysis
-Depends: phylip
+Recommends: phylip
Why: Phylogenetic analysis (Non-free, thus only suggested).
X-Comment: treetool is removed from Debian because it is not maintained upstream since
1995 and cause the Xserver to freeze under Squeeze
-Depends: fastlink, loki, plink, plink1.9, r-cran-qtl, r-cran-genabel
+Recommends: fastlink, loki, plink, plink1.9, r-cran-qtl, r-cran-genabel
Why: Genetics
X-Begin-Category: Sequence alignments and related programs.
-Depends: amap-align
+Recommends: amap-align
Remark: Dead upstream
The homepage of this project vanished as well as the Download area. An
old unmaintained version remained at code.google.com. Please drop the
maintainer a note if you have any news of this project.
-Depends: boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4, tabix, tophat, wise
+Recommends: boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4, tabix, tophat, wise
-Depends: maqview
+Recommends: maqview
-Depends: blasr
+Recommends: blasr
-Depends: daligner
+Recommends: daligner
Suggests: dascrubber
-Depends: mhap
+Recommends: mhap
-Depends: bwa
+Recommends: bwa
-Depends: mummer, e-mem
+Recommends: mummer, e-mem
-Depends: ncbi-blast+-legacy, plast
+Recommends: ncbi-blast+-legacy, plast
-Depends: ncbi-blast+
+Recommends: ncbi-blast+
-Depends: mafft
+Recommends: mafft
-Depends: sra-toolkit
+Recommends: sra-toolkit
-Depends: t-coffee
+Recommends: t-coffee
-Depends: kalign
+Recommends: kalign
-Depends: hmmer
+Recommends: hmmer
-Depends: exonerate
+Recommends: exonerate
-Depends: dialign
+Recommends: dialign
-Depends: dialign-tx
+Recommends: dialign-tx
-Depends: poa
+Recommends: poa
-Depends: probcons
+Recommends: probcons
-Depends: proda
+Recommends: proda
-Depends: seaview
+Recommends: seaview
-Depends: sigma-align
+Recommends: sigma-align
-Depends: emboss
+Recommends: emboss
-Depends: embassy-domalign, embassy-domainatrix, embassy-domsearch, embassy-phylip
+Recommends: embassy-domalign, embassy-domainatrix, embassy-domsearch, embassy-phylip
Suggests: emboss-explorer
Why: The EMBOSS sequence analysis suite and its galaxy.
-Depends: arb
+Recommends: arb
Why: Sequence alignments and related programs (Non-free, thus only suggested).
-Depends: clustalx, clustalo
+Recommends: clustalx, clustalo
-Depends: clustalw
+Recommends: clustalw
-Depends: mothur, bowtie, bowtie2
+Recommends: mothur, bowtie, bowtie2
-Depends: transtermhp
+Recommends: transtermhp
X-End-Category: Sequence alignments and related programs.
X-Begin-Category: high-throughput sequencing
-Depends: last-align, maq, ssake, velvet | velvet-long
+Recommends: last-align, maq, ssake, velvet | velvet-long
-Depends: qiime
+Recommends: qiime
X-End-Category: high-throughput sequencing
X-Begin-Category: Analysis of RNA sequences.
-Depends: infernal
+Recommends: infernal
-Depends: rnahybrid
+Recommends: rnahybrid
X-Category: Target duplex prediction
X-End-Category: Analysis of RNA sequences.
X-Begin-Category: Molecular modelling and molecular dynamics
-Depends: adun-core
+Recommends: adun-core
Suggests: adun.app
-Depends: garlic, gamgi, gdpc, ghemical, jmol, pymol, r-cran-bio3d, massxpert
+Recommends: garlic, gamgi, gdpc, ghemical, jmol, pymol, r-cran-bio3d, massxpert
-Depends: gromacs
+Recommends: gromacs
-Depends: rasmol
+Recommends: rasmol
-Depends: modeller
+Recommends: modeller
Homepage: http://salilab.org/modeller/
Pkg-URL: http://salilab.org/modeller/release.html#deb
Remark: The package is created independently from Debian Med or Debian Science.
@@ -145,35 +145,35 @@ Pkg-Description: MODELLER provides three dimensional structures of proteins by s
X-End-Category: Molecular modelling and molecular dynamics
-Depends: plasmidomics
+Recommends: plasmidomics
Why: Presentation
X-Begin-Category: Tools for the molecular biologist.
-Depends: gff2ps, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, readseq, tigr-glimmer
+Recommends: gff2ps, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, readseq, tigr-glimmer
-Depends: melting
+Recommends: melting
Suggests: melting-gui
Comment: I think it makes sense to point users to GUI applications as well as to
the console applications - in this case melting (Andreas Tille)
-Depends: mipe
+Recommends: mipe
-Depends: primer3
+Recommends: primer3
X-End-Category: Tools for the molecular biologist.
X-Begin-Category: Genome Browser
-Depends: artemis
+Recommends: artemis
-Depends: gbrowse
+Recommends: gbrowse
X-Importance: Academic ones are really expensive for commercial use
X-End-Category: Genome Browser
-Depends: python3-biomaj3
+Recommends: python3-biomaj3
Suggests: biomaj
Why: Suggests since mysql setup might be overkill for default client installation
@@ -186,178 +186,178 @@ Remark: biofox was removed from Debian (see #727689)
the removal. Please keep us informed if you become aware about
upstream changes that enable using this plugin for firefox >= 10.
-Depends: glam2
+Recommends: glam2
Why: Motif search
-Depends: raster3d
+Recommends: raster3d
-Depends: phyml
+Recommends: phyml
-Depends: autodock
+Recommends: autodock
Why: Molecular modelling and molecular dynamics.
-Depends: autogrid
+Recommends: autogrid
-Depends: autodock-vina
+Recommends: autodock-vina
-Depends: autodocktools, mgltools-pmv, mgltools-vision, mgltools-cadd
+Recommends: autodocktools, mgltools-pmv, mgltools-vision, mgltools-cadd
-Depends: mustang
+Recommends: mustang
-Depends: probabel
+Recommends: probabel
-Depends: theseus
+Recommends: theseus
-Depends: staden-io-lib-utils
+Recommends: staden-io-lib-utils
-Depends: samtools, bedtools, filo, datamash
+Recommends: samtools, bedtools, filo, datamash
-Depends: gassst
+Recommends: gassst
-Depends: r-bioc-hilbertvis
+Recommends: r-bioc-hilbertvis
Remark: It would be interesting to package HilbertVisGUI (see below) as well.
-Depends: r-other-mott-happy.hbrem
+Recommends: r-other-mott-happy.hbrem
-Depends: seq-gen
+Recommends: seq-gen
-Depends: snp-sites
+Recommends: snp-sites
-Depends: mira-assembler
+Recommends: mira-assembler
-Depends: alien-hunter
+Recommends: alien-hunter
-Depends: seqan-apps
+Recommends: seqan-apps
-Depends: ncoils
+Recommends: ncoils
-Depends: gentle
+Recommends: gentle
-Depends: gmap
+Recommends: gmap
-Depends: igv
+Recommends: igv
-Depends: picard-tools
+Recommends: picard-tools
-Depends: acedb-other-dotter, acedb-other-belvu, acedb-other
+Recommends: acedb-other-dotter, acedb-other-belvu, acedb-other
-Depends: python-cogent
+Recommends: python-cogent
-Depends: paml
+Recommends: paml
-Depends: velvetoptimiser
+Recommends: velvetoptimiser
-Depends: ensembl
+Recommends: ensembl
Pkg-URL: http://snapshot.debian.org/package/ensembl/63-1/
Remark: Ensembl was removed from Debian due #645487
Ensembl used to be in Debian experimental branch but was removed for formal reasons which
are explained in http://bugs.debian.org/645487
-Depends: mrbayes
+Recommends: mrbayes
-Depends: pdb2pqr
+Recommends: pdb2pqr
-Depends: squizz
+Recommends: squizz
-Depends: clonalframe
+Recommends: clonalframe
-Depends: dssp
+Recommends: dssp
-Depends: jellyfish
+Recommends: jellyfish
-Depends: ballview
+Recommends: ballview
-Depends: pynast
+Recommends: pynast
-Depends: raxml
+Recommends: raxml
-Depends: mlv-smile
+Recommends: mlv-smile
Suggests: cain
-Depends: cd-hit
+Recommends: cd-hit
-Depends: cufflinks
+Recommends: cufflinks
-Depends: r-bioc-cummerbund
+Recommends: r-bioc-cummerbund
-Depends: eigensoft
+Recommends: eigensoft
-Depends: grinder
+Recommends: grinder
-Depends: jalview
+Recommends: jalview
-Depends: reprof
+Recommends: reprof
-Depends: tm-align
+Recommends: tm-align
-Depends: norsnet
+Recommends: norsnet
-Depends: norsp
+Recommends: norsp
-Depends: predictnls
+Recommends: predictnls
-Depends: prime-phylo
+Recommends: prime-phylo
-Depends: proftmb
+Recommends: proftmb
-Depends: profbval
+Recommends: profbval
-Depends: profisis
+Recommends: profisis
-Depends: hhsuite
+Recommends: hhsuite
-Depends: ffindex
+Recommends: ffindex
-Depends: flexbar
+Recommends: flexbar
-Depends: blimps-utils
+Recommends: blimps-utils
-Depends: sift
+Recommends: sift
-Depends: neobio
+Recommends: neobio
-Depends: ray
+Recommends: ray
-Depends: ugene
+Recommends: ugene
-Depends: logol-bin
+Recommends: logol-bin
-Depends: soapdenovo, soapdenovo2
+Recommends: soapdenovo, soapdenovo2
-Depends: microbiomeutil, chimeraslayer, nast-ier, wigeon
+Recommends: microbiomeutil, chimeraslayer, nast-ier, wigeon
-Depends: minia
+Recommends: minia
-Depends: trimmomatic
+Recommends: trimmomatic
-Depends: saint
+Recommends: saint
-Depends: rtax
+Recommends: rtax
-Depends: rate4site
+Recommends: rate4site
-Depends: rna-star
+Recommends: rna-star
-Depends: topp, openms
+Recommends: topp, openms
-Depends: scythe
+Recommends: scythe
-Depends: sickle
+Recommends: sickle
-Depends: kmc
+Recommends: kmc
-Depends: king-probe
+Recommends: king-probe
-Depends: ncl-tools
+Recommends: ncl-tools
-Depends: tvc
+Recommends: tvc
Suggests: science-workflow
-Depends: libvcflib-tools
+Recommends: libvcflib-tools
-Depends: bppsuite, bppphyview
+Recommends: bppsuite, bppphyview
Suggests: getdata
@@ -365,180 +365,180 @@ X-Mark: Prospective packages are starting here
X-Mark: Packages in Vcs - Information about these is queried from UDD as well
-Depends: acacia
+Recommends: acacia
-Depends: adapterremoval
+Recommends: adapterremoval
-Depends: aegean
+Recommends: aegean
-Depends: andi
+Recommends: andi
-Depends: arden
+Recommends: arden
-Depends: artfastqgenerator, art-nextgen-simulation-tools
+Recommends: artfastqgenerator, art-nextgen-simulation-tools
-Depends: augustus
+Recommends: augustus
-Depends: baitfisher
+Recommends: baitfisher
-Depends: beagle
+Recommends: beagle
-Depends: bedops
+Recommends: bedops
-Depends: biceps
+Recommends: biceps
Remark: Mentioned at http://www.renard.it/, developed in RKI
-Depends: cnvkit
+Recommends: cnvkit
-Depends: diamond-aligner
+Recommends: diamond-aligner
-Depends: emperor
+Recommends: emperor
-Depends: euler2, euler-sr
+Recommends: euler2, euler-sr
-Depends: fitgcp
+Recommends: fitgcp
-Depends: gasic
+Recommends: gasic
-Depends: giira
+Recommends: giira
-Depends: ipig
+Recommends: ipig
-Depends: aevol
+Recommends: aevol
-Depends: alter-sequence-alignment
+Recommends: alter-sequence-alignment
-Depends: amos-assembler, hawkeye
+Recommends: amos-assembler, hawkeye
Language: Perl
-Depends: anfo
+Recommends: anfo
-Depends: apollo
+Recommends: apollo
-Depends: aragorn
+Recommends: aragorn
-Depends: ariba
+Recommends: ariba
-Depends: atac
+Recommends: atac
-Depends: axe-demultiplexer
+Recommends: axe-demultiplexer
-Depends: axparafit, axpcoords
+Recommends: axparafit, axpcoords
-Depends: barrnap
+Recommends: barrnap
-Depends: bamtools
+Recommends: bamtools
-Depends: bagpipe
+Recommends: bagpipe
-Depends: bcftools
+Recommends: bcftools
WNPP: 804007
-Depends: bigsdb
+Recommends: bigsdb
-Depends: bio-eagle
+Recommends: bio-eagle
-Depends: bio-tradis
+Recommends: bio-tradis
-Depends: bitseq
+Recommends: bitseq
-Depends: blat
+Recommends: blat
-Depends: blobology
+Recommends: blobology
-Depends: bio-rainbow
+Recommends: bio-rainbow
-Depends: card-rgi
+Recommends: card-rgi
-Depends: cassiopee
+Recommends: cassiopee
-Depends: ccs
+Recommends: ccs
-Depends: cdbfasta
+Recommends: cdbfasta
-Depends: cgview, brig
+Recommends: cgview, brig
-Depends: cinema
+Recommends: cinema
Language: Java
-Depends: circlator
+Recommends: circlator
-Depends: clearcut
+Recommends: clearcut
-Depends: clonalorigin
+Recommends: clonalorigin
-Depends: cluster3
+Recommends: cluster3
-Depends: codonw
+Recommends: codonw
-Depends: condetri
+Recommends: condetri
-Depends: contrafold
+Recommends: contrafold
-Depends: crac
+Recommends: crac
-Depends: crossbow
+Recommends: crossbow
X-Category: Sequencing
-Depends: crux-toolkit
+Recommends: crux-toolkit
-Depends: cutadapt
+Recommends: cutadapt
-Depends: cytoscape
+Recommends: cytoscape
-Depends: dawg
+Recommends: dawg
-Depends: dazzdb
+Recommends: dazzdb
-Depends: dazzle
+Recommends: dazzle
-Depends: deepnano
+Recommends: deepnano
Remark: There is no intend to keep continue the existing packaging since
the program nanocall seems to serve the intended purpose better
-Depends: dindel
+Recommends: dindel
-Depends: dwgsim
+Recommends: dwgsim
-Depends: ea-utils
+Recommends: ea-utils
-Depends: ecell
+Recommends: ecell
-Depends: ecopcr
+Recommends: ecopcr
-Depends: edtsurf
+Recommends: edtsurf
-Depends: emmax
+Recommends: emmax
-Depends: examl, raxml-ng
+Recommends: examl, raxml-ng
-Depends: exabayes
+Recommends: exabayes
-Depends: berkeley-express
+Recommends: berkeley-express
-Depends: falcon
+Recommends: falcon
-Depends: fasta3
+Recommends: fasta3
-Depends: fasttree
+Recommends: fasttree
-Depends: fastahack
+Recommends: fastahack
-Depends: fastaq
+Recommends: fastaq
-Depends: fastml
+Recommends: fastml
-Depends: fastqc
+Recommends: fastqc
-Depends: fastqtl
+Recommends: fastqtl
-Depends: ffp
+Recommends: ffp
-Depends: unc-fish
+Recommends: unc-fish
-Depends: fml-asm
+Recommends: fml-asm
-Depends: forester
+Recommends: forester
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-amd64
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
BioLinux was following the upstream name change to archaeopteryx and thus the
@@ -546,11 +546,11 @@ Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
.
The binary package is full of JARs without source.
-Depends: freecontact
+Recommends: freecontact
-Depends: freebayes
+Recommends: freebayes
-Depends: fsa
+Recommends: fsa
Enhances: t-coffee
Remark: Precondition for T-Coffee
see http://wiki.debian.org/DebianMed/TCoffee
@@ -558,296 +558,296 @@ Remark: Precondition for T-Coffee
Upstream address bounced when contacting about segfaults so it seems to be
dead upstream and no good code quality.
-Depends: fsm-lite
+Recommends: fsm-lite
-Depends: garli
+Recommends: garli
-Depends: gatk
+Recommends: gatk
-Depends: genometools
+Recommends: genometools
-Depends: grabix
+Recommends: grabix
-Depends: graphlan
+Recommends: graphlan
-Depends: grogui
+Recommends: grogui
-Depends: gwama
+Recommends: gwama
-Depends: gubbins
+Recommends: gubbins
-Depends: haploview
+Recommends: haploview
-Depends: harvest-tools
+Recommends: harvest-tools
-Depends: hilive
+Recommends: hilive
-Depends: hisat2
+Recommends: hisat2
-Depends: hmmer2
+Recommends: hmmer2
Remark: This older version of HMMER is used in some applications
While Debian has HMMER 3 since some time there are users of
HMMER 2 interested in having this old version available and
thus the package is reintroduced.
