[Blends-commit] [Git][blends-team/med][master] Update bio - substituted (most) recommendations with suggestions
Steffen Möller
gitlab at salsa.debian.org
Tue Jun 23 17:56:46 BST 2020
Steffen Möller pushed to branch master at Debian Blends Team / med
Commits:
d2729893 by Steffen Möller at 2020-06-23T16:56:33+00:00
Update bio - substituted (most) recommendations with suggestions
- - - - -
1 changed file:
- tasks/bio
Changes:
=====================================
tasks/bio
=====================================
@@ -371,7 +371,7 @@ Suggests: flexbar
Suggests: blimps-utils
-Recommends: sift
+Suggests: sift
Suggests: neobio
@@ -687,409 +687,409 @@ Suggests: fsm-lite
Suggests: garli
-Recommends: gatb-core
+Suggests: gatb-core
-Recommends: gatk
+Suggests: gatk
-Recommends: genometester
+Suggests: genometester
-Recommends: genomethreader
+Suggests: genomethreader
-Recommends: genometools
+Suggests: genometools
-Recommends: gerp++
+Suggests: gerp++
-Recommends: gffread
+Suggests: gffread
-Recommends: grabix
+Suggests: grabix
-Recommends: graphlan
+Suggests: graphlan
-Recommends: graphmap2
+Suggests: graphmap2
-Recommends: gwama
+Suggests: gwama
-Recommends: gubbins
+Suggests: gubbins
-Recommends: haploview-cran-amap
+Suggests: haploview-cran-amap
-Recommends: harvest-tools
+Suggests: harvest-tools
-Recommends: hilive
+Suggests: hilive
-Recommends: hisat2
+Suggests: hisat2
-Recommends: hmmer2
+Suggests: 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.
-Recommends: htqc
+Suggests: htqc
-Recommends: idba
+Suggests: idba
-Recommends: idefix
+Suggests: idefix
-Recommends: igdiscover
+Suggests: igdiscover
-Recommends: indelible
+Suggests: indelible
-Recommends: insilicoseq
+Suggests: insilicoseq
-Recommends: iqtree
+Suggests: iqtree
-Recommends: iva
+Suggests: iva
-Recommends: jaligner
+Suggests: jaligner
-Recommends: jbrowse
+Suggests: jbrowse
-Recommends: jmodeltest
+Suggests: jmodeltest
-Recommends: kaptive, kleborate
+Suggests: kaptive, kleborate
-Recommends: kempbasu
+Suggests: kempbasu
-Recommends: kineticstools
+Suggests: kineticstools
-Recommends: kissplice
+Suggests: kissplice
-Recommends: kma
+Suggests: kma
-Recommends: kmerresistance
+Suggests: kmerresistance
-Recommends: kraken, kraken2
+Suggests: kraken, kraken2
-Recommends: lagan
+Suggests: lagan
X-Category: Comparative genomics
-Recommends: lambda-align, lambda-align2
+Suggests: lambda-align, lambda-align2
-Recommends: lastz
+Suggests: lastz
-Recommends: leaff
+Suggests: leaff
-Recommends: ltrsift
+Suggests: ltrsift
-Recommends: lofreq
+Suggests: lofreq
-Recommends: kallisto
+Suggests: kallisto
-Recommends: khmer
+Suggests: khmer
-Recommends: kmer
+Suggests: kmer
-Recommends: radiant
+Suggests: radiant
-Recommends: lefse
+Suggests: lefse
-Recommends: lighter
+Suggests: lighter
-Recommends: lumpy-sv
+Suggests: lumpy-sv
-Recommends: mach-haplotyper
+Suggests: mach-haplotyper
-Recommends: macs
+Suggests: macs
-Recommends: macsyfinder
+Suggests: macsyfinder
-Recommends: maffilter
+Suggests: maffilter
-Recommends: mage2tab, tab2mage
+Suggests: mage2tab, tab2mage
-Recommends: malt
+Suggests: malt
-Recommends: manta
+Suggests: manta
-Recommends: mapdamage
+Suggests: mapdamage
-Recommends: martj
+Suggests: martj
-Recommends: mash
+Suggests: mash
-Recommends: progressivemauve
+Suggests: progressivemauve
X-Category: Multiple genome alignment
X-Importance: efficient
-Recommends: mauve-aligner
+Suggests: mauve-aligner
-Recommends: medaka
+Suggests: medaka
-Recommends: meme
+Suggests: meme
License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)
-Recommends: meryl
+Suggests: meryl
-Recommends: metabit
+Suggests: metabit
-Recommends: metaphlan2
+Suggests: metaphlan2
-Recommends: metastudent
+Suggests: metastudent
Suggests: metastudent-data, metastudent-data-2
-Recommends: microbegps
+Suggests: microbegps
-Recommends: mindthegap
+Suggests: mindthegap
-Recommends: miniasm
+Suggests: miniasm
-Recommends: minimac4
+Suggests: minimac4
-Recommends: minimap, minimap2
+Suggests: minimap, minimap2
-Recommends: mirtop
+Suggests: mirtop
-Recommends: molekel
+Suggests: molekel
