[Blends-commit] [Git][blends-team/med][master] Update bio
Steffen Möller
gitlab at salsa.debian.org
Sun Jun 21 17:06:42 BST 2020
Steffen Möller pushed to branch master at Debian Blends Team / med
Commits:
82fef035 by Steffen Möller at 2020-06-21T16:06:35+00:00
Update bio
- - - - -
1 changed file:
- tasks/bio
Changes:
=====================================
tasks/bio
=====================================
@@ -6,128 +6,128 @@ Description: Debian Med bioinformatics packages
X-Begin-Category: Phylogenetic analysis
-Recommends: altree
+Suggests: altree
-Recommends: beast-mcmc, beast2-mcmc
+Suggests: beast-mcmc, beast2-mcmc
-Recommends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle
+Suggests: fastdnaml, njplot, tree-puzzle | tree-ppuzzle
-Recommends: probalign
+Suggests: probalign
-Recommends: treeviewx
+Suggests: treeviewx
-Recommends: figtree
+Suggests: figtree
-Recommends: hyphy-mpi | hyphy-pt
+Suggests: hyphy-mpi | hyphy-pt
-Recommends: spread-phy
+Suggests: spread-phy
-Recommends: omegamap
+Suggests: omegamap
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Recommends: sweed
+Suggests: sweed
X-End-Category: Phylogenetic analysis
-Recommends: phylip
-Why: Phylogenetic analysis (Non-free, thus only suggested).
+Suggests: phylip
+Why: Phylogenetic analysis
X-Comment: treetool is removed from Debian because it is not maintained upstream since
1995 and cause the Xserver to freeze under Squeeze
-Recommends: fastlink, loki, plink, plink1.9, r-cran-qtl, r-cran-genabel, gemma, bolt-lmm
+Suggests: fastlink, loki, plink, plink1.9, r-cran-qtl, r-cran-genabel, gemma, bolt-lmm
Why: Genetics
X-Begin-Category: Sequence alignments and related programs.
-Recommends: amap-align
+Suggests: amap-align
Remark: Dead upstream
The homepage of this project vanished as well as the Download area. An
old unmaintained version remained at code.google.com. Please drop the
maintainer a note if you have any news of this project.
-Recommends: boxshade, gff2aplot, muscle, sim4, sibsim4, tabix, wise
+Suggests: boxshade, gff2aplot, muscle, sim4, sibsim4, tabix, wise
-Recommends: maqview
+Suggests: maqview
-Recommends: blasr
+Suggests: blasr
Recommends: daligner
Suggests: dascrubber
-Recommends: mhap
+Suggests: mhap
-Recommends: bwa
+Suggests: bwa
-Recommends: megahit
+Suggests: megahit
-Recommends: metabat
+Suggests: metabat
-Recommends: mummer, e-mem
+Suggests: mummer, e-mem
-Recommends: ncbi-blast+-legacy, plast
+Suggests: ncbi-blast+-legacy, plast
-Recommends: ncbi-blast+
+Suggests: ncbi-blast+
-Recommends: mafft
+Suggests: mafft
-Recommends: sra-toolkit
+Suggests: sra-toolkit
-Recommends: t-coffee
+Suggests: t-coffee
-Recommends: kalign
+Suggests: kalign
-Recommends: ghmm, hmmer
+Suggests: ghmm, hmmer
-Recommends: gramalign
+Suggests: gramalign
-Recommends: exonerate
+Suggests: exonerate
-Recommends: elph
+Suggests: elph
-Recommends: dialign
+Suggests: dialign
-Recommends: dialign-tx
+Suggests: dialign-tx
-Recommends: poa
+Suggests: poa
-Recommends: probcons
+Suggests: probcons
-Recommends: proda
+Suggests: proda
-Recommends: seaview
+Suggests: seaview
-Recommends: sigma-align
+Suggests: sigma-align
-Recommends: wham-align
+Suggests: wham-align
-Recommends: emboss
+Suggests: emboss
-Recommends: embassy-domalign, embassy-domainatrix, embassy-domsearch, embassy-phylip
+Suggests: embassy-domalign, embassy-domainatrix, embassy-domsearch, embassy-phylip
Suggests: emboss-explorer
Why: The EMBOSS sequence analysis suite and its galaxy.
-Recommends: arb
+Suggests: arb
Why: Sequence alignments and related programs (Non-free, thus only suggested).
-Recommends: clustalx, clustalo
+Suggests: clustalx, clustalo
-Recommends: clustalw
+Suggests: clustalw
-Recommends: mothur, bowtie, bowtie2
+Suggests: mothur, bowtie, bowtie2
-Recommends: transtermhp
+Suggests: transtermhp
X-End-Category: Sequence alignments and related programs.
X-Begin-Category: high-throughput sequencing
-Recommends: bustools
+Suggests: bustools
Suggests: dnapi
-Recommends: last-align, maq, ssake, velvet | velvet-long
+Suggests: last-align, maq, ssake, velvet | velvet-long
Recommends: qiime
@@ -156,20 +156,20 @@ Suggets: q2-taxa,
q2-quality-control,
q2-fragment-insertion
-Recommends: scoary
+Suggests: scoary
-Recommends: tophat,
+Suggests: tophat,
tophat-recondition
-Recommends: umap
+Suggests: umap
X-End-Category: high-throughput sequencing
X-Begin-Category: Analysis of RNA sequences.