-Depends: htqc
+Recommends: htqc
-Depends: idba
+Recommends: idba
-Depends: indelible
+Recommends: indelible
-Depends: iqtree
+Recommends: iqtree
-Depends: iva
+Recommends: iva
-Depends: jaligner
+Recommends: jaligner
-Depends: jbrowse
+Recommends: jbrowse
-Depends: jmodeltest
+Recommends: jmodeltest
-Depends: kempbasu
+Recommends: kempbasu
-Depends: kineticstools
+Recommends: kineticstools
WNPP: 797676
-Depends: kissplice
+Recommends: kissplice
-Depends: kraken
+Recommends: kraken
-Depends: lagan
+Recommends: lagan
X-Category: Comparative genomics
-Depends: lambda-align
+Recommends: lambda-align
-Depends: leaff
+Recommends: leaff
-Depends: ltrsift
+Recommends: ltrsift
-Depends: lofreq
+Recommends: lofreq
-Depends: logomat-m
+Recommends: logomat-m
-Depends: kclust
+Recommends: kclust
-Depends: khmer
+Recommends: khmer
-Depends: kmer
+Recommends: kmer
-Depends: radiant
+Recommends: radiant
-Depends: lefse
+Recommends: lefse
-Depends: mach-haplotyper
+Recommends: mach-haplotyper
-Depends: macs
+Recommends: macs
-Depends: macsyfinder
+Recommends: macsyfinder
-Depends: maffilter
+Recommends: maffilter
-Depends: mage2tab
+Recommends: mage2tab
-Depends: malt
+Recommends: malt
-Depends: manta
+Recommends: manta
-Depends: mapdamage
+Recommends: mapdamage
-Depends: martj
+Recommends: martj
-Depends: mash
+Recommends: mash
-Depends: progressivemauve
+Recommends: progressivemauve
X-Category: Multiple genome alignment
X-Importance: efficient
-Depends: mauve-aligner
+Recommends: mauve-aligner
-Depends: meme
+Recommends: meme
License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)
-Depends: meryl
+Recommends: meryl
-Depends: metabit
+Recommends: metabit
-Depends: metaphlan2
+Recommends: metaphlan2
-Depends: metastudent
+Recommends: metastudent
Suggests: metastudent-data, metastudent-data-2, metastudent-data-3
-Depends: microbegps
+Recommends: microbegps
-Depends: miniasm
+Recommends: miniasm
-Depends: minimap
+Recommends: minimap
-Depends: molekel
+Recommends: molekel
-Depends: mosaik-aligner
+Recommends: mosaik-aligner
-Depends: mpsqed
+Recommends: mpsqed
Suggests: mrs
Remark: mrs might occupy a lot of space on users disk - so you want to avoid this package from the metapackage recommends
-Depends: mptp
+Recommends: mptp
-Depends: mugsy
+Recommends: mugsy
-Depends: murasaki
+Recommends: murasaki
-Depends: nanocall
+Recommends: nanocall
-Depends: nanopolish
+Recommends: nanopolish
-Depends: ncbi-entrez-direct
+Recommends: ncbi-entrez-direct
WNPP: 810949
-Depends: ncbi-seg
+Recommends: ncbi-seg
-Depends: nextsv
+Recommends: nextsv
-Depends: ngila
+Recommends: ngila
-Depends: ngsqctoolkit
+Recommends: ngsqctoolkit
-Depends: nw-align
+Recommends: nw-align
-Depends: oases
+Recommends: oases
-Depends: obitools
+Recommends: obitools
-Depends: r-other-apmswapp
+Recommends: r-other-apmswapp
-Depends: pal2nal
+Recommends: pal2nal
-Depends: paleomix
+Recommends: paleomix
-Depends: paraclu
+Recommends: paraclu
-Depends: parsinsert
+Recommends: parsinsert
-Depends: parsnp
+Recommends: parsnp
-Depends: partitionfinder
+Recommends: partitionfinder
-Depends: patman
+Recommends: patman
-Depends: patristic
+Recommends: patristic
Language: Java
-Depends: pbalign, pbbarcode, pbdagcon
+Recommends: pbalign, pbbarcode, pbdagcon
-Depends: pbsuite
+Recommends: pbsuite
WNPP: 807802
-Depends: pbgenomicconsensus
+Recommends: pbgenomicconsensus
-Depends: pbjelly, pbhoney
+Recommends: pbjelly, pbhoney
-Depends: pbh5tools
+Recommends: pbh5tools
-Depends: pbsim
+Recommends: pbsim
-Depends: pcma
+Recommends: pcma
Remark: Precondition for T-Coffee
see http://wiki.debian.org/DebianMed/TCoffee
.
Check with authors about licensing, they adopted code from clustalw which is now
free. Thus a change might be possible
-Depends: perm
+Recommends: perm
-Depends: pftools
+Recommends: pftools
-Depends: phast
+Recommends: phast
-Depends: phipack
+Recommends: phipack
-Depends: phybin
+Recommends: phybin
-Depends: phylophlan
+Recommends: phylophlan
Remark: usearch can not be replaced since vsearch does not work with proteins
See https://lists.debian.org/debian-med/2016/05/msg00091.html
-Depends: phyloviz-core
+Recommends: phyloviz-core
Remark: There are several plugins to package
The download page http://www.phyloviz.net/wiki/plugins/ lists several plugins
that should be packaged (single or as bundle) as well.
-Depends: phyutility
+Recommends: phyutility
-Depends: piler
+Recommends: piler
-Depends: pipasic, inspect, tide
+Recommends: pipasic, inspect, tide
-Depends: physamp
+Recommends: physamp
-Depends: pirs
+Recommends: pirs
-Depends: placnet
+Recommends: placnet
-Depends: plato
+Recommends: plato
-Depends: plip
+Recommends: plip
-Depends: poretools
+Recommends: poretools
-Depends: prank
+Recommends: prank
-Depends: predictprotein
+Recommends: predictprotein
-Depends: proalign
+Recommends: proalign
-Depends: prodigal
+Recommends: prodigal
-Depends: prokka
+Recommends: prokka
-Depends: proteinortho
+Recommends: proteinortho
-Depends: prottest
+Recommends: prottest
-Depends: psortb
+Recommends: psortb
-Depends: pscan-tfbs
+Recommends: pscan-tfbs
-Depends: psipred
+Recommends: psipred
-Depends: pssh2
+Recommends: pssh2
-Depends: pycorrfit
+Recommends: pycorrfit
-Depends: pyscanfcs
+Recommends: pyscanfcs
-Depends: python-reaper
+Recommends: python-reaper
-Depends: python-treetime
+Recommends: python-treetime
-Depends: qcumber
+Recommends: qcumber
-Depends: qtltools
+Recommends: qtltools
-Depends: qualimap
+Recommends: qualimap
-Depends: quorum
+Recommends: quorum
-Depends: rambo-k
+Recommends: rambo-k
-Depends: rapmap
+Recommends: rapmap
-Depends: r-bioc-rtracklayer, r-bioc-gviz, r-bioc-biostrings, r-bioc-annotate, r-bioc-genefilter
+Recommends: r-bioc-rtracklayer, r-bioc-gviz, r-bioc-biostrings, r-bioc-annotate, r-bioc-genefilter
-Depends: r-bioc-deseq2, r-bioc-dnacopy, r-bioc-geneplotter
+Recommends: r-bioc-deseq2, r-bioc-dnacopy, r-bioc-geneplotter
-Depends: r-bioc-mergeomics
+Recommends: r-bioc-mergeomics
-Depends: r-bioc-metagenomeseq, r-bioc-phyloseq
+Recommends: r-bioc-metagenomeseq, r-bioc-phyloseq
-Depends: r-bioc-ebseq
+Recommends: r-bioc-ebseq
-Depends: r-bioc-limma, r-bioc-edger
+Recommends: r-bioc-limma, r-bioc-edger
Suggests: r-bioc-annotationhub, r-bioc-aroma.light, r-bioc-ensembldb, r-bioc-go.db
@@ -855,75 +855,75 @@ Suggests: r-bioc-savr
Suggests: r-cran-qqman
-Depends: r-cran-rotl
+Recommends: r-cran-rotl
Suggests: r-cran-rentrez
-Depends: r-cran-adegenet, r-cran-adephylo
+Recommends: r-cran-adegenet, r-cran-adephylo
-Depends: r-cran-distory
+Recommends: r-cran-distory
-Depends: r-cran-metamix
+Recommends: r-cran-metamix
-Depends: r-cran-phangorn
+Recommends: r-cran-phangorn
-Depends: r-cran-pscbs
+Recommends: r-cran-pscbs
Suggests: r-cran-boolnet
-Depends: r-cran-seqinr
+Recommends: r-cran-seqinr
-Depends: r-cran-vegan
+Recommends: r-cran-vegan
Suggests: r-cran-pheatmap
-Depends: relion-bin+gui | relion-bin+mpi+gui, relion-bin | relion-bin+mpi
+Recommends: relion-bin+gui | relion-bin+mpi+gui, relion-bin | relion-bin+mpi
-Depends: r-other-valdar-bagphenotype.library
+Recommends: r-other-valdar-bagphenotype.library
-Depends: rdp-alignment, rdp-readseq, rdp-classifier
+Recommends: rdp-alignment, rdp-readseq, rdp-classifier
-Depends: reapr
+Recommends: reapr
-Depends: repeatmasker-recon
+Recommends: repeatmasker-recon
-Depends: repeatmasker
+Recommends: repeatmasker
-Depends: roadtrips
+Recommends: roadtrips
-Depends: roary
+Recommends: roary
-Depends: roguenarok
+Recommends: roguenarok
-Depends: rosetta
+Recommends: rosetta
-Depends: rsat
+Recommends: rsat
-Depends: rsem
+Recommends: rsem
-Depends: sambamba
+Recommends: sambamba
-Depends: salmon
+Recommends: salmon
-Depends: sap
+Recommends: sap
Remark: Precondition for T-Coffee
see http://wiki.debian.org/DebianMed/TCoffee
-Depends: scrm
+Recommends: scrm
-Depends: sga
+Recommends: sga
-Depends: seer
+Recommends: seer
-Depends: segemehl
+Recommends: segemehl
-Depends: seqprep
+Recommends: seqprep
-Depends: seqsero
+Recommends: seqsero
-Depends: seqtk
+Recommends: seqtk
-Depends: sequenceconverter.app
+Recommends: sequenceconverter.app
Remark: Formerly part of Debian as biococoa.app but removed
The package was part of Debian under the name biococoa.app which is confusing
because biococoa is actually a library for working with sequences under GNUstep.
@@ -935,124 +935,124 @@ Remark: Formerly part of Debian as biococoa.app but removed
newer versions are needed to work under Linux try to convince upstream to
support GNUstep.
-Depends: situs
+Recommends: situs
-Depends: sim4db
+Recommends: sim4db
-Depends: smalt
+Recommends: smalt
Remark: This can be regarded as successor of ssaha2
This program is from the same author as ssaha2 and according to its author
faster and more precise than ssaha2 (except for sequences > 2000bp).
-Depends: smithwaterman
+Recommends: smithwaterman
-Depends: ssw-align
+Recommends: ssw-align
-Depends: smrtanalysis
+Recommends: smrtanalysis
-Depends: snpeff
+Recommends: snpeff
-Depends: snpomatic
+Recommends: snpomatic
-Depends: sortmerna
+Recommends: sortmerna
-Depends: snap-aligner
+Recommends: snap-aligner
-Depends: sniffles
+Recommends: sniffles
-Depends: spaced
+Recommends: spaced
WNPP: 815672
-Depends: spades
+Recommends: spades
-Depends: sparta
+Recommends: sparta
-Depends: sprai
+Recommends: sprai
-Depends: srst2
+Recommends: srst2
-Depends: ssaha
+Recommends: ssaha
Remark: Successor for ssaha2 available: smalt
The program smalt is from the same author is according to its author
faster and more precise than ssaha2 (except for sequences > 2000bp)
-Depends: sspace
+Recommends: sspace
-Depends: staden
+Recommends: staden
-Depends: stacks
+Recommends: stacks
-Depends: strap, strap-base
+Recommends: strap, strap-base
Language: Java
-Depends: subread
+Recommends: subread
-Depends: suitename
+Recommends: suitename
-Depends: sumatra, sumaclust
+Recommends: sumatra, sumaclust
-Depends: sumtrees
+Recommends: sumtrees
-Depends: surankco
+Recommends: surankco
-Depends: swarm
+Recommends: swarm
-Depends: tacg
+Recommends: tacg
X-Category: Motif detection
X-Importance: powerful
-Depends: tantan
+Recommends: tantan
-Depends: toppred
+Recommends: toppred
-Depends: transdecoder
+Recommends: transdecoder
-Depends: tnseq-transit
+Recommends: tnseq-transit
-Depends: tn-seqexplorer
+Recommends: tn-seqexplorer
-Depends: transrate-tools
+Recommends: transrate-tools
-Depends: treeview
+Recommends: treeview
X-Category: Visualisation
-X-Depends: treevolve
+X-Recommends: treevolve
X-Comment: Homepage of software vanished, packaging in SVN is obviosely stalled
Feel free to delete the 'X-' in front if you intend to do something on this package
-Depends: trinityrnaseq
+Recommends: trinityrnaseq
-Depends: uc-echo
+Recommends: uc-echo
X-Category: NGS
-Depends: varna
+Recommends: varna
-Depends: varmatch
+Recommends: varmatch
-Depends: varscan
+Recommends: varscan
-Depends: vienna-rna
+Recommends: vienna-rna
X-Category: Secondary structure of nucleic acids
-Depends: vmd
+Recommends: vmd
-Depends: vsearch
+Recommends: vsearch
-Depends: canu
+Recommends: canu
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Depends: zalign
+Recommends: zalign
-Depends: zodiac-zeden
+Recommends: zodiac-zeden
Language: C, C++
-Depends: discosnp, mapsembler2
+Recommends: discosnp, mapsembler2
-Depends: dnaclust
+Recommends: dnaclust
X-Mark: The information below needs to be checked whether it can be obtained from Vcs or needs to stay here
-Depends: copycat
+Recommends: copycat
Homepage: http://www-ab.informatik.uni-tuebingen.de/software/copycat/welcome.html
License: Use of the program is free for academic purposes at an academic institute. For all other uses, please contact the authors.
Pkg-Description: fast access to cophylogenetic analyses
@@ -1063,7 +1063,7 @@ Pkg-Description: fast access to cophylogenetic analyses
creation of customized host-parasite association data and the
computation of phylogenetic host/parasite trees based on the NCBI taxonomy.
-Depends: btk-core
+Recommends: btk-core
Homepage: http://sourceforge.net/projects/btk/
Responsible: Morten Kjeldgaard <mok at bioxray.au.dk>
License: GPL
@@ -1074,7 +1074,7 @@ Pkg-Description: biomolecule Toolkit C++ library
for common tasks in structural biology to facilitate the development of
molecular modeling, design and analysis tools.
-Depends: asap
+Recommends: asap
Homepage: http://asap.ahabs.wisc.edu/software/asap/
Responsible: Andreas Tille <tille at debian.org>
License: GPL
@@ -1102,7 +1102,7 @@ Pkg-Description: organize the data associated with a genome
inter-operable between sites.
X-Category: Annotation
-Depends: cactus
+Recommends: cactus
Homepage: http://www.cactuscode.org/Community/Biology.html
License: GPL
Pkg-Description:
@@ -1116,7 +1116,7 @@ Pkg-Description:
Metacomputing Toolkit, HDF5 parallel file I/O, the PETSc scientific library,
adaptive mesh refinement, web interfaces, and advanced visualization tools.
-Depends: contralign
+Recommends: contralign
Homepage: http://contra.stanford.edu/contralign/
License: Public Domain
Pkg-Description: parameter learning framework for protein pairwise sequence alignment
@@ -1127,14 +1127,14 @@ Pkg-Description: parameter learning framework for protein pairwise sequence alig
previously unseen sequences and avoid overfitting by controlling model
complexity through regularization.
-Depends: concavity
+Recommends: concavity
Homepage: http://compbio.cs.princeton.edu/concavity/
-Depends: conservation-code
+Recommends: conservation-code
Homepage: http://compbio.cs.princeton.edu/conservation/
WNPP: 690058
-Depends: galaxy
+Recommends: galaxy
Homepage: http://g2.trac.bx.psu.edu/
License: MIT
WNPP: 432472
@@ -1145,7 +1145,7 @@ Pkg-Description: manipulate sequences and annotation files
strong ties with the UCSC genome browser, and makes it easy to
visualise modified annotation files as a custom track.