-Recommends: mosaik-aligner
+Suggests: mosaik-aligner
-Recommends: mosdepth
+Suggests: mosdepth
-Recommends: mmseqs2
+Suggests: mmseqs2
-Recommends: mpsqed
+Suggests: 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
-Recommends: mptp
+Suggests: mptp
-Recommends: mugsy
+Suggests: mugsy
-Recommends: multiqc
+Suggests: multiqc
-Recommends: murasaki | murasaki-mpi
+Suggests: murasaki | murasaki-mpi
-Recommends: mview
+Suggests: mview
-Recommends: nanocall
+Suggests: nanocall
-Recommends: nanook
+Suggests: nanook
-Recommends: nanopolish
+Suggests: nanopolish
-Recommends: nanolyse
+Suggests: nanolyse
-Recommends: nanofilt
+Suggests: nanofilt
-Recommends: nanoplot
+Suggests: nanoplot
-Recommends: nanosv
+Suggests: nanosv
-Recommends: ncbi-acc-download
+Suggests: ncbi-acc-download
-Recommends: ncbi-entrez-direct
+Suggests: ncbi-entrez-direct
-Recommends: ncbi-magicblast
+Suggests: ncbi-magicblast
-Recommends: ncbi-seg
+Suggests: ncbi-seg
-Recommends: nextsv
+Suggests: nextsv
-Recommends: ngila
+Suggests: ngila
-Recommends: ngmlr
+Suggests: ngmlr
-Recommends: ngsqctoolkit
+Suggests: ngsqctoolkit
-Recommends: nw-align
+Suggests: nw-align
-Recommends: oases
+Suggests: oases
-Recommends: obitools
+Suggests: obitools
-Recommends: oncofuse
+Suggests: oncofuse
-Recommends: optimir
+Suggests: optimir
-Recommends: optitype
+Suggests: optitype
-Recommends: paipline
+Suggests: paipline
-Recommends: python3-pairtools
+Suggests: python3-pairtools
-Recommends: pal2nal
+Suggests: pal2nal
-Recommends: paleomix
+Suggests: paleomix
-Recommends: paraclu
+Suggests: paraclu
-Recommends: parasail
+Suggests: parasail
-Recommends: parsinsert
+Suggests: parsinsert
-Recommends: parsnp
+Suggests: parsnp
-Recommends: partitionfinder
+Suggests: partitionfinder
-Recommends: patman
+Suggests: patman
-Recommends: patristic
+Suggests: patristic
Language: Java
-Recommends: pbdagcon
+Suggests: pbdagcon
-Recommends: pbsuite
+Suggests: pbsuite
-Recommends: pbgenomicconsensus
+Suggests: pbgenomicconsensus
-Recommends: pbjelly, pbhoney
+Suggests: pbjelly, pbhoney
-Recommends: pbsim
+Suggests: pbsim
-Recommends: pcma
+Suggests: 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
-Recommends: perm
+Suggests: perm
-Recommends: pftools
+Suggests: pftools
-Recommends: phast
+Suggests: phast
-Recommends: phipack
+Suggests: phipack
-Recommends: phybin
+Suggests: phybin
-Recommends: phylophlan
+Suggests: 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
-Recommends: phyloviz-core
+Suggests: 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.
-Recommends: phyutility
+Suggests: phyutility
-Recommends: phyx
+Suggests: phyx
-Recommends: physamp
+Suggests: physamp
-Recommends: picopore
+Suggests: picopore
-Recommends: piler
+Suggests: piler
-Recommends: pilercr
+Suggests: pilercr
-Recommends: pilon
+Suggests: pilon
-Recommends: pipasic, inspect, tide
+Suggests: pipasic, inspect, tide
-Recommends: pirs
+Suggests: pirs
-Recommends: placnet
+Suggests: placnet
-Recommends: plasmidid
+Suggests: plasmidid
-Recommends: plasmidseeker
+Suggests: plasmidseeker
-Recommends: plato
+Suggests: plato
-Recommends: plip
+Suggests: plip
-Recommends: pomoxis
+Suggests: pomoxis
-Recommends: poretools
+Suggests: poretools
-Recommends: porechop
+Suggests: porechop
-Recommends: pplacer
+Suggests: pplacer
-Recommends: prank
+Suggests: prank
-Recommends: predictprotein
+Suggests: predictprotein
-Recommends: proalign
+Suggests: proalign
-Recommends: prodigal
+Suggests: prodigal
-Recommends: prokka
+Suggests: prokka
-Recommends: proteinortho
+Suggests: proteinortho
-Recommends: prottest
+Suggests: prottest
-Recommends: psortb
+Suggests: psortb
-Recommends: pscan-tfbs, pscan-chip
+Suggests: pscan-tfbs, pscan-chip
-Recommends: psipred
+Suggests: psipred
-Recommends: pssh2
+Suggests: pssh2
Recommends: pufferfish
Suggests: python3-alignlib
-Recommends: python3-cogent
+Suggests: python3-cogent
-Recommends: pycorrfit
+Suggests: pycorrfit
-Recommends: pyscanfcs
+Suggests: pyscanfcs
-Recommends: python3-deeptools, python3-deeptoolsintervals
+Suggests: python3-deeptools, python3-deeptoolsintervals
