Re: Please do not do heavy changes on metapackages without discussion (Was: [Git][blends-team/med][master] Update bio - substituted (most) recommendations with suggestions)

[Steffen Möller <steffen_moeller@gmx.de>]

Hi Andreas,


On 24.06.20 18:44, Andreas Tille wrote:
> Hi Steffen,
>
> your recent change to the bio task was quite invasive.  I think
> we should discuss those things here first.  Leaving just daligner,
> jalview (which is severely broken due to missing upgradres), qiime
> and r-cran-rotl does not make sense at all.

you are right. I should not have done that. Sorry.

No, those leftovers should not be recommended either. ;o)


> So please, before any massive change is done that changes the nature of
> metapackages and might break user expectations that have grown over time
> should be discussed here.
>
> As I explained I have created a new branch demote-recommends that
> can be used as a sandbox for a more fine grained metapackage layout.
> But please do not to massive changes in the production branch without
> any discussion.

In the past you explained (or I understood) you meant the "bio" task to
be a bit of a summary of everything available and a superset of bio-dev
and bio-ngs. And I agree that we need something like this - just for us
to see what should be updated, basically, and of others to see what is
out there, that is more then the Debian Med QA page. But to auto-derive
an installation of these packages - this is no longer feasible, I tend
to think and I feel that we agree on that.

My expectation is that our users are after on or two use cases/workflows
that will vertically install all the required tools. They don't install
five different workflows for RNA-seq analyses but decide for one (or
two). We have no means to express "please make a pick among those
packages that are equal", though.

So, the bio-task list I suggest not to install anything. And likely
neither the bio-dev task list. And then we need something expressing
(partial) functional equivalence to support a user-driven selection. My
hunch is, and I think also the somewhat unspoken idea from the last
sprints, that the EDAM ontology directs us towards it. For the moment,
that annotation is too sparse and not detailed enough - but ... to
describe a few tens of packages properly from where we then derive
installation directions - that sounds doable. I imagine to derive the
kind of lists you are vaguely describing in an automated manner from the
UDD (which you had engineered to parse the d/u/edam annotation already).

Best,

Steffen


> On Tue, Jun 23, 2020 at 04:56:46PM +0000, Steffen Möller wrote:
> > 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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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@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
> > You're receiving this email because of your account on salsa.debian.org.
> >
> >
> > _______________________________________________
> > Blends-commit mailing list
> > Blends-commit@alioth-lists.debian.net
> > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/blends-commit