-Depends: genographer
+Recommends: genographer
Homepage: http://hordeum.oscs.montana.edu/genographer/
License: GPL
Pkg-Description: read data and reconstruct them into a gel image
@@ -1157,7 +1157,7 @@ Pkg-Description: read data and reconstruct them into a gel image
The program is written in Java and uses the Java 1.3 API. Therefore,
it should run on any machine that can run java.
-Depends: pftools
+Recommends: pftools
Homepage: ftp://us.expasy.org/databases/prosite/tools/ps_scan/sources
License: GPL
Pkg-Description: tools to handle profiles of protein domains from PROSITE
@@ -1175,7 +1175,7 @@ Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: phylographer
+Recommends: phylographer
Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html
License: GPL
X-Category: Graphical representation of sequence conservation
@@ -1196,7 +1196,7 @@ Remark: Outdated upstream, better alternatives available
The former packaging effort of this package was dropped. It seems
that http://cytoscape.org/ is a reasonable replacement.
-Depends: phylowin
+Recommends: phylowin
Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html
WNPP: 395840
License: unknown
@@ -1221,7 +1221,7 @@ Remark: Issuer of previous ITP said:
Probably it makes sense to remove this project from the prospective packages
list.
-Depends: gbioseq
+Recommends: gbioseq
Homepage: http://www.bioinformatics.org/project/?group_id=94
License: GPL
Pkg-Description: DNA sequence editor for Linux
@@ -1229,14 +1229,14 @@ Pkg-Description: DNA sequence editor for Linux
The goal is to provide an easy to use software to edit DNA sequences under
Linux, Windows, MacOsX, using GTK C# (Mono).
-Depends: phpphylotree
+Recommends: phpphylotree
Homepage: http://www.bioinformatics.org/project/?group_id=372
License: GPL
Pkg-Description: draw phylogenetic trees
PhpPhylotree is a web application that is able to draw phylogenetic trees.
It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.
-Depends: tracetuner
+Recommends: tracetuner
Homepage: http://www.jcvi.org/cms/research/software/tracetuner/overview
License: GPL; but US Patent #6,681,186
Pkg-Description: DNA sequencing and trace processing
@@ -1265,7 +1265,7 @@ Pkg-Description: DNA sequencing and trace processing
and conditions of the GNU General Public License, version 2, as published by the
Free Software Foundation (the "GNU General Public License").
-Depends: twain
+Recommends: twain
Homepage: http://cbcb.umd.edu/software/pirate/twain/twain.shtml
License: Open Source
Pkg-Description: syntenic genefinder employing a Generalized Pair Hidden Markov Model
@@ -1288,7 +1288,7 @@ Pkg-Description: syntenic genefinder employing a Generalized Pair Hidden Markov
Slides from a talk at Computational Genomics 2004 are now available.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Depends: rose
+Recommends: rose
Homepage: http://www.cbcb.umd.edu/software/rose/Rose.html
License: Open Source
Pkg-Description: Region-Of-Synteny Extractor
@@ -1307,7 +1307,7 @@ Pkg-Description: Region-Of-Synteny Extractor
boundaries of the output region.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Depends: glimmerhmm
+Recommends: glimmerhmm
Homepage: http://www.cbcb.umd.edu/software/glimmerhmm/
License: Artistic
Pkg-Description: Eukaryotic Gene-Finding System
@@ -1322,7 +1322,7 @@ Pkg-Description: Eukaryotic Gene-Finding System
user manual can be consulted here.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Depends: genezilla
+Recommends: genezilla
Homepage: http://www.genezilla.org/
License: Artistic
Language: C++
@@ -1352,7 +1352,7 @@ Pkg-Description: eukaryotic gene finder
for the comparative gene finder TWAIN.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Depends: exalt
+Recommends: exalt
Homepage: http://www.cbcb.umd.edu/software/exalt/
License: Artistic
Pkg-Description: phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
@@ -1366,7 +1366,7 @@ Pkg-Description: phylogenetic generalized hidden Markov model for predicting alt
run on other species.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Depends: jigsaw
+Recommends: jigsaw
Homepage: http://www.cbcb.umd.edu/software/jigsaw/
License: Artistic
Pkg-Description: gene prediction using multiple sources of evidence
@@ -1394,7 +1394,7 @@ Pkg-Description: gene prediction using multiple sources of evidence
custom tracks in the UCSC Human Genome Browser
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Depends: genesplicer
+Recommends: genesplicer
Homepage: http://www.cbcb.umd.edu/software/GeneSplicer/
License: Artistic
Pkg-Description: computational method for splice site prediction
@@ -1438,7 +1438,7 @@ Pkg-Description: motif discovery tool
On the other hand the SMILE author told us in private mail that he
thinks that RISO is dead and SMILE continues to have some importance.
-Depends: mummergpu
+Recommends: mummergpu
Homepage: http://mummergpu.sourceforge.net/
License: Artistic
Pkg-Description: High-throughput sequence alignment using Graphics Processing Units
@@ -1466,7 +1466,7 @@ Pkg-Description: High-throughput sequence alignment using Graphics Processing Un
technologies.
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Depends: amoscmp
+Recommends: amoscmp
Homepage: http://amos.sourceforge.net/docs/pipeline/AMOScmp.html
License: Artistic
Pkg-Description: comparative genome assembly package
@@ -1495,7 +1495,7 @@ Pkg-Description: comparative genome assembly package
modular open-source framework for assembly development.
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Depends: minimus
+Recommends: minimus
Homepage: http://amos.sourceforge.net/docs/pipeline/minimus.html
License: Artistic
Pkg-Description: AMOS lightweight assembler
@@ -1587,7 +1587,7 @@ Pkg-Description: Transcript Annotation Prioritization and Screening System
Remark: Found at
http://gforge.nci.nih.gov/softwaremap/trove_list.php?form_cat=337
-Depends: bambus
+Recommends: bambus
Homepage: http://amos.sourceforge.net/docs/bambus/
License: Artistic
Pkg-Description: hierarchical approach to building contig scaffolds
@@ -1602,7 +1602,7 @@ Pkg-Description: hierarchical approach to building contig scaffolds
integrated with the AMOS package (see http://amos.sourceforge.net/)
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Depends: gmv
+Recommends: gmv
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?GMV
License: GPL
Pkg-Description: comparative genome browser for Murasaki
@@ -1610,14 +1610,14 @@ Pkg-Description: comparative genome browser for Murasaki
anchors from Murasaki, annotation data from GenBank files, and
expression / prediction score from GFF files.
-Depends: pyrophosphate-tools
+Recommends: pyrophosphate-tools
Homepage: http://www-naweb.iaea.org/nafa/ipc/public/d4_pbl_6a.html
License: not specified
Pkg-Description: for assembling and searching pyrophosphate sequence data
Simple tools for assembling and searching high-density picolitre
pyrophosphate sequence data.
-Depends: figaro
+Recommends: figaro
Homepage: http://amos.sourceforge.net/Figaro/Figaro.html
License: Artistic
Pkg-Description: novel vector trimming software
@@ -1630,7 +1630,7 @@ Pkg-Description: novel vector trimming software
part of the AMOS suite.
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Depends: mirbase
+Recommends: mirbase
Homepage: http://microrna.sanger.ac.uk/
License: Public Domain
WNPP: 420938
@@ -1653,7 +1653,7 @@ Pkg-Description: The microRNA sequence database
It is possible that mirbase will not be a package from the main archive, but
will be autogenerated as part of a larger data packaging effort.
-Depends: elph
+Recommends: elph
Homepage: http://www.cbcb.umd.edu/software/ELPH/
License: Artistic
Pkg-Description: motif finder that can find ribosome binding sites, exon splicing enhancers, or regulatory sites
@@ -1671,7 +1671,7 @@ Pkg-Description: motif finder that can find ribosome binding sites, exon splicin
http://www.cbcb.umd.edu/software/SeeEse/index.html .
Remark: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
-X-Depends: repeatfinder
+X-Recommends: repeatfinder
X-Homepage: http://www.cbcb.umd.edu/software/RepeatFinder/
X-License: Artistic
X-Pkg-Description: finding repetitive sequences complete and draft genomes
@@ -1685,7 +1685,7 @@ X-Pkg-Description: finding repetitive sequences complete and draft genomes
Kurtz's REPuter.
X-Note: Depends from non-distributable code reputer (see below)
-X-Depends: reputer
+X-Recommends: reputer
X-Homepage: http://citeseer.ist.psu.edu/kurtz95reputer.html
X-License: non-commercial
X-Pkg-Description: fast computation of maximal repeats in complete genomes
@@ -1694,7 +1694,7 @@ X-Pkg-Description: fast computation of maximal repeats in complete genomes
X-Note: Code is not redistributable see mailing list discussion at
http://lists.debian.org/debian-med/2012/07/msg00195.html
-Depends: uniprime
+Recommends: uniprime
Homepage: http://code.google.com/p/uniprime/
License: GPL-3+
Responsible: Charles Plessy <plessy at debian.org>
@@ -1710,7 +1710,7 @@ Pkg-Description: workflow-based platform for universal primer design
generates successful cross-species primers that take into account the
biological aspects of the PCR.
-Depends: genetrack
+Recommends: genetrack
Homepage: http://sysbio.bx.psu.edu/genetrack.html
License: MIT
Responsible: Charles Plessy <plessy at debian.org>
@@ -1720,7 +1720,7 @@ Pkg-Description: genomic data storage and visualization framework
analyze data obtained via high-throughput rapid sequencing platforms such as
the 454 and Solexa as well as tiling array data based on various platforms.
-Depends: operondb
+Recommends: operondb
Homepage: http://www.cbcb.umd.edu/cgi-bin/operons/operons.cgi
License: to be clarified
Pkg-Description: detect and analyze conserved gene pairs
@@ -1749,7 +1749,7 @@ Remark: Other sequence analysis tools (http://www.cbcb.umd.edu/software/);
no info about license or downloadable code found, but tried to
contact authors.
-Depends: trnascan-se
+Recommends: trnascan-se
WNPP: 803542
Comment: If you stumble upon alfresco at
@@ -1763,7 +1763,7 @@ Comment: If you stumble upon angler at
this is probably also not for us except somebody has real interest
and volunteers to clarify the license.
-Depends: cdna-db
+Recommends: cdna-db
Homepage: http://www.sanger.ac.uk/Software/analysis/cdna_db/
License: Artistic
Pkg-Description: quality-control checking of finished cDNA clone sequences
@@ -1790,7 +1790,7 @@ Pkg-Description: quality-control checking of finished cDNA clone sequences
dump cDNA clones sequences (such as those that passed the QC
checking) from the cdna_db.
-Depends: das-proserver
+Recommends: das-proserver
Homepage: http://www.sanger.ac.uk/Software/analysis/proserver/
License: Same as Perl
Pkg-Description: lightweight Distributed Annotation System (DAS) server
@@ -1827,7 +1827,7 @@ Pkg-Description: lightweight Distributed Annotation System (DAS) server
last years we have also seen growing acceptance in the protein
sequence and structure communities.
-Depends: spice
+Recommends: spice
Homepage: http://www.efamily.org.uk/software/dasclients/spice/
License: GPL
Pkg-Description: Distributed Annotation System (DAS) client
@@ -1841,7 +1841,7 @@ Pkg-Description: Distributed Annotation System (DAS) client
possible to add new annotations to SPICE, and to compare them with
the already available information.
-Depends: decipher
+Recommends: decipher
Homepage: http://www.sanger.ac.uk/Software/analysis/decipher/
License: To be clarified
Pkg-Description: tracks duplications and deletions of DNA in patients
@@ -1853,7 +1853,7 @@ Pkg-Description: tracks duplications and deletions of DNA in patients
of these conditions. DECIPHER makes use of DAS technology to
integrate with Ensembl, the world's leading genome browser.
-Depends: est-db
+Recommends: est-db
Homepage: http://www.sanger.ac.uk/Software/analysis/est_db/
License: Artistic
Pkg-Description: Software suite for expressed sequence tag (EST) sequencing
@@ -1884,7 +1884,7 @@ Pkg-Description: Software suite for expressed sequence tag (EST) sequencing
available free of charge, and, where possible, similarly
open-licensed components have been used in its development.
-Depends: finex
+Recommends: finex
Homepage: http://www.sanger.ac.uk/Software/analysis/finex/
License: To be clarified
Pkg-Description: sequence homology searching
@@ -1895,7 +1895,7 @@ Pkg-Description: sequence homology searching
Please note FINEX is no longer supported but is available for
download.
-Depends: hexamer
+Recommends: hexamer
Homepage: http://www.sanger.ac.uk/Software/analysis/hexamer/
License: GPL
Pkg-Description: scan DNA sequences to look for likely coding regions
@@ -1922,13 +1922,13 @@ Pkg-Description: scan DNA sequences to look for likely coding regions
converted to 'c'.
The output of hexamer is in General Feature Format (GFF) format.
-Depends: coot
+Recommends: coot
-Depends: r-cran-ape
+Recommends: r-cran-ape
-Depends: r-cran-treescape
+Recommends: r-cran-treescape
-Depends: caftools
+Recommends: caftools
Homepage: http://www.sanger.ac.uk/Software/formats/CAF/userguide.shtml
License: Free for non-commercial purposes
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -1952,7 +1952,7 @@ Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html
Format) or GAP4. This package includes tools to convert assemblies
from Newbler's ace format for loading into a gap4 assembly.
-Depends: roche454ace2caf
+Recommends: roche454ace2caf
Homepage: http://genome.imb-jena.de/software/roche454ace2caf/
License: not specified
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -1979,7 +1979,7 @@ Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html
Format) or GAP4. This package includes tools to convert assemblies
from Newbler's ace format for loading into a gap4 assembly.
-Depends: big-blast
+Recommends: big-blast
Homepage: ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/extra/big_blast.pl
License: not specified
Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -1990,7 +1990,7 @@ Pkg-Description: Helper tool to run blast on large sequences
containing the hits.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: blixem
+Recommends: blixem
Homepage: http://bioinformatics.abc.hu/tothg/biocomp/other/Blixem.html
License: not specified
Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
@@ -2002,7 +2002,7 @@ Pkg-Description: interactive browser of pairwise Blast matches
Remark: The link to the source archive on the web pages is not valid any more - it might be a problem to obtain the source.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: cap3
+Recommends: cap3
Homepage: http://genome.cs.mtu.edu/cap/cap3.html
License: free for governmental agency or a non-profit educational institution
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2032,7 +2032,7 @@ Comment: BioLinux contains a clcworkbench package which is available
at http://www.clcbio.com/index.php?id=28 but this seems to be only
"free as in beer" binary download - so this is not for us ...
-Depends: coalesce
+Recommends: coalesce
Homepage: http://evolution.gs.washington.edu/lamarc/coalesce.html
License: not specified
Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
@@ -2057,7 +2057,7 @@ Comment: BioLinux contains a dendroscope package which is available
at http://www.dendroscope.org but this project has only a
"free as in beer" binary download - so this is not for us ...
-Depends: estferret
+Recommends: estferret
Homepage: http://legr.liv.ac.uk/EST-ferret/index.htm
License: to be clarified
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2104,7 +2104,7 @@ Pkg-Description: processes, clusters and annotates EST data
a MySQL database or web-browsable search tool.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: estscan
+Recommends: estscan
Homepage: http://estscan.sourceforge.net/
License: free
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2137,7 +2137,7 @@ Pkg-Description: detect coding regions in DNA sequences, even if of low quality
EST sequences. Proc Int Conf Intell Syst Mol Biol.138-48.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: fasta
+Recommends: fasta
Homepage: http://www.ebi.ac.uk/Tools/fasta/
License: no inclusion into commercial product
Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2158,7 +2158,7 @@ Pkg-Description: searching DNA and protein databases
several nearby hits.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: fluctuate
+Recommends: fluctuate
Homepage: http://evolution.gs.washington.edu/lamarc/fluctuate.html
License: not specified
Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
@@ -2179,7 +2179,7 @@ Remark: This software is probably outdated
BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
a package.