-Recommends: python3-geneimpacts
+Suggests: python3-geneimpacts
-Recommends: python3-gffutils
+Suggests: python3-gffutils
Suggests: python3-loompy
-Recommends: python3-pybel
+Suggests: python3-pybel
Suggests: python3-pychopper
Suggests: python3-py2bit
-Recommends: python3-pybedtools
+Suggests: python3-pybedtools
-Recommends: python3-sqt
+Suggests: python3-sqt
-Recommends: qtlreaper
+Suggests: qtlreaper
Suggests: python3-tinyalign
-Recommends: python3-treetime
+Suggests: python3-treetime
-Recommends: purple
+Suggests: purple
-Recommends: pycoqc
+Suggests: pycoqc
-Recommends: qcat
+Suggests: qcat
-Recommends: qcumber
+Suggests: qcumber
-Recommends: quicktree
+Suggests: quicktree
-Recommends: qtltools
+Suggests: qtltools
-Recommends: qualimap
+Suggests: qualimap
-Recommends: quast
+Suggests: quast
-Recommends: quorum
+Suggests: quorum
-Recommends: ragout
+Suggests: ragout
-Recommends: rambo-k
+Suggests: rambo-k
-Recommends: rapmap
+Suggests: rapmap
Suggests: r-bioc-ctc
-Recommends: r-bioc-cummerbund
+Suggests: r-bioc-cummerbund
-Recommends: r-bioc-rtracklayer, r-bioc-gviz, r-bioc-biostrings, r-bioc-annotate, r-bioc-genefilter
+Suggests: r-bioc-rtracklayer, r-bioc-gviz, r-bioc-biostrings, r-bioc-annotate, r-bioc-genefilter
-Recommends: r-bioc-deseq2, r-bioc-dnacopy, r-bioc-geneplotter
+Suggests: r-bioc-deseq2, r-bioc-dnacopy, r-bioc-geneplotter
-Recommends: r-bioc-geoquery
+Suggests: r-bioc-geoquery
Suggests: r-bioc-grohmm
@@ -1103,7 +1103,7 @@ Suggests: r-cran-corrplot
Suggests: r-cran-dynamictreecut
-Recommends: r-bioc-ebseq
+Suggests: r-bioc-ebseq
Suggests: r-cran-forecast
@@ -1111,23 +1111,23 @@ Suggests: r-cran-gprofiler
Suggests: r-cran-fitdistrplus
-Recommends: r-bioc-impute
+Suggests: r-bioc-impute
-Recommends: r-bioc-mergeomics
+Suggests: r-bioc-mergeomics
-Recommends: r-bioc-metagenomeseq, r-bioc-phyloseq
+Suggests: r-bioc-metagenomeseq, r-bioc-phyloseq
-Recommends: r-bioc-mofa
+Suggests: r-bioc-mofa
-Recommends: r-bioc-multiassayexperiment
+Suggests: r-bioc-multiassayexperiment
-Recommends: r-bioc-mutationalpatterns
+Suggests: r-bioc-mutationalpatterns
-Recommends: r-bioc-limma, r-bioc-edger
+Suggests: r-bioc-limma, r-bioc-edger
-Recommends: r-bioc-bitseq, r-bioc-pcamethods, r-cran-samr
+Suggests: r-bioc-bitseq, r-bioc-pcamethods, r-cran-samr
-Recommends: r-bioc-htsfilter
+Suggests: r-bioc-htsfilter
Suggests: r-bioc-annotationhub, r-bioc-aroma.light, r-bioc-ensembldb,
@@ -1141,33 +1141,33 @@ Recommends: r-cran-rotl
Suggests: r-cran-rentrez
-Recommends: r-cran-adegenet, r-cran-adephylo
+Suggests: r-cran-adegenet, r-cran-adephylo
-Recommends: r-cran-ape
+Suggests: r-cran-ape
Suggests: r-cran-boolnet
-Recommends: r-cran-distory
+Suggests: r-cran-distory
-Recommends: r-cran-drinsight
+Suggests: r-cran-drinsight
-Recommends: r-cran-kaos
+Suggests: r-cran-kaos
Suggests: r-cran-minerva
-Recommends: r-cran-metamix
+Suggests: r-cran-metamix
Suggests: r-cran-optimalcutpoints
Suggests: r-cran-parmigene
-Recommends: r-cran-phangorn
+Suggests: r-cran-phangorn
Suggests: r-cran-pheatmap
-Recommends: r-cran-phytools
+Suggests: r-cran-phytools
-Recommends: r-cran-pscbs
+Suggests: r-cran-pscbs
Suggests: r-cran-rsgcc
@@ -1175,92 +1175,92 @@ Suggests: r-bioc-savr
Suggests: r-cran-sctransform
-Recommends: r-cran-seurat
+Suggests: r-cran-seurat
-Recommends: r-cran-seqinr
+Suggests: r-cran-seqinr
-Recommends: r-cran-spp
+Suggests: r-cran-spp
-Recommends: r-bioc-tfbstools, r-bioc-cner
+Suggests: r-bioc-tfbstools, r-bioc-cner
-Recommends: r-cran-treescape
+Suggests: r-cran-treescape
-Recommends: r-cran-tsne
+Suggests: r-cran-tsne
Suggests: r-bioc-tximport
-Recommends: r-cran-vegan
+Suggests: r-cran-vegan
-Recommends: r-cran-webgestaltr
+Suggests: r-cran-webgestaltr
-Recommends: r-other-apmswapp
+Suggests: r-other-apmswapp
-Recommends: r-other-hms-dbmi-spp
+Suggests: r-other-hms-dbmi-spp
-Recommends: r-cran-wgcna
+Suggests: r-cran-wgcna
-Recommends: r-other-ascat
+Suggests: r-other-ascat
-Recommends: readucks
+Suggests: readucks
-Recommends: recan
+Suggests: recan