-Depends: lamarc
+Recommends: lamarc
Homepage: http://evolution.gs.washington.edu/lamarc/
License: Apache V2.0
Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
@@ -2196,7 +2196,7 @@ Pkg-Description: estimate population-genetic parameters
effectively on workstations.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: lucy
+Recommends: lucy
Homepage: http://rcc.uga.edu/applications/bioinformatics/lucy.html
License: GPL
Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
@@ -2222,7 +2222,7 @@ Pkg-Description: DNA sequence quality and vector trimming tool
See also the SourceForge page at http://lucy.sourceforge.net/.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: maxd
+Recommends: maxd
Homepage: http://www.bioinf.man.ac.uk/microarray/maxd/
License: Artistic
Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2240,9 +2240,9 @@ Pkg-Description: data warehouse and visualisation environment for genomic expres
maxdSetup - installation management utility
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: mesquite
+Recommends: mesquite
-Depends: migrate
+Recommends: migrate
Homepage: http://popgen.scs.fsu.edu/Migrate-n.html
License: to be clarified
Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
@@ -2264,7 +2264,7 @@ Pkg-Description: estimation of population sizes and gene flow using the coalesce
surfaces for all populations and all loci.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: msatfinder
+Recommends: msatfinder
Homepage: http://www.genomics.ceh.ac.uk/msatfinder/
License: GPL
Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2279,7 +2279,7 @@ Pkg-Description: identification and characterization of microsatellites in a com
FASTA, EMBL and Swissprot formats are supported.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: mview
+Recommends: mview
Homepage: http://bio-mview.sourceforge.net/
License: GPL
Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2295,7 +2295,7 @@ Pkg-Description: reformat results of a sequence database search or a multiple al
is it a general purpose alignment editor.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: oligoarrayaux
+Recommends: oligoarrayaux
Homepage: http://dinamelt.bioinfo.rpi.edu/OligoArrayAux.php
License: non-free (fre academical use)
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2322,7 +2322,7 @@ Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
this and so it might make soem sense to list it here - further
investigation is needed.
-Depends: omegamap
+Recommends: omegamap
Homepage: http://www.danielwilson.me.uk/software.html
License: to be clarified
Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2342,7 +2342,7 @@ Pkg-Description: detecting natural selection and recombination in DNA or RNA seq
Genetics doi:10.1534/genetics.105.044917.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: partigene
+Recommends: partigene
Homepage: http://www.nematodes.org/bioinformatics/PartiGene/
License: GPL
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2356,7 +2356,7 @@ Pkg-Description: generating partial gemomes
(putative genes) which we term a partial genome.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: pfaat
+Recommends: pfaat
Homepage: http://pfaat.sourceforge.net/
License: GPL
Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
@@ -2374,7 +2374,7 @@ Comment: priam
project has only a "free as in beer" binary download - so this is not
for us ...
-Depends: prot4est
+Recommends: prot4est
Homepage: http://xyala.cap.ed.ac.uk/bioinformatics/prot4EST/index.shtml
License: GPL
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2386,7 +2386,7 @@ Pkg-Description: EST protein translation suite
translating ESTs.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: qtlcart
+Recommends: qtlcart
Homepage: http://statgen.ncsu.edu/qtlcart/
License: GPL
Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
@@ -2399,7 +2399,7 @@ Pkg-Description: map quantitative traits using a map of molecular markers
simulation studies of experiments.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: rbs-finder
+Recommends: rbs-finder
Homepage: http://www.genomics.jhu.edu/RBSfinder/
License: not specified
Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2416,7 +2416,7 @@ Pkg-Description: find ribosome binding sites(RBS)
http://nbc11.biologie.uni-kl.de/docbook/doc_userguide_bioinformatics_server/chunk/ch01s06.html
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: recombine
+Recommends: recombine
Homepage: http://evolution.genetics.washington.edu/lamarc/recombine.html
License: not specified
Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
@@ -2438,7 +2438,7 @@ Remark: This software might be outdated
BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
a package.
-Depends: splitstree
+Recommends: splitstree
Homepage: http://www-ab.informatik.uni-tuebingen.de/software/splitstree3/welcome.html
License: to be clarified
Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2470,7 +2470,7 @@ Pkg-Description: Analyzing and Visualizing Evolutionary Data
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: taverna
+Recommends: taverna
Homepage: http://taverna.sourceforge.net/
License: LGPL
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2495,7 +2495,7 @@ Pkg-Description: designing and executing myGrid workflows for bioinformatics
collaboration with the open source community.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: taxinspector
+Recommends: taxinspector
Homepage: http://nebc.nox.ac.uk/projects/taxinspector.html
License: Artistic + other free licenses
Responsible: BioLinux - Tim Booth <tbooth at ceh.ac.uk>
@@ -2506,7 +2506,7 @@ Pkg-Description: browser for entries in the NCBI taxonomy
and Pedro, but also has a standalone mode.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: tetra
+Recommends: tetra
Homepage: http://www.megx.net/tetra/
License: free academic
Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2524,7 +2524,7 @@ Remark: for the Linux version
Linux version might happen when REALbasic's Linux IDE is more mature.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: trace2dbest
+Recommends: trace2dbest
Homepage: http://www.nematodes.org/bioinformatics/trace2dbEST/
License: GPL
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2547,11 +2547,11 @@ Pkg-Description: process trace files into dbEST submissions
(optionaly) BLAST.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Depends: profit
+Recommends: profit
WNPP: 525428
Remark: The authors need to change the license, still.
-Depends: obo-edit
+Recommends: obo-edit
Homepage: http://www.geneontology.org
X-Comment: Find the license here [1] and [2].
[1] http://geneontology.svn.sourceforge.net/viewvc/geneontology/java/oboedit/tags/2.2/release_resources/LICENSE?revision=4863&view=markup
@@ -2564,7 +2564,7 @@ Pkg-Description: editor for biological ontologies
is the GeneOntology.
-Depends: jstreeview
+Recommends: jstreeview
Homepage: http://www.sanger.ac.uk/Users/lh3/treeview.shtml
License: MIT/X11
Language: JavaScript
@@ -2578,7 +2578,7 @@ Pkg-Description: Editor for Phylogenetic Trees
The source can be downloaded at
http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip
-Depends: phagefinder
+Recommends: phagefinder
Homepage: http://phage-finder.sourceforge.net/
License: GPL
Language: Perl
@@ -2599,7 +2599,7 @@ Pkg-Description: heuristic computer program to identify prophage regions within
will facilitate future studies on the biology and evolution of these prophages by providing
a level of microbial genome annotation that was previously void.
-Depends: compclust
+Recommends: compclust
Homepage: http://woldlab.caltech.edu/compclust/
License: MLX (http://woldlab.caltech.edu/compclust/LICENSE.txt)
Language: Python
@@ -2621,7 +2621,7 @@ Pkg-Description: explore and quantify relationships between clustering results
maker/line color, etc. These plots are intrinsically linked to the dataset, the
View and the Labeling classes found within pyMLX.
-Depends: treebuilder3d
+Recommends: treebuilder3d
Homepage: http://www.bcgsc.ca/platform/bioinfo/software/treebuilder
License: GPL
Language: Java
@@ -2634,7 +2634,7 @@ Pkg-Description: viewer of SAGE and other types of gene expression data
analyzing differences in expression profiles of SAGE libraries, serves as an
alternative to Venn diagrams.
-Depends: excavator
+Recommends: excavator
Homepage: http://csbl.bmb.uga.edu/downloads/excavator/
License: GPL
Language: Java
@@ -2657,42 +2657,42 @@ Pkg-Description: gene expression data clustering
* numerical comparison between different clustering results of the same data set
* runnable on command line as well as through a Java GUI
-Depends: treetime
+Recommends: treetime
Homepage: http://treetime.linhi.com/
License: GPL
Pkg-Description: Bayesian sampling of phylogenetic trees from molecular data
TreeTime is controlled by input files in nexus format and does
bayesian sampling of phylogenetic trees from these data.
-Depends: abacas
+Recommends: abacas
-Depends: profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun
+Recommends: profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun
-Depends: profphd-net, profphd-utils
+Recommends: profphd-net, profphd-utils
-Depends: profphd
+Recommends: profphd
-Depends: abyss
+Recommends: abyss
-Depends: ampliconnoise
+Recommends: ampliconnoise
-Depends: disulfinder
+Recommends: disulfinder
-Depends: circos, runcircos-gui
+Recommends: circos, runcircos-gui
-Depends: populations
+Recommends: populations
-Depends: raccoon
+Recommends: raccoon
-Depends: librg-utils-perl
+Recommends: librg-utils-perl
-Depends: snap
+Recommends: snap
-Depends: vcftools
+Recommends: vcftools
Suggests: mobyle, mobyle-programs, mobyle-tutorials
-Depends: hilbertvisgui
+Recommends: hilbertvisgui
Homepage: http://www.bioconductor.org/help/bioc-views/2.7/bioc/html/HilbertVisGUI.html
License: GPL-3
Pkg-Description: interactive tool to visualize long vectors of integer data by means of Hilbert curves
@@ -2701,7 +2701,7 @@ Pkg-Description: interactive tool to visualize long vectors of integer data by m
interesting for giving users some comfort. Until this software is not yet packaged
you can follow the hint at the homepage how to use it with R.
-Depends: beads
+Recommends: beads
Homepage: http://pappso.inra.fr/bioinfo/beads
License: CeCILL
Pkg-URL: https://launchpad.net/~olivier-langella/+archive/ppa/+packages
@@ -2710,7 +2710,7 @@ Pkg-Description: 2-DE electrophoresis gel image spot detection
an analogy with beads flowing uphill on the surface of the gel image and
on the analysis of their paths
-Depends: x-tandem-pipeline
+Recommends: x-tandem-pipeline
Homepage: http://pappso.inra.fr/bioinfo/xtandempipeline/
License: GPL
Language: Java
@@ -2735,7 +2735,7 @@ Pkg-Description: peptide/protein identification from MS/MS mass spectra
Suggests: maude
-Depends: forge
+Recommends: forge
Homepage: http://combiol.org/forge/
License: Apache 2.0
Pkg-Description: genome assembler for mixed read types
@@ -2759,7 +2759,7 @@ Remark: Competitor to MIRA2 and wgs-assembler
This package was requested by William Spooner <whs at eaglegenomics.com> as
a competitor to MIRA2 and wgs-assembler.
-Depends: metarep
+Recommends: metarep
License: MIT
Homepage: http://www.jcvi.org/metarep/
Pkg-Description: JCVI Metagenomics Reports
@@ -2779,7 +2779,7 @@ Pkg-Description: JCVI Metagenomics Reports
X-Comment: Not sure whether this can be distributed at all - asking
might not harm because I've got a serious hint that this software
is quite interesting
-X-Depends: megan
+X-Recommends: megan
X-License: Registriation required
X-Homepage: http://www-ab.informatik.uni-tuebingen.de/software/megan
X-Pkg-Description: MEtaGenome ANalyzer
@@ -2792,7 +2792,7 @@ X-Pkg-Description: MEtaGenome ANalyzer
projects. In consequence, there is a dramatic increase in the volume of
sequence data to be analyzed.
-Depends: arachne
+Recommends: arachne
Homepage: http://www.broadinstitute.org/crd/wiki/index.php/Arachne
License: free
Pkg-Description: toolkit for Whole Genome Shotgun Assembly
@@ -2811,7 +2811,7 @@ Pkg-Description: toolkit for Whole Genome Shotgun Assembly
numerous modules, to analyze, visualize and manipulate assemblies. New
and improved algorithms are becoming available on a regular basis.
-Depends: maker2
+Recommends: maker2
Homepage: http://www.yandell-lab.org/software/maker.html
License: GPL / Artistic
Pkg-Description: annotate genomes and create genome databases
@@ -2831,7 +2831,7 @@ Pkg-Description: annotate genomes and create genome databases
especially useful for emerging model organism projects with minimal
bioinformatics expertise and computer resources
-Depends: rmblast
+Recommends: rmblast
Homepage: http://tandem.bu.edu/trf/trf.html
License: Same as blast2
Pkg-Description: RepeatMasker compatible version of the standard NCBI BLAST
@@ -2845,7 +2845,7 @@ Pkg-Description: RepeatMasker compatible version of the standard NCBI BLAST
scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm.
Support for cross_match-like masklevel filtering.
-Depends: e-hive
+Recommends: e-hive
Homepage: http://www.ensembl.org/info/docs/eHive/index.html
License: Not specified
Pkg-Description: distributed processing system based on 'autonomous agents'
@@ -2855,14 +2855,14 @@ Pkg-Description: distributed processing system based on 'autonomous agents'
to codify any program, algorithm, or parallel processing job control system.
It is not bound to any processing 'farm' system and can be adapted to any GRID.
-Depends: cmap
+Recommends: cmap
Homepage: http://gmod.org/wiki/CMap
License: Not specified
Pkg-Description: view comparisons of genetic and physical maps
CMap is a web-based tool that allows users to view comparisons of genetic and
physical maps. The package also includes tools for curating map data.
-Depends: gbrowse-syn
+Recommends: gbrowse-syn
Homepage: http://gmod.org/wiki/GBrowse_syn
License: Not specified
Pkg-Description: Generic Synteny Browser
@@ -2875,7 +2875,7 @@ Pkg-Description: Generic Synteny Browser
later). Working examples can be seen at TAIR and WormBase.
-Depends: tripal
+Recommends: tripal
Homepage: http://www.genome.clemson.edu/software/tripal
License: GPL ( as Drupal a derivative )
Pkg-Description: collection of Drupal modules for genomic research
@@ -2890,14 +2890,14 @@ Pkg-Description: collection of Drupal modules for genomic research
databases are projects of the Main Bioinformatics Laboratory at Washington
State University
-Depends: genemark
+Recommends: genemark
Homepage: http://exon.biology.gatech.edu/
License: Academic License Agreement
Pkg-Description: family of gene prediction programs
A family of gene prediction programs developed at Georgia Institute of
Technology, Atlanta, Georgia, USA.
-Depends: python-orange
+Recommends: python-orange
License: GPLv3
Homepage: http://orange.biolab.si/
Pkg-URL: http://orange.biolab.si/debian/
@@ -2908,7 +2908,7 @@ Pkg-Description: Data mining framework
techniques. It can be used through a nice and intuitive user interface
or, for more advanced users, as a module for Python programming language.
-Depends: tigr-glimmer-mg
+Recommends: tigr-glimmer-mg
Comment: Several related R packages are listed at CRAN:
http://cran.r-project.org/web/views/Genetics.html
diff --git a/tasks/bio-dev b/tasks/bio-dev
index a62139e..11e6bd6 100644
--- a/tasks/bio-dev
+++ b/tasks/bio-dev
@@ -4,54 +4,54 @@ 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
+Recommends: bioperl, bioperl-run, libncbi6-dev
-Depends: mcl
+Recommends: mcl
X-Category: Analysis of network structure
X-Importance: Clustering of graphs
-Depends: biosquid
+Recommends: biosquid
-Depends: libvibrant6-dev
+Recommends: libvibrant6-dev
-Depends: python3-biopython | python-biopython
+Recommends: python3-biopython | python-biopython
Suggests: python3-biopython-sql | python-biopython-sql, python-biopython-doc
-Depends: python-cogent
+Recommends: python-cogent
-Depends: python-screed
+Recommends: python-screed
-Depends: python3-cutadapt | python-cutadapt
+Recommends: python3-cutadapt | python-cutadapt
-Depends: ruby-bio
+Recommends: ruby-bio
-Depends: libbiojava-java, libbiojava4-java
+Recommends: libbiojava-java, libbiojava4-java
-Depends: libgenome-1.3-dev, libmuscle-3.7-dev, libmems-1.6-dev
+Recommends: libgenome-1.3-dev, libmuscle-3.7-dev, libmems-1.6-dev
-Depends: libhtsjdk-java
+Recommends: libhtsjdk-java
-Depends: libai-fann-perl
+Recommends: libai-fann-perl
-Depends: libbio-mage-perl
+Recommends: libbio-mage-perl
Why: Useful for the submission of microarray data to public repositories.