-Recommends: relion-bin+gui | relion-bin+mpi+gui, relion-bin | relion-bin+mpi
+Suggests: relion-bin+gui | relion-bin+mpi+gui, relion-bin | relion-bin+mpi
-Recommends: rdp-alignment, rdp-readseq, rdp-classifier
+Suggests: rdp-alignment, rdp-readseq, rdp-classifier
-Recommends: reapr
+Suggests: reapr
-Recommends: repeatmasker-recon
+Suggests: repeatmasker-recon
-Recommends: repeatmasker
+Suggests: repeatmasker
-Recommends: resfinder
+Suggests: resfinder
-Recommends: roadtrips
+Suggests: roadtrips
-Recommends: roary
+Suggests: roary
-Recommends: roguenarok
+Suggests: roguenarok
-Recommends: rsat
+Suggests: rsat
-Recommends: rsem
+Suggests: rsem
-Recommends: sambamba
+Suggests: sambamba
-Recommends: samblaster
+Suggests: samblaster
-Recommends: salmon
+Suggests: salmon
-Recommends: samclip
+Suggests: samclip
-Recommends: sap
+Suggests: sap
Remark: Precondition for T-Coffee
see http://wiki.debian.org/DebianMed/TCoffee
-Recommends: scrappie
+Suggests: scrappie
-Recommends: scrm
+Suggests: scrm
-Recommends: seer
+Suggests: seer
-Recommends: segemehl
+Suggests: segemehl
-Recommends: sepp
+Suggests: sepp
-Recommends: seq-seq-pan
+Suggests: seq-seq-pan
Remark: Needs blat which is not re-distributable
-Recommends: seqmagick
+Suggests: seqmagick
-Recommends: seqprep
+Suggests: seqprep
-Recommends: seqsero
+Suggests: seqsero
-Recommends: seqtk
+Suggests: seqtk
-Recommends: sequenceconverter.app
+Suggests: 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.
@@ -1272,195 +1272,195 @@ 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.
-Recommends: seqwish
+Suggests: seqwish
-Recommends: sga
+Suggests: sga
-Recommends: shovill
+Suggests: shovill
-Recommends: signalalign
+Suggests: signalalign
-Recommends: sibelia
+Suggests: sibelia
-Recommends: sina
+Suggests: sina
-Recommends: sistr
+Suggests: sistr
-Recommends: situs
+Suggests: situs
-Recommends: sim4db
+Suggests: sim4db
-Recommends: skesa
+Suggests: skesa
-Recommends: smalt
+Suggests: 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).
-Recommends: smithwaterman
+Suggests: smithwaterman
-Recommends: smrtanalysis
+Suggests: smrtanalysis
-Recommends: snpeff
+Suggests: snpeff
-Recommends: snpomatic
+Suggests: snpomatic
-Recommends: solvate
+Suggests: solvate
-Recommends: sortmerna
+Suggests: sortmerna
-Recommends: snap-aligner
+Suggests: snap-aligner
-Recommends: sniffles
+Suggests: sniffles
-Recommends: sourmash
+Suggests: sourmash
-Recommends: spaced
+Suggests: spaced
-Recommends: spades
+Suggests: spades
-Recommends: spaln
+Suggests: spaln
-Recommends: sparta
+Suggests: sparta
-Recommends: sprai
+Suggests: sprai
-Recommends: srst2
+Suggests: srst2
-Recommends: ssaha
+Suggests: 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)
-Recommends: sspace
+Suggests: sspace
-Recommends: ssw-align
+Suggests: ssw-align
-Recommends: staden
+Suggests: staden
-Recommends: stacks
+Suggests: stacks
-Recommends: strap, strap-base
+Suggests: strap, strap-base
Language: Java
-Recommends: strelka
+Suggests: strelka
-Recommends: stringtie
+Suggests: stringtie
-Recommends: subread
+Suggests: subread
-Recommends: suitename
+Suggests: suitename
-Recommends: sumatra, sumaclust
+Suggests: sumatra, sumaclust
-Recommends: sumtrees
+Suggests: sumtrees
-Recommends: surankco
+Suggests: surankco
-Recommends: swarm
+Suggests: swarm
-Recommends: tacg
+Suggests: tacg
X-Category: Motif detection
X-Importance: powerful
-Recommends: tantan
+Suggests: tantan
-Recommends: thesias
+Suggests: thesias
-Recommends: tiddit
+Suggests: tiddit
-Recommends: toppred
+Suggests: toppred
-Recommends: transdecoder
+Suggests: transdecoder
-Recommends: tnseq-transit
+Suggests: tnseq-transit
-Recommends: tn-seqexplorer
+Suggests: tn-seqexplorer
-Recommends: toil
+Suggests: toil
-Recommends: tombo
+Suggests: tombo
-Recommends: tracetuner
+Suggests: tracetuner
-Recommends: transrate-tools
+Suggests: transrate-tools
-Recommends: treeview
+Suggests: treeview
X-Category: Visualisation
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
-Recommends: trinityrnaseq
+Suggests: trinityrnaseq
-Recommends: uc-echo
+Suggests: uc-echo
X-Category: NGS