-Depends: libnhgri-blastall-perl
+Recommends: libnhgri-blastall-perl
-Depends: libtfbs-perl
+Recommends: libtfbs-perl
-Depends: libfreecontact-dev, libfreecontact-perl
+Recommends: libfreecontact-dev, libfreecontact-perl
Suggests: libfreecontact-doc
-Depends: libgo-perl
+Recommends: libgo-perl
-Depends: r-cran-genetics, r-cran-haplo.stats, r-cran-phylobase
+Recommends: r-cran-genetics, r-cran-haplo.stats, r-cran-phylobase
-Depends: r-cran-rncl, r-cran-rnexml
+Recommends: r-cran-rncl, r-cran-rnexml
-Depends: octave-bioinfo
+Recommends: 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
@@ -68,40 +68,40 @@ Pkg-Description: bioinformatic functions for Octave
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
+Recommends: libbio-graphics-perl, libbio-coordinate-perl
-Depends: libbio-primerdesigner-perl
+Recommends: libbio-primerdesigner-perl
-Depends: libace-perl
+Recommends: libace-perl
-Depends: libbiococoa-dev
+Recommends: libbiococoa-dev
-Depends: libstaden-read-dev
+Recommends: libstaden-read-dev
-Depends: libsrf-dev
+Recommends: libsrf-dev
-Depends: libzerg0-dev, libzerg-perl
+Recommends: libzerg0-dev, libzerg-perl
-Depends: librg-reprof-bundle-perl
+Recommends: librg-reprof-bundle-perl
-Depends: python-corepywrap, librcsb-core-wrapper0-dev
+Recommends: python-corepywrap, librcsb-core-wrapper0-dev
-Depends: libsbml5-dev, sbmltoolbox
+Recommends: 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
+Recommends: seqan-dev
-Depends: libbio-mage-utils-perl
+Recommends: libbio-mage-utils-perl
-Depends: libchado-perl
+Recommends: libchado-perl
-Depends: libpal-java
+Recommends: libpal-java
-Depends: libjebl2-java
+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
@@ -136,87 +136,87 @@ Suggests: r-cran-rentrez
Suggests: ruby-rgfa
-Depends: r-bioc-biobase
+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/
-Depends: libffindex0-dev
+Recommends: libffindex0-dev
-Depends: librostlab3-dev
+Recommends: librostlab3-dev
Suggests: librostlab-doc
-Depends: librostlab-blast0-dev
+Recommends: librostlab-blast0-dev
Suggests: librostlab-blast-doc
-Depends: librg-blast-parser-perl
+Recommends: librg-blast-parser-perl
-Depends: libsort-key-top-perl
+Recommends: libsort-key-top-perl
-Depends: libhmsbeagle-dev
+Recommends: libhmsbeagle-dev
-Depends: libforester-java
+Recommends: 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
+Recommends: libbambamc-dev
-Depends: libbamtools-dev
+Recommends: libbamtools-dev
-Depends: libpbbam-dev
+Recommends: libpbbam-dev
-Depends: libbio-das-lite-perl
+Recommends: libbio-das-lite-perl
-Depends: python-mmtk
+Recommends: python-mmtk
Language: C, Python
-Depends: libopenms-dev
+Recommends: libopenms-dev
-Depends: libgenometools0-dev
+Recommends: libgenometools0-dev
-Depends: librdp-taxonomy-tree-java
+Recommends: librdp-taxonomy-tree-java
-Depends: python-biom-format
+Recommends: python-biom-format
-Depends: python-rdkit
+Recommends: python-rdkit
Suggests: libswarm2-dev
-Depends: libgenome-perl, libgenome-model-tools-music-perl
+Recommends: libgenome-perl, libgenome-model-tools-music-perl
-Depends: pyfai
+Recommends: pyfai
-Depends: libhts-dev
+Recommends: libhts-dev
-Depends: python-htseq
+Recommends: python-htseq
-Depends: python3-intervaltree-bio | python-intervaltree-bio
+Recommends: python3-intervaltree-bio | python-intervaltree-bio
-Depends: python3-csb | python-csb
+Recommends: python3-csb | python-csb
-Depends: python3-misopy | python-misopy
+Recommends: python3-misopy | python-misopy
-Depends: python-freecontact
+Recommends: python-freecontact
-Depends: python3-pymummer
+Recommends: python3-pymummer
Suggests: libgtextutils-dev
-Depends: libkmer-dev
+Recommends: libkmer-dev
-Depends: libsnp-sites1-dev
+Recommends: libsnp-sites1-dev
-Depends: libssm-dev
+Recommends: libssm-dev
-Depends: librelion-dev
+Recommends: librelion-dev
-Depends: libdivsufsort-dev
+Recommends: libdivsufsort-dev
-Depends: bioclipse
+Recommends: bioclipse
Homepage: http://www.bioclipse.net/
License: Eclipse Public License (EPL) + exception
Pkg-Description: platform for chemo- and bioinformatics based on Eclipse
@@ -237,9 +237,9 @@ Pkg-Description: platform for chemo- and bioinformatics based on Eclipse
followed on the Bioclipse Wiki where we document the progress and
ideas of the development on a daily basis.
-Depends: libgff-dev
+Recommends: libgff-dev
-Depends: libgff-perl
+Recommends: libgff-perl
Homepage: http://www.sanger.ac.uk/Software/formats/GFF/
Responsible: David Paleino <d.paleino at gmail.com>
License: GPL-1+
@@ -250,35 +250,35 @@ Pkg-Description: Perl bindings for GFF Annotation Protocol
.
This package provides a Perl module to use GFF objects.
-Depends: python-pysam
+Recommends: python-pysam
-Depends: python-pbcore, python-pbh5tools
+Recommends: python-pbcore, python-pbh5tools
-Depends: python-cobra
+Recommends: python-cobra
-Depends: libtabixpp-dev
+Recommends: libtabixpp-dev
-Depends: python3-ruffus | python-ruffus
+Recommends: python3-ruffus | python-ruffus
-Depends: python3-hyphy | python-hyphy
+Recommends: python3-hyphy | python-hyphy
-Depends: python3-dendropy | python-dendropy
+Recommends: python3-dendropy | python-dendropy
-Depends: python3-skbio
+Recommends: python3-skbio
-Depends: python3-pbconsensuscore | python-pbconsensuscore
+Recommends: python3-pbconsensuscore | python-pbconsensuscore
-Depends: python3-consensuscore2 | python-consensuscore2, libconsensuscore-dev
+Recommends: python3-consensuscore2 | python-consensuscore2, libconsensuscore-dev
-Depends: python-pbcommand
+Recommends: python-pbcommand
-Depends: python3-pyvcf | python-pyvcf
+Recommends: python3-pyvcf | python-pyvcf
-Depends: python3-pyfaidx | python-pyfaidx
+Recommends: python3-pyfaidx | python-pyfaidx
-Depends: python-kineticstools
+Recommends: python-kineticstools
-Depends: python3-pyfasta | python-pyfasta
+Recommends: 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
@@ -287,25 +287,25 @@ Remark: Testsuite uncovers problems and code is not actively maintained
Suggests: libbam-dev
-Depends: libqes-dev
+Recommends: libqes-dev
-Depends: libfast5-dev, python3-fast5 | python-fast5
+Recommends: libfast5-dev, python3-fast5 | python-fast5
-Depends: libpbseq-dev, libpbdata-dev, libpbihdf-dev, libblasr-dev
+Recommends: libpbseq-dev, libpbdata-dev, libpbihdf-dev, libblasr-dev
Suggests: libpbcopper-dev
-Depends: libminimap-dev
+Recommends: libminimap-dev
-Depends: libncl-dev
+Recommends: libncl-dev
-Depends: libngs-sdk-dev, libngs-java, python3-ngs | python-ngs, libncbi-vdb-dev
+Recommends: libngs-sdk-dev, libngs-java, python3-ngs | python-ngs, libncbi-vdb-dev
-Depends: libqcpp-dev
+Recommends: 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
+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
-Depends: octace-bioinfo
+Recommends: octace-bioinfo
Homepage: http://octave.sourceforge.net/bioinfo/index.html
License: GPL-2+
Pkg-Description: Bioinformatics manipulation for Octave
@@ -320,53 +320,53 @@ Pkg-Description: Bioinformatics manipulation for Octave
seqreverse
Reverse a nucleotide sequence.
-Depends: ruby-crb-blast
+Recommends: ruby-crb-blast
-Depends: libsmithwaterman-dev
+Recommends: libsmithwaterman-dev
-Depends: libfastahack-dev
+Recommends: libfastahack-dev
-Depends: mgltools-networkeditor, mgltools-vision, mgltools-pybabel
+Recommends: mgltools-networkeditor, mgltools-vision, mgltools-pybabel
Suggests: libdisorder-dev
-Depends: libssw-dev, libssw-java
+Recommends: libssw-dev, libssw-java
-Depends: libfml-dev
+Recommends: libfml-dev
-Depends: libgkarrays-dev
+Recommends: libgkarrays-dev
-Depends: libjloda-java
+Recommends: libjloda-java
-Depends: libvcflib-dev
+Recommends: libvcflib-dev
-Depends: libswiss-perl
+Recommends: libswiss-perl
-Depends: python3-pybedtools
+Recommends: python3-pybedtools
-Depends: python3-gffutils
+Recommends: python3-gffutils
WNPP: 851488
-Depends: python3-bx | python-bx
+Recommends: python3-bx | python-bx
WNPP: 851242
-Depends: python3-bd2k | python-bd2k
+Recommends: python3-bd2k | python-bd2k
WNPP: 851341
-Depends: libbio-eutilities-perl
+Recommends: libbio-eutilities-perl
-Depends: libseqlib-dev
+Recommends: libseqlib-dev
-Depends: libroadrunner-dev, python-roadrunner
+Recommends: libroadrunner-dev, python-roadrunner
-Depends: python3-biotools | python-biotools
+Recommends: python3-biotools | python-biotools
-Depends: bio-tradis
+Recommends: bio-tradis
-Depends: python3-biomaj3 | python-biomaj3
+Recommends: python3-biomaj3 | python-biomaj3
Suggests: python-pyflow
Suggests: r-cran-natserv
-Depends: libbiod-dev
+Recommends: libbiod-dev
diff --git a/tasks/bio-ngs b/tasks/bio-ngs
index 886fd35..6b721d0 100644
--- a/tasks/bio-ngs
+++ b/tasks/bio-ngs
@@ -7,7 +7,7 @@ Description: Debian Med bioinformatics applications usable in Next Generation Se
Comment: Do not build a metapackage because it is not clear in how far this set of
packages is complete regarding NGS.
-Depends:
+Recommends:
bedtools,
bwa,
bowtie,
@@ -31,33 +31,33 @@ Depends:
vcftools,
velvet
-Depends: sprai
+Recommends: sprai
-Depends: mothur
+Recommends: mothur
-Depends: qiime
+Recommends: qiime
-Depends: cufflinks
+Recommends: cufflinks
-Depends: hinge
+Recommends: hinge
-Depends: mira-assembler
+Recommends: mira-assembler
X-Mark: Prospective packages are starting here.
-Depends: kissplice
+Recommends: kissplice
X-Mark: Packages in Vcs - Information about these is queried from UDD as well
-Depends: scoary
+Recommends: scoary
-Depends: umap
+Recommends: umap
-Depends: dindel
+Recommends: dindel
-Depends: mosaik-aligner
+Recommends: mosaik-aligner
-Depends: forge
+Recommends: forge
Homepage: http://combiol.org/forge/
License: Apache 2.0
Pkg-Description: genome assembler for mixed read types
@@ -81,9 +81,9 @@ Remark: Competitor to MIRA2 and wgs-assembler
This package was requested by William Spooner <whs at eaglegenomics.com> as
a competitor to MIRA2 and wgs-assembler.
-Depends: uc-echo
+Recommends: uc-echo
-Depends: annovar
+Recommends: annovar
Homepage: http://www.openbioinformatics.org/annovar/
License: Open Source for non-profit
Pkg-Description: annotate genetic variants detected from diverse genomes
diff --git a/tasks/bio-phylogeny b/tasks/bio-phylogeny
index b3aac2c..a608e90 100644
--- a/tasks/bio-phylogeny
+++ b/tasks/bio-phylogeny
@@ -11,17 +11,17 @@ Comment: Do not build a metapackage because it is not clear in how far this set
X-Begin-Category: Phylogenetic analysis
-Depends: altree
+Recommends: altree
-Depends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle
+Recommends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle
-Depends: probalign
+Recommends: probalign
-Depends: treeviewx
+Recommends: treeviewx
X-End-Category: Phylogenetic analysis
-Depends: phylip
+Recommends: phylip
Why: Phylogenetic analysis (Non-free, thus only suggested).
X-Comment: treetool is removed from Debian because it is not maintained upstream since
@@ -29,66 +29,66 @@ X-Comment: treetool is removed from Debian because it is not maintained upstream
X-Begin-Category: Sequence alignments and related programs.
-Depends: muscle
+Recommends: muscle
-Depends: t-coffee
+Recommends: t-coffee
-Depends: kalign
+Recommends: kalign
-Depends: hmmer
+Recommends: hmmer
-Depends: exonerate
+Recommends: exonerate
-Depends: dialign
+Recommends: dialign
-Depends: dialign-tx
+Recommends: dialign-tx
-Depends: poa
+Recommends: poa
-Depends: probcons
+Recommends: probcons
-Depends: proda
+Recommends: proda
-Depends: seaview
+Recommends: seaview
-Depends: sigma-align
+Recommends: sigma-align
-Depends: gmap
+Recommends: gmap
-Depends: clustalx
+Recommends: clustalx
Why: Sequence alignments and related programs (Non-free, thus only suggested).
-Depends: clustalw
+Recommends: clustalw
-Depends: mustang
+Recommends: mustang
X-End-Category: Sequence alignments and related programs.
X-Begin-Category: Models of nucleotide/amino acid evolution
-Depends: phyml
+Recommends: phyml
X-End-Category: Models of nucleotide/amino acid evolution
-Depends: beast-mcmc
+Recommends: beast-mcmc
-Depends: tm-align
+Recommends: tm-align
-Depends: mrbayes
+Recommends: mrbayes
-Depends: figtree
+Recommends: figtree
-Depends: populations
+Recommends: populations
X-Mark: Packages in Vcs - Information about these is queried from UDD as well
-Depends: proalign
+Recommends: proalign
-Depends: prottest
+Recommends: prottest
-Depends: treeview
+Recommends: treeview
-Depends: phylowin
+Recommends: phylowin
Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html
WNPP: 395840
License: unknown
@@ -114,7 +114,7 @@ Remark: Issuer of previous ITP said:
list.
-Depends: gbioseq
+Recommends: gbioseq
Homepage: http://www.bioinformatics.org/project/?group_id=94
License: GPL
Pkg-Description: DNA sequence editor for Linux
@@ -122,14 +122,14 @@ Pkg-Description: DNA sequence editor for Linux
The goal is to provide an easy to use software to edit DNA sequences under
Linux, Windows, MacOsX, using GTK C# (Mono).
-Depends: phpphylotree
+Recommends: phpphylotree
Homepage: http://www.bioinformatics.org/project/?group_id=372
License: GPL
Pkg-Description: draw phylogenetic trees
PhpPhylotree is a web application that is able to draw phylogenetic trees.
It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.
-Depends: jstreeview
+Recommends: jstreeview
Homepage: http://www.sanger.ac.uk/Users/lh3/treeview.shtml
License: MIT/X11
Language: JavaScript
@@ -143,20 +143,20 @@ Pkg-Description: Editor for Phylogenetic Trees
The source can be downloaded at
http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip
-Depends: treetime
+Recommends: treetime
Homepage: http://treetime.linhi.com/
License: GPL
Pkg-Description: Bayesian sampling of phylogenetic trees from molecular data
TreeTime is controlled by input files in nexus format and does
bayesian sampling of phylogenetic trees from these data.
-Depends: jmodeltest
+Recommends: jmodeltest
-Depends: forester
+Recommends: forester
-Depends: patristic
+Recommends: patristic
Language: Java
-Depends: spread-phy
+Recommends: spread-phy
-Depends: iqtree
+Recommends: iqtree
diff --git a/tasks/cloud b/tasks/cloud
index 39cdbd8..6fbb755 100644
--- a/tasks/cloud
+++ b/tasks/cloud
@@ -6,19 +6,19 @@ Description: Debian Med bioinformatics applications usable in cloud computing
in cloud computing clusters, where space can be limited.
X-Begin-Category: Phylogenetic analysis
-Depends: \
+Recommends: \
altree, clearcut, fastdnaml, fasttree, parsinsert, phyml, phyutility,
prime-phylo, mrbayes, tree-puzzle | tree-ppuzzle
X-End-Category: Phylogenetic analysis
X-Begin-Category: Genetics and genomics
-Depends: \
+Recommends: \
alien-hunter, bagpipe, fastlink, loki, gasic, genometools, plink,
probabel, r-cran-qtl, r-other-valdar-bagphenotype.library, r-other-mott-happy.hbrem
X-End-Category: Genetics
X-Begin-Category: Sequence alignments and related programs.
-Depends: \
+Recommends: \
amap-align, blast2, biosquid, boxshade, cassiopee, cdbfasta, cd-hit,
clustalo, clustalw, conservation-code, dialign, dialign-tx,
emboss, embassy-domalign, embassy-domainatrix, embassy-domsearch,
@@ -29,54 +29,54 @@ Depends: \
X-End-Category: Sequence alignments and related programs.
X-Begin-Category: High throughput sequencing
-Depends: \
+Recommends: \
bamtools, bedtools, fastx-toolkit, flexbar, picard-tools, samtools,
tabix, vcftools
Comment: Processing
-Depends: \
+Recommends: \
anfo, cufflinks, bowtie, bowtie2, bwa, last-align, maq, perm, tophat, smalt,
soapdenovo, soapdenovo2
Comment: Aligners
-Depends: \
+Recommends: \
abyss, mapsembler2, idba, minia, mira-assembler, ssake, velvet
Comment: Assembly
-Depends: \
+Recommends: \
ampliconnoise, arden, fastqc
Comment: Filtering and QC
-Depends: \
+Recommends: \
discosnp, dnaclust, fitgcp, giira, grinder, kissplice, macs, mothur,
paraclu, r-bioc-hilbertvis, sra-toolkit
Comment: Other
X-End-Category: High throughput sequencing
X-Begin-Category: Analysis of RNA sequences.
-Depends: \
+Recommends: \
aragorn, infernal, rnahybrid, rtax
X-End-Category: Analysis of RNA sequences.
X-Begin-Category: Molecular modelling and molecular dynamics
-Depends: \
+Recommends: \
autodock, autodock-vina, autogrid, concavity, dssp, freecontact,
gromacs, hhsuite, mustang, pdb2pqr, raster3d, theseus
Comment: non-free
X-End-Category: Molecular modelling and molecular dynamics
X-Begin-Category: Tools for the molecular biologist.
-Depends: \
+Recommends: \
melting, mipe, ncbi-epcr, primer3
Comment: Oligonucleotides and PCR
-Depends: \
+Recommends: \
acedb-other, disulfinder, ncbi-tools-bin, ncoils, python-cogent,
readseq, tigr-glimmer, seqan-apps, staden-io-lib-utils
X-End-Category: Tools for the molecular biologist.
X-Begin-Category: Others
-Depends: \
+Recommends: \
aevol, biomaj, bioperl, bioperl-run, cain, clonalframe, circos, datamash, filo,
prodigal, python-biopython, python3-biopython, qiime, r-bioc-edger,
r-cran-pvclust, r-cran-vegan
diff --git a/tasks/data b/tasks/data
index 081d009..34e6058 100644
--- a/tasks/data
+++ b/tasks/data
@@ -4,14 +4,14 @@ Description: Debian Med drug databases
applications. The database can be accessed by any EMR using
the application.
-Depends: freediams, freemedforms-freedata
+Recommends: freediams, freemedforms-freedata
-Depends: python-hl7
+Recommends: python-hl7
Suggests: sleepyhead
WNPP: 780060
-Depends: drugref.org
+Recommends: drugref.org
Homepage: http://savannah.nongnu.org/projects/php-drugref/
License: GPL2+
Pkg-Description: pharmaceutical reference database
diff --git a/tasks/dental b/tasks/dental
index c5b728d..b1f9701 100644
--- a/tasks/dental
+++ b/tasks/dental
@@ -3,8 +3,8 @@ Description: Debian Med packages related to dental practice
This metapackage contains dependencies for a collection of software
which might be helpful for dentists to manage their practice.
-Depends: openmolar
+Recommends: openmolar
-Depends: imagetooth
+Recommends: imagetooth
-Depends: entangle
+Recommends: entangle
diff --git a/tasks/epi b/tasks/epi
index 3aa6675..83904a0 100644
--- a/tasks/epi
+++ b/tasks/epi
@@ -6,39 +6,39 @@ Description: Debian Med epidemiology related packages
"A short introduction to R for Epidemiology" at
http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
-Depends: epigrass
+Recommends: epigrass
Suggests: r-cran-msm
-Depends: r-cran-epibasix
+Recommends: r-cran-epibasix
-Depends: r-cran-epitools
+Recommends: r-cran-epitools
X-Comment: See also: http://sites.google.com/site/medepi/epitools
-Depends: r-cran-surveillance
+Recommends: r-cran-surveillance
-Depends: r-cran-epi
+Recommends: r-cran-epi
-Depends: r-cran-diagnosismed, r-cran-epicalc, r-cran-epir
+Recommends: r-cran-diagnosismed, r-cran-epicalc, r-cran-epir
-Depends: r-cran-seroincidence
+Recommends: r-cran-seroincidence
X-Comment: Needs to wait for processing of r-cran-knitr
Suggests: r-cran-cmprsk
-Depends: ushahidi
+Recommends: ushahidi
Suggests: shiny-server
-Depends: r-cran-lexrankr
+Recommends: r-cran-lexrankr
-Depends: python-treetime
+Recommends: python-treetime
-Depends: netepi-analysis
+Recommends: netepi-analysis
Remark: See also: http://www.stockholmchallenge.se/data/2123 and
http://www.publish.csiro.au/?act=view_file&file_id=NB07103.pdf
-Depends: netepi-collection
+Recommends: netepi-collection
Remark: See also: http://www.stockholmchallenge.se/data/2123 and
http://www.publish.csiro.au/?act=view_file&file_id=NB07103.pdf
diff --git a/tasks/his b/tasks/his
index 6b43ad3..fa6559c 100644
--- a/tasks/his
+++ b/tasks/his
@@ -6,18 +6,18 @@ Description: Debian Med suggestions for Hospital Information Systems
only preconditions are finished but hopefully helpful in hospitals
anyway.
-Depends: care2x
+Recommends: care2x
Pkg-URL: http://sourceforge.net/projects/care2002/files/CARE2X/Care2X%202.6%20alpha/
-Depends: fis-gtm
+Recommends: fis-gtm
-Depends: vista-foia
+Recommends: vista-foia
-Depends: ewd-920
+Recommends: ewd-920
-Depends: orthanc-wsi
+Recommends: orthanc-wsi
-Depends: tryton-modules-health
+Recommends: tryton-modules-health
Pkg-URL: http://debian.tryton.org/debian/pool/main/t/tryton-modules-health/
Remark: Docker instance and apt repository
GNUHealth is packaged by the Debian Tryton Maintainers. Here you can
@@ -29,7 +29,7 @@ Remark: Docker instance and apt repository
containing
deb http://debian.tryton.org/debian/ <debian-dist>-<tryton-series> main
-Depends: openmaxims
+Recommends: openmaxims
Homepage: https://github.com/IMS-MAXIMS/openMAXIMS
License: AGPL
Pkg-Description: patient administration system and electronic patient record
@@ -59,7 +59,7 @@ Pkg-Description: patient administration system and electronic patient record
with third-party systems.
Comment: see http://www.pro-linux.de/news/1/22883/krankenhaus-in-grossbritannien-nutzt-open-source-fuer-krankenakten.html
-Depends: world-vista
+Recommends: world-vista
Homepage: http://worldvista.org/World_VistA_EHR
License: GPL v2
Responsible: K.S. Bhaskar <ks.bhaskar at fnis.com>
@@ -80,7 +80,7 @@ Pkg-Description: repackage and extended version of VistA produced by WorldVistA
electronic data to other entities such as laboratories), and security
(ability to keep patients' information safe).
-Depends: ipath
+Recommends: ipath
Homepage: http://ipath.sourceforge.net/
License: GPL
Pkg-Description: telemedicine platform
@@ -88,7 +88,7 @@ Pkg-Description: telemedicine platform
case disucssions, virtual staff meetings, etc. It was originally developed at University
of Basel where a public iPath server for projects with developing countries is hosted.
-Depends: patientos
+Recommends: patientos
Homepage: http://www.patientos.org/
License: GPL v3
Language: Java
@@ -115,10 +115,10 @@ Pkg-Description: Healthcare Information System (HIS) for small hospitals and cli
* Add-ons are available to add new features or functionality including plugins, custom forms, themes, and translations
* Supports multiple languages
-Depends: openmrs
+Recommends: openmrs
Pkg-URL: http://mentors.debian.net/debian/pool/main/o/openmrs/
-Depends: hkma-cms
+Recommends: hkma-cms
Homepage: http://www.hkma.org/taoyuan/
License: free
Pkg-Description: clinic management system
@@ -129,7 +129,7 @@ Pkg-Description: clinic management system
(OGCIO) under the Sector-specific Programme (SSP) for the Medical and
Health Sector, and was developed by Mobigator Technology Group.
-Depends: oscar-mcmaster
+Recommends: oscar-mcmaster
License: to be clarified
Homepage: http://oscarmanual.org
Pkg-URL: http://sourceforge.net/projects/oscarmcmaster/files/
@@ -152,7 +152,7 @@ Pkg-Description: Oscar (Web) A medical web application for electronic medical re
* Diagnostic imaging results and consultation notes can be scanned
into the EMR where required
-Depends: openeyes
+Recommends: openeyes
Homepage: http://www.openeyes.org.uk
License: GPLv3
Pkg-Description: ophthalmology electronic patient record system
diff --git a/tasks/imaging b/tasks/imaging
index 707c7dd..b1e0863 100644
--- a/tasks/imaging
+++ b/tasks/imaging
@@ -11,23 +11,23 @@ Description: Debian Med image processing and visualization packages
- either from a graphical user interface, the command line, or implemented in
workflows.
-Depends: amide, ctsim, ctn, dicomnifti, imagej, minc-tools, medcon, python-nibabel, python-dicom, xmedcon, dcmtk
+Recommends: amide, ctsim, ctn, dicomnifti, imagej, minc-tools, medcon, python-nibabel, python-dicom, xmedcon, dcmtk
Suggests: imagemagick, pngquant, imview, trimage
-Depends: nifti-bin
+Recommends: nifti-bin
-Depends: aeskulap
+Recommends: aeskulap
-Depends: fsl
+Recommends: fsl
-Depends: fslview
+Recommends: fslview
Remark: fslview was removed from Debian (see #647810)
The bug log (http://bugs.debian.org/647810) explains the reasons for
the removal. The maintainers did never respond whether they plan
to bring back a more recent version of this package
-Depends: via-bin
+Recommends: via-bin
Pkg-URL: http://snapshot.debian.org/package/via/2.0.4-2.1/
WNPP: 732129
Comment: removed from Debian and only available in Wheezy or snapshot.debian.org
@@ -35,18 +35,18 @@ Comment: removed from Debian and only available in Wheezy or snapshot.debian.org
transition. A very similar library is provided by the mia package
(see bug #732129).
-Depends: gwyddion
+Recommends: gwyddion
-Depends: sofa-apps
+Recommends: sofa-apps
-Depends: python-mvpa2
+Recommends: python-mvpa2
Why: Suggested by maintainer Michael Hanke <michael.hanke at gmail.com>
-Depends: python-nipy
+Recommends: python-nipy
Why: Although listed in -dev task, it also has a strong focus on interactive
data analysis.
-Depends: python-nipype
+Recommends: python-nipype
Why: Although listed in -dev task, it also has a strong focus on interactive
data analysis.
@@ -54,44 +54,44 @@ Recommends: python-nitime
Why: Although listed in -dev task, it also has a strong focus on interactive
data analysis.
-Depends: caret
+Recommends: caret
-Depends: libgdcm-tools
+Recommends: libgdcm-tools
-Depends: slicer
+Recommends: slicer
Remark: slicer was removed from Debian (see #644352)
The bug log (http://bugs.debian.org/644352) explains the reasons for
the removal and the conditions when a new version might be back
-Depends: lipsia
+Recommends: lipsia
Remark: lipsia was removed from Debian (see #674295)
The bug log (http://bugs.debian.org/674295) explains the reasons for
the removal and the conditions when a new version might be back
-Depends: dicom3tools
+Recommends: dicom3tools
-Depends: imagevis3d
+Recommends: imagevis3d
-Depends: odin
+Recommends: odin
Published-Title: ODIN: Object-oriented development interface for NMR
Published-Authors: Thies H. Jochimsen, Michael von Mengershausen
Published-In: Journal of Magnetic Resonance 170:67-78
Published-Year: 2004
Published-URL: http://od1n.sourceforge.net/odin.pdf
-Depends: dicomscope
+Recommends: dicomscope
-Depends: pixelmed-apps
+Recommends: pixelmed-apps
-Depends: vmtk
+Recommends: vmtk
-Depends: gofigure2
+Recommends: gofigure2
-Depends: ginkgocadx
+Recommends: ginkgocadx
-Depends: openslide-tools
+Recommends: openslide-tools
-Depends: volview
+Recommends: volview
Pkg-URL: http://snapshot.debian.org/package/volview/3.4%2Bdfsg-1/
WNPP: 745023
Comment: removed from Debian and only available in Wheezy or snapshot.debian.org
@@ -99,29 +99,29 @@ Comment: removed from Debian and only available in Wheezy or snapshot.debian.org
is currently abandoned upstream. Apparently VolViewNinja would be the
successor (see bug #745023).
-Depends: conquest-common
+Recommends: conquest-common
Suggests: conquest-dbase, conquest-mysql, conquest-postgres, conquest-sqlite
Suggests: paraview
-Depends: camitk-imp
+Recommends: camitk-imp
-Depends: crea
+Recommends: crea
-Depends: orthanc
+Recommends: orthanc
Suggests: orthanc-webviewer, orthanc-dicomweb, orthanc-imagej, orthanc-postgresql
-Depends: teem-apps
+Recommends: teem-apps
-Depends: bioimagesuite
+Recommends: bioimagesuite
Remark: Contact to upstream
There is a forum at BioImage Suite site for discussion of
compiling it from source and packaging issues at
http://research.yale.edu/bioimagesuite/forum/index.php?board=12.0
-Depends: drjekyll
+Recommends: drjekyll
Homepage: http://drjekyll.sourceforge.net
License: GPL
Pkg-Description: interactive voxel editor for viewing and editing three-dimensional images
@@ -132,14 +132,14 @@ Pkg-Description: interactive voxel editor for viewing and editing three-dimensio
a final polishing process.
Why: Hint given by Petter Reinholdtsen
-Depends: libdcm4che-java
+Recommends: libdcm4che-java
Remark: Needs jai_imageio as prerequsite
Building the package using the packaging code in SVN works up to a point
were jai_imageio.jar is required. For the status of packaging this
prerequisite see the Debian Java mailing list at
http://lists.debian.org/debian-java/2011/04/msg00045.html
-Depends: dcm4chee
+Recommends: dcm4chee
Homepage: http://www.dcm4che.org/
License: LGPL, MPL, Apache, other (also non-free)
Pkg-Description: Clinical Image and Object Management (enterprise)
@@ -153,7 +153,7 @@ Pkg-Description: Clinical Image and Object Management (enterprise)
role of several IHE actors for the sake of interoperability, the
application provides many robust and scalable services.
-Depends: piano
+Recommends: piano
Homepage: http://mbi.dkfz-heidelberg.de/mbi/software/
License: BSD
Pkg-Description: medical image processing library for surgical planning
@@ -161,7 +161,7 @@ Pkg-Description: medical image processing library for surgical planning
multi-dimensional medical image processing, analysis and visualization.
It is used in the field of surgical planning.
-Depends: mesa-test-tools
+Recommends: mesa-test-tools
Homepage: http://ihedoc.wustl.edu/mesasoftware/
License: free
Pkg-Description: IHE Test Software for Radiology
@@ -194,7 +194,7 @@ Pkg-Description: IHE Test Software for Radiology
of CTN software in those tools does not have a separate release number
but is more current than version 3.0.6."
-Depends: devide
+Recommends: devide
Homepage: http://code.google.com/p/devide/
License: BSD
WNPP: 509110
@@ -208,13 +208,13 @@ Pkg-Description: Delft Visualization and Image processing Development Environmen
.
See the DeVIDE website at http://visualisation.tudelft.nl/Projects/DeVIDE
-Depends: dicom4j
+Recommends: dicom4j
Homepage: http://dicom4j.sourceforge.net/
License: GPL
Pkg-Description: Java framework for Dicom
Java framework for Dicom
-Depends: opendicom.net
+Recommends: opendicom.net
Homepage: http://opendicom.sourceforge.net/
License: LGPL
Responsible: Albert Gnandt <agnandt at users.sourceforge.net>
@@ -263,10 +263,10 @@ Pkg-Description: API to DICOM in C# for Mono
All GUI applications focus the popular GNOME desktop, but are 100%
platform independent by relying on Mono.
-Depends: afni
+Recommends: afni
Pkg-URL: http://neuro.debian.net/pkgs/afni.html
-Depends: blox
+Recommends: blox
Homepage: http://sourceforge.net/projects/blox/
License: GPL
Pkg-Description: medical imaging and visualization program
@@ -277,7 +277,7 @@ Pkg-Description: medical imaging and visualization program
(http://pni.med.jhu.edu/methods/morph.htm).
-Depends: ecg2png
+Recommends: ecg2png
X-Homepage-old: http://www.cardiothink.com/downloads
Homepage: http://www.freshports.org/graphics/ecg2png/
License: GPL
@@ -302,9 +302,9 @@ Remark: Homepage vanished
can be downloaded fro instance from
http://www.freshports.org/graphics/ecg2png/ .
-Depends: kradview
+Recommends: kradview
-Depends: opensourcepacs
+Recommends: opensourcepacs
Homepage: http://www.mii.ucla.edu/index.php/MainSite:OpenSourcePacsHome
License: GPL
WNPP: 509113
@@ -341,7 +341,7 @@ Pkg-Description: visualization and graphical analysis tool for viewing scientifi
VisIt was designed to handle very large data set sizes in the terascale
range and yet can also handle small data sets in the kilobyte range.