-Recommends: ufasta
+Suggests: ufasta
-Recommends: umap-learn
+Suggests: umap-learn
-Recommends: umis
+Suggests: umis
-Recommends: unanimity
+Suggests: unanimity
-Recommends: unicycler
+Suggests: unicycler
-Recommends: varna
+Suggests: varna
-Recommends: varmatch
+Suggests: varmatch
-Recommends: varscan
+Suggests: varscan
-Recommends: vcfanno
+Suggests: vcfanno
-Recommends: vdjtools
+Suggests: vdjtools
-Recommends: vg
+Suggests: vg
-Recommends: vienna-rna
+Suggests: vienna-rna
X-Category: Secondary structure of nucleic acids
-Recommends: virulencefinder
+Suggests: virulencefinder
-Recommends: vmatch
+Suggests: vmatch
-Recommends: vmd
+Suggests: vmd
-Recommends: vsearch
+Suggests: vsearch
-Recommends: vt
+Suggests: vt
-Recommends: yaha
+Suggests: yaha
-Recommends: yanagiba
+Suggests: yanagiba
-Recommends: yanosim
+Suggests: yanosim
-Recommends: canu
+Suggests: canu
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Recommends: zalign
+Suggests: zalign
-Recommends: zodiac-zeden
+Suggests: zodiac-zeden
Language: C, C++
-Recommends: discosnp, mapsembler2
+Suggests: discosnp, mapsembler2
-Recommends: dnaclust
+Suggests: dnaclust
-Recommends: r-cran-tcr, r-cran-tigger, r-cran-alakazam, r-cran-shazam, igor, r-cran-sdmtools, presto, changeo
+Suggests: r-cran-tcr, r-cran-tigger, r-cran-alakazam, r-cran-shazam, igor, r-cran-sdmtools, presto, changeo
-Recommends: ncbi-igblast
+Suggests: ncbi-igblast
Suggests: python3-pyflow
-Recommends: pigx-rnaseq, pigx-scrnaseq
+Suggests: pigx-rnaseq, pigx-scrnaseq
X-Mark: The information below needs to be checked whether it can be obtained from Vcs or needs to stay here
-Recommends: copycat
+Suggests: 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
@@ -1471,7 +1471,7 @@ 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.
-Recommends: btk-core
+Suggests: btk-core
Homepage: http://sourceforge.net/projects/btk/
Responsible: Morten Kjeldgaard <mok at bioxray.au.dk>
License: GPL
@@ -1482,7 +1482,7 @@ Pkg-Description: biomolecule Toolkit C++ library
for common tasks in structural biology to facilitate the development of
molecular modeling, design and analysis tools.
-Recommends: asap
+Suggests: asap
Homepage: http://asap.ahabs.wisc.edu/software/asap/
Responsible: Andreas Tille <tille at debian.org>
License: GPL
@@ -1510,7 +1510,7 @@ Pkg-Description: organize the data associated with a genome
inter-operable between sites.
X-Category: Annotation
-Recommends: cactus
+Suggests: cactus
Homepage: http://www.cactuscode.org/Community/Biology.html
License: GPL
Pkg-Description:
@@ -1524,7 +1524,7 @@ Pkg-Description:
Metacomputing Toolkit, HDF5 parallel file I/O, the PETSc scientific library,
adaptive mesh refinement, web interfaces, and advanced visualization tools.
-Recommends: contralign
+Suggests: contralign
Homepage: http://contra.stanford.edu/contralign/
License: Public Domain
Pkg-Description: parameter learning framework for protein pairwise sequence alignment
@@ -1535,13 +1535,13 @@ Pkg-Description: parameter learning framework for protein pairwise sequence alig
previously unseen sequences and avoid overfitting by controlling model
complexity through regularization.
-Recommends: concavity
+Suggests: concavity
-Recommends: conservation-code
+Suggests: conservation-code
-Recommends: galaxy
+Suggests: galaxy
-Recommends: genographer
+Suggests: genographer
Homepage: https://sourceforge.net/projects/genographer/
License: GPL
Pkg-Description: read data and reconstruct them into a gel image
@@ -1553,7 +1553,7 @@ 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.
-Recommends: phylographer
+Suggests: phylographer
Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html
License: GPL
X-Category: Graphical representation of sequence conservation
@@ -1574,7 +1574,7 @@ 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.
-Recommends: phylowin
+Suggests: phylowin
Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html
WNPP: 395840
License: unknown
@@ -1599,14 +1599,14 @@ Remark: Issuer of previous ITP said:
Probably it makes sense to remove this project from the prospective packages
list.
-Recommends: phpphylotree
+Suggests: 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.
-Recommends: twain
+Suggests: 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
@@ -1629,7 +1629,7 @@ 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/)
-Recommends: rose
+Suggests: rose
Homepage: http://www.cbcb.umd.edu/software/rose/Rose.html
License: Open Source
Pkg-Description: Region-Of-Synteny Extractor
@@ -1648,7 +1648,7 @@ Pkg-Description: Region-Of-Synteny Extractor
boundaries of the output region.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Recommends: glimmerhmm
+Suggests: glimmerhmm
Homepage: http://www.cbcb.umd.edu/software/glimmerhmm/
License: Artistic
Pkg-Description: Eukaryotic Gene-Finding System
@@ -1663,7 +1663,7 @@ Pkg-Description: Eukaryotic Gene-Finding System
user manual can be consulted here.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Recommends: genezilla
+Suggests: genezilla
Homepage: http://www.genezilla.org/
License: Artistic
Language: C++
@@ -1693,7 +1693,7 @@ Pkg-Description: eukaryotic gene finder
for the comparative gene finder TWAIN.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Recommends: exalt
+Suggests: exalt
Homepage: http://www.cbcb.umd.edu/software/exalt/
License: Artistic
Pkg-Description: phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
@@ -1707,7 +1707,7 @@ Pkg-Description: phylogenetic generalized hidden Markov model for predicting alt
run on other species.
Remark: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-Recommends: jigsaw
+Suggests: jigsaw
Homepage: http://www.cbcb.umd.edu/software/jigsaw/
License: Artistic
Pkg-Description: gene prediction using multiple sources of evidence
@@ -1735,7 +1735,7 @@ 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/)
-Recommends: genesplicer
+Suggests: genesplicer
Homepage: http://www.cbcb.umd.edu/software/GeneSplicer/
License: Artistic
Pkg-Description: computational method for splice site prediction
@@ -1779,7 +1779,7 @@ 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.
-Recommends: mummergpu
+Suggests: mummergpu
Homepage: http://mummergpu.sourceforge.net/
License: Artistic
Pkg-Description: High-throughput sequence alignment using Graphics Processing Units
@@ -1807,7 +1807,7 @@ 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/)
-Recommends: amoscmp
+Suggests: amoscmp
Homepage: http://amos.sourceforge.net/docs/pipeline/AMOScmp.html
License: Artistic
Pkg-Description: comparative genome assembly package
@@ -1836,7 +1836,7 @@ 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/)
-Recommends: minimus
+Suggests: minimus
Homepage: http://amos.sourceforge.net/docs/pipeline/minimus.html
License: Artistic
Pkg-Description: AMOS lightweight assembler
@@ -1869,7 +1869,7 @@ Pkg-Description: AMOS lightweight assembler
develop a modular open-source framework for assembly development.
Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-Ignore: catissuecore
+Suggests: catissuecore
Homepage: https://cabig.nci.nih.gov/tools/catissuecore
License: to be clarified, NCICB Open Source Project Site
Pkg-Description: biospecimen inventory, tracking, and basic annotation
@@ -1928,7 +1928,7 @@ Pkg-Description: Transcript Annotation Prioritization and Screening System
Remark: Found at
http://gforge.nci.nih.gov/softwaremap/trove_list.php?form_cat=337
-Recommends: bambus
+Suggests: bambus
Homepage: http://amos.sourceforge.net/docs/bambus/
License: Artistic
Pkg-Description: hierarchical approach to building contig scaffolds
@@ -1943,7 +1943,7 @@ 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/)
-Recommends: gmv
+Suggests: gmv
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?GMV
License: GPL
Pkg-Description: comparative genome browser for Murasaki
@@ -1951,14 +1951,14 @@ Pkg-Description: comparative genome browser for Murasaki
anchors from Murasaki, annotation data from GenBank files, and
expression / prediction score from GFF files.
-Recommends: pyrophosphate-tools
+Suggests: 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.
-Recommends: figaro
+Suggests: figaro
Homepage: http://amos.sourceforge.net/Figaro/Figaro.html
License: Artistic
Pkg-Description: novel vector trimming software
@@ -1971,7 +1971,7 @@ 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/)
-Recommends: mirbase
+Suggests: mirbase
Homepage: http://microrna.sanger.ac.uk/
License: Public Domain
WNPP: 420938
@@ -2017,7 +2017,7 @@ 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
-Recommends: uniprime
+Suggests: uniprime
Homepage: http://code.google.com/p/uniprime/
License: GPL-3+
Responsible: Charles Plessy <plessy at debian.org>
@@ -2033,7 +2033,7 @@ Pkg-Description: workflow-based platform for universal primer design
generates successful cross-species primers that take into account the
biological aspects of the PCR.
-Recommends: genetrack
+Suggests: genetrack
Homepage: http://sysbio.bx.psu.edu/genetrack.html
License: MIT
Responsible: Charles Plessy <plessy at debian.org>
@@ -2043,7 +2043,7 @@ 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.