-Depends: mni-autoreg
+Recommends: mni-autoreg
Homepage: http://www.bic.mni.mcgill.ca/software/mni_autoreg/
License: no-free, but GPLed parts
Responsible: NeuroDebian Team <team at neuro.debian.net>
@@ -356,7 +356,7 @@ Pkg-Description: MNI average brain (305 MRI) stereotaxic registration model
* average_305_mask.mnc - a mask of the brain in average_305.mnc
* average_305_headmask.mnc - another mask, required for nonlinear mode
-Depends: mni-n3
+Recommends: mni-n3
Homepage: http://www.bic.mni.mcgill.ca/software/N3/
License: BSDish
Responsible: NeuroDebian Team <team at neuro.debian.net>
@@ -368,7 +368,7 @@ Pkg-Description: MNI Non-parametric Non-uniformity Normalization
* mni-n3 - provides 'nu_correct'
* libebtks-dev - MNI support library with numerical types and algorithms
-Depends: brainvisa
+Recommends: brainvisa
Homepage: http://brainvisa.info/
License: Free? (CeCill License)
Pkg-Description: image processing factory for MR images
@@ -387,7 +387,7 @@ Pkg-Description: image processing factory for MR images
labeling of the cortical folds according to a nomenclature of the
main sulci.
-Depends: maris
+Recommends: maris
Homepage: http://maris.homelinux.org/
License: GPL
Pkg-Description: package suite for Radiological Workflow
@@ -398,7 +398,7 @@ Pkg-Description: package suite for Radiological Workflow
that is an ensemble of single pieces that cooperate together using
IHE profiles.
-Depends: micromanager
+Recommends: micromanager
Pkg-URL: http://mentors.debian.net/package/micromanager
Remark: Partially problematic licenses
Unfortunately there is a pile of dirty licenses involved so I'm not sure
@@ -417,7 +417,7 @@ Pkg-Description: simulator for magnetic resonance imaging data
parameters (TR, TE ...) to be specified and then produces simulated
images with noise. Currently, no artifacts are implemented.
-Depends: fiji
+Recommends: fiji
Homepage: http://pacific.mpi-cbg.de/
Responsible: Mark Longair <mark-debianlists at longair.net>
Pkg-URL: http://pacific.mpi-cbg.de/wiki/index.php/Downloads
@@ -450,7 +450,7 @@ Remark: About packaging status the authors said:
packages in Debian, but now that these are in sid we should
eventually be able to switch to using those.
-Depends: cdmedicpacs
+Recommends: cdmedicpacs
Homepage: http://cdmedicpacsweb.sourceforge.net/
License: GPL2
Pkg-URL: http://sourceforge.net/projects/cdmedicpacsweb/files/
@@ -474,7 +474,7 @@ Pkg-Description: web interface to PACS to access DICOM study images
Viewers/Work Stations.
* Good DICOM interaction with free DICOM Viewers Aeskulap
-Depends: stir
+Recommends: stir
Homepage: http://stir.sourceforge.net/
License: GPL
Pkg-Description: Software for Tomographic Image Reconstruction
@@ -489,10 +489,10 @@ Pkg-Description: Software for Tomographic Image Reconstruction
the PARAPET project..
Remark: Even if this is GPLed software the download requires registration.
-Depends: openelectrophy
+Recommends: openelectrophy
Pkg-URL: http://neuro.debian.net/pkgs/openelectrophy.html
-Depends: invesalius
+Recommends: invesalius
X-Screenshot: http://dl.dropbox.com/u/4053278/invesalius_trac/screenshots/invesalius3_promed_0446_bone.png
This screenshot is done on iOSX :-(
@@ -501,16 +501,16 @@ Comment: Several related R packages are listed at CRAN:
http://cran.r-project.org/web/views/MedicalImaging.html
-Depends: mricron
+Recommends: mricron
Published-Title: Improving lesion-symptom mapping
Published-Authors: Chris Rorden, Hans-Otto Karnath, Leonardo Bonilha
Published-In: Journal of Cognitive Neuroscience, 19: 1081-1088
Published-Year: 2007
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/17583985
-Depends: voxbo
+Recommends: voxbo
-Depends: mrtrix
+Recommends: mrtrix
Published-Title: Robust determination of the fibre orientation distribution in diffusion MRI: Non-negativity constrained super-resolved spherical deconvolution
Published-Authors: J-Donald Tournier, Fernando Calamantea, Alan Connelly
Published-In: NeuroImage, 35: 1459-1472
@@ -518,7 +518,7 @@ Published-Year: 2007
Published-DOI: 10.1016/j.neuroimage.2007.02.016
-Depends: ants
+Recommends: ants
Published-Title: The optimal template effect in hippocampus studies of diseased populations
Published-Authors: Brian B. Avants, Paul Yushkevich, John Pluta, David Minkoff, Marc Korczykowski, John Detre and James C. Gee
Published-In: NeuroImage, 49: 2457-2466
@@ -527,13 +527,13 @@ Published-DOI: 10.1016/j.neuroimage.2009.09.062
X-Institution: UCLA Center for Computation Biology
-Depends: itksnap
+Recommends: itksnap
-Depends: mriconvert
+Recommends: mriconvert
-Depends: mia-tools, mialmpick, mia-viewit
+Recommends: mia-tools, mialmpick, mia-viewit
-Depends: ismrmrd-tools
+Recommends: ismrmrd-tools
; Added by blends-inject 0.0.7. [Please note here if modified manually]
Suggests: connectomeviewer
@@ -544,11 +544,11 @@ Published-Title: The Connectome Viewer Toolkit: An open source framework to mana
Published-Year: 2011
; Added by blends-inject 0.0.7. [Now official package]
-Depends: sigviewer
+Recommends: sigviewer
-Depends: python-tifffile
+Recommends: python-tifffile
-Depends: mni-icbm152-nlin-2009
+Recommends: mni-icbm152-nlin-2009
Homepage: http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
License: custom, DFSG-compliant
Responsible: NeuroDebian Team <team at neuro.debian.net>
@@ -570,17 +570,17 @@ Published-Year: 2009
Remark: This package is waiting for the Debian data package archive to become available.
-Depends: mni-colin27-nifti
+Recommends: mni-colin27-nifti
Pkg-URL: http://neuro.debian.net/pkgs/mni-colin27-nifti.html
-Depends: mipav
+Recommends: mipav
Pkg-URL: http://neuro.debian.net/pkgs/mipav.html
-Depends: jist
+Recommends: jist
-Depends: openmeeg-tools
+Recommends: openmeeg-tools
-Depends: jemris
+Recommends: jemris
License: GPL-2+
Responsible: NeuroDebian Team <team at neuro.debian.net>
WNPP: 590469
@@ -597,10 +597,10 @@ Published-In: Magnetic Resonance in Medicine
Published-Year: 2010
Published-DOI: 10.1002/mrm.22406
-Depends: insightapplications
+Recommends: insightapplications
Language: C++, Python, Tcl
-Depends: tempo
+Recommends: tempo
Homepage: http://code.google.com/p/tempo/
License: BSD
Language: C++, Qt
@@ -615,7 +615,7 @@ Pkg-Description: 3D visualization of brain electrical activity
publishing.
Remark: Packaged for OpenSuSE http://en.opensuse.org/TEMPO
-Depends: dti-query
+Recommends: dti-query
Homepage: http://graphics.stanford.edu/projects/dti/software/index.html
License: MIT
Language: C++
@@ -655,9 +655,9 @@ Recommends: python-dipy
Why: Although listed in -dev task, it also has a strong focus on interactive
data analysis.
-Depends: plastimatch
+Recommends: plastimatch
-Depends: medisnap
+Recommends: medisnap
Homepage: http://medisnap.sourceforge.net/
License: GPL-3
Pkg-Description: photograph, manage, view, compare, document and archive medical photos
@@ -674,7 +674,7 @@ Pkg-Description: photograph, manage, view, compare, document and archive medical
the current patient in your system
* easily print selected photos and archive or give them to your patients
-Depends: gimias
+Recommends: gimias
Homepage: http://www.gimias.org/
X-SF-URL: http://gimias.sourceforge.net
License: BSD-like
@@ -751,7 +751,7 @@ Remark: At the moment available only for Windows, but author says
there should be no major showstoppers to build it on Linux -- just
needs building infrastructure
-Depends: mayam
+Recommends: mayam
Language: Java
; Added by blends-inject 0.0.7. [extra information removed because package uploaded to Debian]
@@ -785,7 +785,7 @@ Published-Year: 2007
Registration: http://www.xnat.org/download-xnat.html
; Added by blends-inject 0.0.7. [Removed unneeded publication data]
-Depends: biosig-tools
+Recommends: biosig-tools
; Added by blends-inject 0.0.7. [Please note here if modified manually]
Suggests: isis
@@ -826,15 +826,15 @@ Pkg-Description: evaluate fMRI scanner stability
on the FBIRN quality assurance test protocal. Any 4D volumetric timeseries
image in NIfTI format is support input. Output is a rich HTML report.
-Depends: python-surfer
+Recommends: python-surfer
-Depends: dicoogle
+Recommends: dicoogle
-Depends: cellprofiler
+Recommends: cellprofiler
-Depends: bioimagexd
+Recommends: bioimagexd
-Depends: omero
+Recommends: omero
Homepage: http://www.openmicroscopy.org
License: GPL
Pkg-Description: coming standard LIMS for microscopy images
@@ -864,11 +864,11 @@ Published-Title: A National Human Neuroimaging Collaboratory Enabled
Published-Year: 2008
Registration: http://www.nitrc.org/account/register.php
-Depends: king
+Recommends: king
-Depends: vtk-dicom-tools
+Recommends: vtk-dicom-tools
-Depends: gdf-tools
+Recommends: gdf-tools
Suggests: incf-nidash-oneclick-clients
Homepage: http://xnat.incf.org/
@@ -883,15 +883,15 @@ Responsible: NeuroDebian Team <team at neuro.debian.net>
Vcs-Git: https://github.com/INCF/one_click.git
Vcs-Browser: https://github.com/INCF/one_click
-Depends: fw4spl
+Recommends: fw4spl
-Depends: bart
+Recommends: bart
-Depends: bart-view
+Recommends: bart-view
WNPP: 851431
Suggests: science-workflow
-Depends: dcm2niix
+Recommends: dcm2niix
-Depends: orthanc-wsi
+Recommends: orthanc-wsi
diff --git a/tasks/imaging-dev b/tasks/imaging-dev
index b0ad076..cf4d130 100644
--- a/tasks/imaging-dev
+++ b/tasks/imaging-dev
@@ -4,32 +4,32 @@ Description: Debian Med image processing and visualization packages development
for developing applications for medical image processing and
visualization.
-Depends: ctn-dev, cimg-dev, libminc-dev, libmdc2-dev, libvtk6-dev
+Recommends: ctn-dev, cimg-dev, libminc-dev, libmdc2-dev, libvtk6-dev
Suggests: libvtkedge-dev
-Depends: libnifti-dev
+Recommends: libnifti-dev
-Depends: libigstk4-dev
+Recommends: libigstk4-dev
Suggests: igstk-examples
-Depends: libinsighttoolkit4-dev
+Recommends: libinsighttoolkit4-dev
Suggests: libnifti-doc
Suggests: libfreeimage-dev
-Depends: libvolpack1-dev
+Recommends: libvolpack1-dev
-Depends: libgdcm2-dev
-Depends: python-gdcm
+Recommends: libgdcm2-dev
+Recommends: python-gdcm
Suggests: libics-dev
-Depends: libopensurgsim-dev
+Recommends: libopensurgsim-dev
-Depends: libmaxflow-dev
+Recommends: libmaxflow-dev
Suggests: liblimereg-dev
@@ -52,42 +52,42 @@ Remark: Homepage shows some potential medical applications
latest snapshot from http://snapshot.debian.org/package/libavg/1.0.1-1/ or use
the packaging in collab-maint for reintroducing.
-Depends: python-mvpa2
+Recommends: python-mvpa2
Why: Suggested by maintainer Michael Hanke <michael.hanke at gmail.com>
-Depends: python-nipy
+Recommends: python-nipy
-Depends: python-nipype
+Recommends: python-nipype
-Depends: python-nitime
+Recommends: python-nitime
-Depends: python-casmoothing
+Recommends: python-casmoothing
-Depends: libvia-dev
+Recommends: libvia-dev
-Depends: odin
+Recommends: odin
-Depends: libcv-dev
+Recommends: libcv-dev
-Depends: libvxl1-dev
+Recommends: libvxl1-dev
-Depends: libteem-dev
+Recommends: libteem-dev
-Depends: gmic
+Recommends: gmic
-Depends: libgiftiio-dev
+Recommends: libgiftiio-dev
-Depends: libvistaio-dev
+Recommends: libvistaio-dev
-Depends: libmia-2.4-dev, libmiaviewit-dev, libmialm-dev
+Recommends: libmia-2.4-dev, libmiaviewit-dev, libmialm-dev
-Depends: python-mia | python3-mia
+Recommends: python-mia | python3-mia
-Depends: libopenigtlink-dev
+Recommends: libopenigtlink-dev
-Depends: r-cran-rniftilib
+Recommends: r-cran-rniftilib
-Depends: libmni-perllib-perl
+Recommends: libmni-perllib-perl
Homepage: http://packages.bic.mni.mcgill.ca/tgz/
License: Artistic License
Responsible: NeuroDebian Team <team at neuro.debian.net>
@@ -100,15 +100,15 @@ Remark: There was some previous work on this software which is stalled currently
http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=libmni-perllib-perl
to Debian Med svn and start group maintenance.
-Depends: python-dicom
+Recommends: python-dicom
License: MIT
Pkg-URL: http://neuro.debian.net/pkgs/python-dicom.html
-Depends: libopenmeeg-dev
+Recommends: libopenmeeg-dev
-Depends: python-nibabel
+Recommends: python-nibabel
-Depends: libgdf-dev, octave-gdf
+Recommends: libgdf-dev, octave-gdf
; Added by blends-inject 0.0.6. [Please note here if modified manually]
Suggests: emokit
@@ -120,23 +120,23 @@ Vcs-Git: git://github.com/daeken/Emokit.git
Pkg-Description: Emotiv EPOC headset Python interface
Emotive is an interface to a budget Emotiv EPOC EEG headset.
-Depends: python-pyxnat
+Recommends: python-pyxnat
-Depends: python-dipy
+Recommends: python-dipy
-Depends: libbiosig-dev
+Recommends: libbiosig-dev
-Depends: libctk-dev
+Recommends: libctk-dev
-Depends: python-cfflib
+Recommends: python-cfflib
-Depends: libopenslide-dev
+Recommends: libopenslide-dev
-Depends: python-openslide
+Recommends: python-openslide
-Depends: libopenslide-java
+Recommends: libopenslide-java
-Depends: libbio-formats-java
+Recommends: libbio-formats-java
Language: Java
Remark: This library would enhance the package imagej
@@ -144,36 +144,36 @@ Suggests: libeegdev-dev
Suggests: libxdffileio-dev
-Depends: octave-dicom
+Recommends: octave-dicom
Homepage: http://octave.sourceforge.net/dicom/
License: GPL-v3+
Pkg-Description: Dicom support in Octave
Digital communications in medicine (DICOM) file io. Depends on Grassroots DICOM (GDCM)
-Depends: libcamitk-dev
+Recommends: libcamitk-dev
-Depends: libpapyrus3-dev
+Recommends: libpapyrus3-dev
-Depends: python-mne
+Recommends: python-mne
Suggests: python-tifffile
-Depends: python-vmtk, libvmtk-dev
+Recommends: python-vmtk, libvmtk-dev
-Depends: libvigraimpex-dev, python-vigra
+Recommends: libvigraimpex-dev, python-vigra
-Depends: libvtk-dicom-dev, libvtk-dicom-java
+Recommends: libvtk-dicom-dev, libvtk-dicom-java
-Depends: libedf-dev
+Recommends: libedf-dev
-Depends: python-imageio
+Recommends: python-imageio
-Depends: libismrmrd-dev
+Recommends: libismrmrd-dev
-Depends: libodil0-dev
+Recommends: libodil0-dev
-Depends: libbart-dev, octave-bart
+Recommends: libbart-dev, octave-bart
Suggests: libcamp-dev
-Depends: libcifti-dev
+Recommends: libcifti-dev
diff --git a/tasks/laboratory b/tasks/laboratory
index 294cf6c..a4894bc 100644
--- a/tasks/laboratory
+++ b/tasks/laboratory
@@ -3,11 +3,11 @@ Description: Debian Med suggestions for medical laboratories
This metapackage contains dependencies for software and that could
be useful ro run a medical laboratory.