-Recommends: operondb
+Suggests: operondb
Homepage: http://www.cbcb.umd.edu/cgi-bin/operons/operons.cgi
License: to be clarified
Pkg-Description: detect and analyze conserved gene pairs
@@ -2072,7 +2072,7 @@ Remark: Other sequence analysis tools (http://www.cbcb.umd.edu/software/);
no info about license or downloadable code found, but tried to
contact authors.
-Recommends: trnascan-se
+Suggests: trnascan-se
Comment: If you stumble upon alfresco at
http://www.sanger.ac.uk/Software/Alfresco/ - it seems outdated and
@@ -2085,7 +2085,7 @@ 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.
-Recommends: cdna-db
+Suggests: cdna-db
Homepage: http://www.sanger.ac.uk/Software/analysis/cdna_db/
License: Artistic
Pkg-Description: quality-control checking of finished cDNA clone sequences
@@ -2112,9 +2112,9 @@ 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.
-Recommends: coot
+Suggests: coot
-Recommends: caftools
+Suggests: caftools
Recommends: roche454ace2caf
Homepage: http://genome.imb-jena.de/software/roche454ace2caf/
@@ -2143,7 +2143,7 @@ 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.
-Recommends: big-blast
+Suggests: 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>
@@ -2154,7 +2154,7 @@ 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
-Recommends: estferret
+Suggests: estferret
Homepage: http://legr.liv.ac.uk/EST-ferret/index.htm
License: to be clarified
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2201,11 +2201,11 @@ 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
-Recommends: lamarc
+Suggests: lamarc
-Recommends: lucy
+Suggests: lucy
-Recommends: maxd
+Suggests: maxd
Homepage: http://www.bioinf.man.ac.uk/microarray/maxd/
License: Artistic
Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2223,9 +2223,9 @@ 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
-Recommends: mesquite
+Suggests: mesquite
-Recommends: migrate
+Suggests: 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>
@@ -2247,7 +2247,7 @@ 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
-Recommends: msatfinder
+Suggests: msatfinder
Homepage: http://www.genomics.ceh.ac.uk/msatfinder/
License: GPL
Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2262,7 +2262,7 @@ 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
-Recommends: oligoarrayaux
+Suggests: oligoarrayaux
Homepage: http://dinamelt.bioinfo.rpi.edu/OligoArrayAux.php
License: non-free (fre academical use)
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2289,7 +2289,7 @@ 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.
-Recommends: partigene
+Suggests: partigene
Homepage: http://www.nematodes.org/bioinformatics/PartiGene/
License: GPL
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2303,7 +2303,7 @@ 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
-Recommends: pfaat
+Suggests: pfaat
Homepage: http://pfaat.sourceforge.net/
License: GPL
Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
@@ -2321,7 +2321,7 @@ Comment: priam
project has only a "free as in beer" binary download - so this is not
for us ...
-Recommends: prot4est
+Suggests: prot4est
Homepage: http://xyala.cap.ed.ac.uk/bioinformatics/prot4EST/index.shtml
License: GPL
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2333,7 +2333,7 @@ Pkg-Description: EST protein translation suite
translating ESTs.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Recommends: qtlcart
+Suggests: qtlcart
Homepage: http://statgen.ncsu.edu/qtlcart/
License: GPL
Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
@@ -2346,7 +2346,7 @@ 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
-Recommends: rbs-finder
+Suggests: rbs-finder
Homepage: http://www.genomics.jhu.edu/RBSfinder/
License: not specified
Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2363,7 +2363,7 @@ 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
-Recommends: splitstree
+Suggests: 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>
@@ -2395,7 +2395,7 @@ Pkg-Description: Analyzing and Visualizing Evolutionary Data
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Recommends: taverna
+Suggests: taverna
Homepage: http://taverna.sourceforge.net/
License: LGPL
Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2420,7 +2420,7 @@ 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
-Recommends: taxinspector
+Suggests: taxinspector
Homepage: http://nebc.nox.ac.uk/projects/taxinspector.html
License: Artistic + other free licenses
Responsible: BioLinux - Tim Booth <tbooth at ceh.ac.uk>
@@ -2431,7 +2431,7 @@ 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
-Recommends: tetra
+Suggests: tetra
Homepage: http://www.megx.net/tetra/
License: free academic
Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2449,16 +2449,16 @@ 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
-Recommends: trace2dbest
+Suggests: trace2dbest
-Recommends: estscan
+Suggests: estscan
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Recommends: profit
+Suggests: profit
WNPP: 525428
Remark: The authors need to change the license, still.
-Recommends: obo-edit
+Suggests: 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
@@ -2470,7 +2470,7 @@ Pkg-Description: editor for biological ontologies
and part-of relations. Amongst the databases cureated by this tool
is the GeneOntology.
-Recommends: phagefinder
+Suggests: phagefinder
Homepage: http://phage-finder.sourceforge.net/
License: GPL
Language: Perl
@@ -2491,11 +2491,11 @@ 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.
-Recommends: compclust
+Suggests: compclust
X-Category: Genomics; Clustering analysis (+GUI)
Pkg-URL: http://woldlab.caltech.edu/compclust/debian_install.shtml
-Recommends: treebuilder3d
+Suggests: treebuilder3d
Homepage: http://www.bcgsc.ca/platform/bioinfo/software/treebuilder
License: GPL
Language: Java
@@ -2508,7 +2508,7 @@ 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.