-Depends: opencfu
+Recommends: opencfu
-Depends: orthanc-wsi
+Recommends: orthanc-wsi
-Depends: openelis
+Recommends: openelis
Homepage: http://openelis.uhl.uiowa.edu/
License: UIRF Open-source Based Public Software License
Pkg-Description: Enterprise Laboratory Information System
@@ -22,9 +22,9 @@ Pkg-Description: Enterprise Laboratory Information System
maintenance costs. By using an open source approach, we ensure that the project
will continue to evolve and meet the changing needs of the community.
-Depends: openfreezer
+Recommends: openfreezer
-Depends: catissuesuite
+Recommends: catissuesuite
License: to be clarified
Homepage: https://cabig.nci.nih.gov/tools/catissuesuite
Pkg-Description: tool for biospecimen inventory management
diff --git a/tasks/oncology b/tasks/oncology
index 075bd62..a1a0b74 100644
--- a/tasks/oncology
+++ b/tasks/oncology
@@ -3,11 +3,11 @@ Description: Debian Med packages for oncology
This metapackage will install tools that are useful for radiation
oncology.
-Depends: uw-prism
+Recommends: uw-prism
-Depends: orthanc-wsi
+Recommends: orthanc-wsi
-Depends: planunc
+Recommends: planunc
Homepage: http://planunc.radonc.unc.edu/about/
License: needs to be clarified, registration required
Pkg-Description: tools for radiotherapy treatment planning
@@ -25,4 +25,4 @@ Pkg-Description: tools for radiotherapy treatment planning
therapy, and to support RTP training for dosimetrists, physicists,
radiation therapists, and radiation oncology residents.
-Depends: dicompyler
+Recommends: dicompyler
diff --git a/tasks/pharmacy b/tasks/pharmacy
index 8c6094c..2d37f11 100644
--- a/tasks/pharmacy
+++ b/tasks/pharmacy
@@ -4,11 +4,11 @@ Description: Debian Med packages for pharmaceutical research
collection of software and documentation which is useful for
pharmaceutical research.
-Depends: chemtool
+Recommends: chemtool
-Depends: raccoon
+Recommends: raccoon
-Depends: r-cran-dosefinding
+Recommends: r-cran-dosefinding
Comment: Several related R packages are listed at CRAN:
http://cran.r-project.org/web/views/Pharmacokinetics.html
diff --git a/tasks/physics b/tasks/physics
index 41841aa..ee1dca7 100644
--- a/tasks/physics
+++ b/tasks/physics
@@ -5,30 +5,30 @@ Description: Debian Med packages for medical physicists
medical physicists in radiation oncology, diagnostics imaging
and related fields.
-Depends: paw++
+Recommends: paw++
Why: Just depend from the user friendly version because it is easier to
povide a menu item
-Depends: paw
+Recommends: paw
Why: This is for the purists with exactly the same functionality as paw++
Suggests: paw-demos
-Depends: octave
+Recommends: octave
-Depends: r-base
+Recommends: r-base
X-Comment: removed " | r-base-core" which desturbs tasks page and does not
harm to just use the metapackage in the dependency list
Why: "r-base" is a metapackage and it is better to have a default
alternative -- Dirk Eddelbuettel <edd at debian.org>
-Depends: biosig-tools
+Recommends: biosig-tools
Suggests: libbiosig-dev, python-biosig, octave-biosig
-Depends: gdf-tools
+Recommends: gdf-tools
-Depends: gate
+Recommends: gate
Homepage: http://www.opengatecollaboration.org
License: LGPL
WNPP: 431425
diff --git a/tasks/practice b/tasks/practice
index ad84312..0c449fa 100644
--- a/tasks/practice
+++ b/tasks/practice
@@ -3,30 +3,30 @@ Description: Debian Med packages for practice management
This metapackage contains dependencies for a collection of software
which might be helpful for practitioners to manage their practice.
-Depends: gnumed-client
+Recommends: gnumed-client
-Depends: gnumed-server
+Recommends: gnumed-server
-Depends: libchipcard-tools
+Recommends: libchipcard-tools
Why: Reading German "Gesundheitskarte"
-Depends: ginkgocadx
+Recommends: ginkgocadx
Suggests: libctapimkt1
-Depends: freediams, freemedforms-emr
+Recommends: freediams, freemedforms-emr
-Depends: r-cran-medadherence
+Recommends: r-cran-medadherence
-Depends: entangle
+Recommends: entangle
-Depends: sleepyhead
+Recommends: sleepyhead
-Depends: orthanc
+Recommends: orthanc
-Depends: orthanc-wsi
+Recommends: orthanc-wsi
-Depends: medintux
+Recommends: medintux
Homepage: http://medintux.org/medintux/en/
License: CeCILL (free)
Pkg-Description: Medical practice management system
@@ -43,7 +43,7 @@ Pkg-Description: Medical practice management system
Any person with real french to english skill is wellcome.
Please, contact Gérard Delafond : gerard-at-delafond.org
-Depends: mirth
+Recommends: mirth
Homepage: http://www.mirthproject.org/
License: MPL 1.1
Pkg-Description: HL7 integration engine
@@ -58,7 +58,7 @@ Pkg-Description: HL7 integration engine
Mirth also supports filters written in Java if you require more complex
filtering options.
-Depends: tinyheb
+Recommends: tinyheb
Homepage: http://tinyheb.sourceforge.net/
License: GPL
Pkg-URL: http://home.arcor.de/thomas.baum/tinyheb/source/
@@ -102,7 +102,7 @@ Comment: I do not really remember why this is set to "Ignore" - my
repository of clearhealth which was linked from http://www.op-en.org/
vanished.
-Depends: mirrormed
+Recommends: mirrormed
Homepage: http://www.mirrormed.org/
License: GPL
Pkg-Description: EHR and practice management system
@@ -111,7 +111,7 @@ Pkg-Description: EHR and practice management system
capable of running a healthcare practice. MirrorMed shares code with
FreeMED, and OpenEMR. MirrorMed is primarily sponsored by SynSeer.
-Depends: elexis
+Recommends: elexis
Homepage: http://sourceforge.net/projects/elexis
License: Eclipse Public License
WNPP: 570433
@@ -123,7 +123,7 @@ Pkg-Description: medical practice managemant system for use in Switzerland
accounting, billing (swiss TARMED-System, other systems to be
developped) and other daily work.
-Depends: freeb
+Recommends: freeb
Homepage: http://freeb.org/
License: GPL
Pkg-Description: Medical Bill formating module
@@ -145,7 +145,7 @@ Pkg-Description: Medical Bill formating module
FreeB 1.0 (Perl) is still used by the OpenEMR project. FreeB 1.0 was rewritten
as REMITT which used by the FreeMED project.
-Depends: freemed
+Recommends: freemed
Homepage: http://www.freemedsoftware.org/
License: GPL
Pkg-URL: http://downloads.sourceforge.net/freemed/freemed_0.8.4-1_all.deb?use_mirror=mesh
@@ -155,7 +155,7 @@ Pkg-Description: Electronic Medical Record and Practice Management system
backend and multiple import and export formats, as well as reporting and other
features.
-Depends: elementalclinic
+Recommends: elementalclinic
Homepage: http://www.elementalclinic.com/
License: GPL2+
Responsible: Hans Dieter Pearcey <hdp at opensourcery.com>
@@ -168,10 +168,10 @@ Pkg-Description: Electronical Medical Health record system for mental health
* Train and support clinicians to get the most from your EMR
* Customize software to fit unique practice needs
-Depends: openemr
+Recommends: openemr
Pkg-URL: http://www.oemr.org/Download_OpenEMR/
-Depends: clearhealth
+Recommends: clearhealth
Homepage: http://www.op-en.org/site/clearhealth
License: GPL
Pkg-Description: Medical practice management system
@@ -254,7 +254,7 @@ Remark: scientific use?
Please read the thread about homeopathic software on the Debian Med mailing
list starting at http://lists.debian.org/debian-med/2009/06/msg00028.html .
-Depends: proteus
+Recommends: proteus
Homepage: http://proteme.org/
License: EPL
Pkg-Description: clinical decision support guidelines model
@@ -263,9 +263,9 @@ Pkg-Description: clinical decision support guidelines model
condition has been created, it can be executed to provide stepwise advice
for any patient having that condition.
-Depends: thera-pi
+Recommends: thera-pi
-Depends: freeshim
+Recommends: freeshim
Homepage: http://freeshim.org/
Pkg-URL: https://launchpad.net/~rufustfirefly/+archive/ppa/+buildjob/2489799/+files/shim_0.1.1-1ubuntu2~maverick_all.deb
Pkg-Description: opensource electronic medical device interface
@@ -278,7 +278,7 @@ Remark: Needs Java prerequisites
* org.hsqldb:hsqldb:2.0.0
* org.reflections:reflections:0.9.5-RC2
-Depends: remitt
+Recommends: remitt
Homepage: http://remitt.org/
License: GPL
Pkg-Description: preparing and submitting medical billing data
@@ -290,4 +290,4 @@ Pkg-Description: preparing and submitting medical billing data
or PM system which implements its application programming interface
(API). The first system to do so has been FreeMED.
-Depends: qrisk2
+Recommends: qrisk2
diff --git a/tasks/psychology b/tasks/psychology
index 09d7548..c8894b5 100644
--- a/tasks/psychology
+++ b/tasks/psychology
@@ -6,14 +6,14 @@ Description: Debian Med packages for psychology
Suggests: science-psychophysics
Meta-Suggests: svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/psychophysics
-Depends: python-pyepl
+Recommends: python-pyepl
-Depends: praat
+Recommends: praat
-Depends: r-cran-foreign, psignifit, python-pypsignifit
+Recommends: r-cran-foreign, psignifit, python-pypsignifit
Why: analysis packages of particular relevance for psych. data
-Depends: r-cran-psy
+Recommends: r-cran-psy
Remark: r-cran-psy is orphaned upstream.
Hint to users of statistical psychological software. This package
seems to be orphaned upstream. There are several related packages
@@ -22,7 +22,7 @@ Remark: r-cran-psy is orphaned upstream.
of them.
; Added by blends-inject 0.0.6. [Please note here if modified manually]
-Depends: psychopy
+Recommends: psychopy
Pkg-URL: http://neuro.debian.net/pkgs/psychopy.html
Published-Authors: J. W. Peirce
Published-DOI: 10.1016/j.jneumeth.2006.11.017
@@ -32,7 +32,7 @@ Published-Year: 2007
Suggests: python-visionegg
-Depends: miscpsycho
+Recommends: miscpsycho
Homepage: http://cran.r-project.org/web/packages/MiscPsycho
License: GPL
Language: R
@@ -40,7 +40,7 @@ Pkg-URL: http://debian.cran.r-project.org/cran2deb/debian-amd64/testing/
Pkg-Description: Miscellaneous Psychometric Analyses
Miscellaneous functions for psychometric problems
-Depends: psych
+Recommends: psych
Homepage: http://cran.r-project.org/web/packages/psych/
License: GPL2+
Language: R
@@ -58,7 +58,7 @@ Pkg-Description: Procedures for Psychological, Psychometric, and Personality Res
personality research. For more information, see the
personality-project.org/r webpage.
-Depends: psychometric
+Recommends: psychometric
Homepage: http://cran.r-project.org/web/packages/psychometric
License: GPL2+
Language: R
@@ -68,7 +68,7 @@ Pkg-Description: Applied Psychometric Theory
(validity-generalization), reliability, item analysis, inter-rater
reliability, and classical utility
-Depends: psychotree
+Recommends: psychotree
Homepage: http://cran.r-project.org/web/packages/psychotree/
License: GPL2
Language: R
@@ -78,7 +78,7 @@ Pkg-Description: Recursive Partitioning Based on Psychometric Models
general MOB algorithm (from package party). Currently, only
Bradley-Terry trees are implemented.
-Depends: psyphy
+Recommends: psyphy
Homepage: http://cran.r-project.org/web/packages/psyphy/
License: GPL
Language: R
diff --git a/tasks/rehabilitation b/tasks/rehabilitation
index a5ae955..1f4d338 100644
--- a/tasks/rehabilitation
+++ b/tasks/rehabilitation
@@ -3,7 +3,7 @@ Description: Debian Med packages for rehabilitation technologies
This metapackage will install tools that are useful for
rehabilitation and therapy.
-Depends: sitplus
+Recommends: sitplus
; Added by blends-inject 0.0.7. [Please note here if modified manually]
Suggests: aghermann
diff --git a/tasks/research b/tasks/research
index e1e6ed8..5f5485c 100644
--- a/tasks/research
+++ b/tasks/research
@@ -3,7 +3,7 @@ Description: Debian Med packages for medical research
This metapackage will install tools that are useful for
medical research.
-Depends: openclinica
+Recommends: openclinica
License: GPL
Homepage: https://openclinica.com/
WNPP: 438868
diff --git a/tasks/statistics b/tasks/statistics
index e29ce61..d665704 100644
--- a/tasks/statistics
+++ b/tasks/statistics
@@ -4,23 +4,23 @@ Description: Debian Med statistics
This metapackage will install packages which are helpful to do statistics
with a special focus on tasks in medical care.
-Depends: r-bioc-edger, r-bioc-limma
+Recommends: r-bioc-edger, r-bioc-limma
Why: Statistical analysis of transcriptome expression assays.
-Depends: r-bioc-qvalue
+Recommends: r-bioc-qvalue
-Depends: r-cran-randomforest
+Recommends: r-cran-randomforest
Suggests: science-statistics
Why: This more or less includes all statistics relevant packages which might be
a bit to much for medical purposes - so it is only suggested.
-Depends: r-cran-beeswarm
+Recommends: r-cran-beeswarm
-Depends: r-cran-pvclust
+Recommends: r-cran-pvclust
-Depends: rstudio
+Recommends: rstudio
-Depends: r-bioc-multtest
+Recommends: r-bioc-multtest
-Depends: r-cran-ade4
+Recommends: r-cran-ade4
diff --git a/tasks/tools b/tasks/tools
index ba12895..c7b236b 100644
--- a/tasks/tools
+++ b/tasks/tools
@@ -3,7 +3,7 @@ Description: Debian Med several tools
This metapackage will install tools for several purposes in health care.
Currently it contains some simple programs for Personal Health.
-Depends: pcalendar
+Recommends: pcalendar
Suggests: cycle
Remark: Use pcalendar instead
@@ -15,40 +15,40 @@ Remark: Use pcalendar instead
Please consider using pcalendar instead of mencal because mencal is outdated,
not maintained any more and pcalendar simply overpasses it.
-Depends: pondus
+Recommends: pondus
-Depends: mssstest
+Recommends: mssstest
-Depends: wgerman-medical, hunspell-de-med
+Recommends: wgerman-medical, hunspell-de-med
-Depends: quitcount
+Recommends: quitcount
-Depends: workrave
+Recommends: workrave
-Depends: edfbrowser
+Recommends: edfbrowser
Suggests: entangle
-Depends: hunspell-en-med
+Recommends: hunspell-en-med
-Depends: python-clips
+Recommends: python-clips
-Depends: cronometer
+Recommends: cronometer
-Depends: python-fitbit
+Recommends: python-fitbit
-Depends: r-cran-fitcoach
+Recommends: r-cran-fitcoach
-Depends: r-cran-fitbitscraper
+Recommends: r-cran-fitbitscraper
-Depends: galileo
+Recommends: galileo
Suggests: goldencheetah
-Depends: nut-nutrition
+Recommends: nut-nutrition
-Depends: nutsqlite
+Recommends: nutsqlite
Suggests: sleepyhead
-Depends: pesco
+Recommends: pesco
diff --git a/tasks/typesetting b/tasks/typesetting
index 7ef3e8c..3673128 100644
--- a/tasks/typesetting
+++ b/tasks/typesetting
@@ -4,7 +4,7 @@ Description: Debian Med support for typesetting and publishing
for typesetting and publishing in medical care and structural
biology.
-Depends: texlive-science
+Recommends: texlive-science
Remark: For biologists specifically biotex.sty and textopo.sty are interesting
The texlive-science package contains a lot of interesting LaTeX styles for
different sciences. As a biologist you are most probably interested in
@@ -15,7 +15,7 @@ Remark: For biologists specifically biotex.sty and textopo.sty are interesting
in
/usr/share/doc/texlive-science-doc/latex/textopo/
-Depends: texlive-latex-extra
+Recommends: texlive-latex-extra
Remark: For biologists specifically texshade.sty is interesting
The texlive-latex-extra package contains a lot of interesting LaTeX styles for
different purposes. As a biologist you are most probably interested in
@@ -33,6 +33,6 @@ Remark:
Desktop tools that help inserting references in LibreOffice, or help managing
PDF collections. This list is probably incomplete.
-Depends: king
+Recommends: king
Suggests: r-cran-qqman
--
Debian Med metapackages
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