-Recommends: excavator
+Suggests: excavator
Homepage: http://csbl.bmb.uga.edu/downloads/excavator/
License: GPL
Language: Java
@@ -2531,44 +2531,44 @@ 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
-Recommends: treetime
+Suggests: 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.
-Recommends: abacas
+Suggests: abacas
-Recommends: profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun
+Suggests: profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun
-Recommends: profphd-net, profphd-utils
+Suggests: profphd-net, profphd-utils
-Recommends: profphd
+Suggests: profphd
-Recommends: abyss
+Suggests: abyss
-Recommends: ampliconnoise
+Suggests: ampliconnoise
-Recommends: disulfinder
+Suggests: disulfinder
-Recommends: circos, runcircos-gui
+Suggests: circos, runcircos-gui
-Recommends: populations
+Suggests: populations
-Recommends: raccoon
+Suggests: raccoon
-Recommends: racon, spoa, rampler
+Suggests: racon, spoa, rampler
-Recommends: librg-utils-perl
+Suggests: librg-utils-perl
-Recommends: snap
+Suggests: snap
-Recommends: pyvcf, vcftools
+Suggests: pyvcf, vcftools
-Recommends: beads
+Suggests: beads
-Recommends: x-tandem-pipeline
+Suggests: x-tandem-pipeline
Homepage: http://pappso.inra.fr/bioinfo/xtandempipeline/
License: GPL
Language: Java
@@ -2593,7 +2593,7 @@ Pkg-Description: peptide/protein identification from MS/MS mass spectra
Suggests: maude
-Recommends: forge
+Suggests: forge
Homepage: http://combiol.org/forge/
License: Apache 2.0
Pkg-Description: genome assembler for mixed read types
@@ -2617,7 +2617,7 @@ 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.
-Recommends: metarep
+Suggests: metarep
License: MIT
Homepage: http://www.jcvi.org/metarep/
Pkg-Description: JCVI Metagenomics Reports
@@ -2650,7 +2650,7 @@ X-Pkg-Description: MEtaGenome ANalyzer
projects. In consequence, there is a dramatic increase in the volume of
sequence data to be analyzed.
-Recommends: arachne
+Suggests: arachne
Homepage: http://www.broadinstitute.org/crd/wiki/index.php/Arachne
License: free
Pkg-Description: toolkit for Whole Genome Shotgun Assembly
@@ -2669,7 +2669,7 @@ 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.
-Recommends: maker2
+Suggests: maker2
Homepage: http://www.yandell-lab.org/software/maker.html
License: GPL / Artistic
Pkg-Description: annotate genomes and create genome databases
@@ -2689,7 +2689,7 @@ Pkg-Description: annotate genomes and create genome databases
especially useful for emerging model organism projects with minimal
bioinformatics expertise and computer resources
-Recommends: rmblast
+Suggests: rmblast
Homepage: http://tandem.bu.edu/trf/trf.html
License: Same as blast2
Pkg-Description: RepeatMasker compatible version of the standard NCBI BLAST
@@ -2703,7 +2703,7 @@ 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.
-Recommends: e-hive
+Suggests: e-hive
Homepage: http://www.ensembl.org/info/docs/eHive/index.html
License: Not specified
Pkg-Description: distributed processing system based on 'autonomous agents'
@@ -2713,14 +2713,14 @@ 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.
-Recommends: cmap
+Suggests: 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.
-Recommends: gbrowse-syn
+Suggests: gbrowse-syn
Homepage: http://gmod.org/wiki/GBrowse_syn
License: Not specified
Pkg-Description: Generic Synteny Browser
@@ -2733,7 +2733,7 @@ Pkg-Description: Generic Synteny Browser
later). Working examples can be seen at TAIR and WormBase.
-Recommends: tripal
+Suggests: tripal
Homepage: http://tripal.info/
License: GPL ( as Drupal a derivative )
Pkg-Description: collection of Drupal modules for genomic research
@@ -2748,14 +2748,14 @@ Pkg-Description: collection of Drupal modules for genomic research
databases are projects of the Main Bioinformatics Laboratory at Washington
State University
-Recommends: genemark
+Suggests: 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.
-Recommends: annovar
+Suggests: annovar
Homepage: http://www.openbioinformatics.org/annovar/
License: Open Source for non-profit
Pkg-Description: annotate genetic variants detected from diverse genomes
@@ -2791,7 +2791,7 @@ Pkg-Description: annotate genetic variants detected from diverse genomes
"variants reduction" procedure, making it practical to handle hundreds
of human genomes in a day.
-Recommends: python3-orange
+Suggests: python3-orange
License: GPLv3
Homepage: http://orange.biolab.si/
Pkg-URL: http://orange.biolab.si/debian/
@@ -2802,7 +2802,7 @@ 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.
-Recommends: tigr-glimmer-mg
+Suggests: tigr-glimmer-mg
Comment: Several related R packages are listed at CRAN:
http://cran.r-project.org/web/views/Genetics.html
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/d272989338037be9ff8eb691a1ed8b8a2216c42d
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/d272989338037be9ff8eb691a1ed8b8a2216c42d
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