-Recommends: infernal
+Suggests: infernal
-Recommends: rnahybrid
+Suggests: rnahybrid
Suggests: python3-anndata
@@ -181,17 +181,17 @@ X-End-Category: Analysis of RNA sequences.
X-Begin-Category: Molecular modelling and molecular dynamics
-Recommends: adun-core
+Suggests: adun-core
Suggests: adun.app
-Recommends: avogadro, garlic, gamgi, gdpc, ghemical, jmol, pymol, r-cran-bio3d, msxpertsuite
+Suggests: avogadro, garlic, gamgi, gdpc, ghemical, jmol, pymol, r-cran-bio3d, msxpertsuite
-Recommends: gromacs
+Suggests: gromacs
-Recommends: rasmol, viewmol, qutemol
+Suggests: rasmol, viewmol, qutemol
-Recommends: modeller
+Suggests: modeller
Pkg-URL: http://salilab.org/modeller/release.html#deb
Remark: The package is created independently from Debian Med or Debian Science.
The source code
@@ -206,31 +206,31 @@ Remark: The package is created independently from Debian Med or Debian Science.
X-End-Category: Molecular modelling and molecular dynamics
-Recommends: plasmidomics
+Suggests: plasmidomics
Why: Presentation
X-Begin-Category: Tools for the molecular biologist.
-Recommends: gff2ps, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, readseq, tigr-glimmer
+Suggests: gff2ps, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, readseq, tigr-glimmer
-Recommends: melting
+Suggests: melting
-Recommends: mipe
+Suggests: mipe
-Recommends: primer3
+Suggests: primer3
X-End-Category: Tools for the molecular biologist.
X-Begin-Category: Genome Browser
-Recommends: artemis
+Suggests: artemis
-Recommends: gbrowse
+Suggests: gbrowse
X-Importance: Academic ones are really expensive for commercial use
X-End-Category: Genome Browser
-Recommends: python3-biomaj3-daemon
+Suggests: python3-biomaj3-daemon
Ignore: mozilla-biofox
Remark: biofox was removed from Debian (see #727689)
@@ -238,66 +238,66 @@ Remark: biofox was removed from Debian (see #727689)
the removal. Please keep us informed if you become aware about
upstream changes that enable using this plugin for firefox >= 10.
-Recommends: glam2
+Suggests: glam2
Why: Motif search
-Recommends: raster3d
+Suggests: raster3d
-Recommends: phyml
+Suggests: phyml
-Recommends: autodock
+Suggests: autodock
Why: Molecular modelling and molecular dynamics.
-Recommends: autogrid
+Suggests: autogrid
-Recommends: autodock-vina
+Suggests: autodock-vina
-Recommends: mustang
+Suggests: mustang
-Recommends: probabel
+Suggests: probabel
-Recommends: theseus
+Suggests: theseus
-Recommends: staden-io-lib-utils
+Suggests: staden-io-lib-utils
-Recommends: samtools, bedtools, datamash
+Suggests: samtools, bedtools, datamash
-Recommends: gassst
+Suggests: gassst
-Recommends: hinge
+Suggests: hinge
-Recommends: r-bioc-hilbertvis
+Suggests: r-bioc-hilbertvis
Remark: It would be interesting to package HilbertVisGUI as well.
-Recommends: r-other-mott-happy.hbrem
+Suggests: r-other-mott-happy.hbrem
-Recommends: seq-gen
+Suggests: seq-gen
-Recommends: snp-sites
+Suggests: snp-sites
-Recommends: mira-assembler
+Suggests: mira-assembler
-Recommends: alien-hunter
+Suggests: alien-hunter
-Recommends: seqan-apps
+Suggests: seqan-apps
-Recommends: ncoils
+Suggests: ncoils
-Recommends: gentle
+Suggests: gentle
-Recommends: gmap
+Suggests: gmap
Recommends: igv
-Recommends: picard-tools
+Suggests: picard-tools
-Recommends: acedb-other
+Suggests: acedb-other
-Recommends: blixem, dotter, belvu
+Suggests: blixem, dotter, belvu
-Recommends: paml
+Suggests: paml
-Recommends: velvetoptimiser
+Suggests: velvetoptimiser
Recommends: ensembl
Pkg-URL: http://snapshot.debian.org/package/ensembl/63-1/
@@ -305,113 +305,113 @@ Remark: Ensembl was removed from Debian due #645487
Ensembl used to be in Debian experimental branch but was removed for formal reasons which
are explained in http://bugs.debian.org/645487
-Recommends: mrbayes
+Suggests: mrbayes
-Recommends: pdb2pqr
+Suggests: pdb2pqr
-Recommends: squizz
+Suggests: squizz
-Recommends: clonalframe, clonalframeml
+Suggests: clonalframe, clonalframeml
-Recommends: dssp
+Suggests: dssp
-Recommends: jellyfish, jellyfish1
+Suggests: jellyfish, jellyfish1
-Recommends: ballview
+Suggests: ballview
-Recommends: pynast
+Suggests: pynast
-Recommends: pizzly
+Suggests: pizzly
-Recommends: raxml
+Suggests: raxml
-Recommends: mlv-smile
+Suggests: mlv-smile
-Recommends: cd-hit
+Suggests: cd-hit
-Recommends: cufflinks
+Suggests: cufflinks
-Recommends: eigensoft
+Suggests: eigensoft
-Recommends: grinder
+Suggests: grinder
Recommends: jalview
-Recommends: reprof
+Suggests: reprof
-Recommends: tm-align
+Suggests: tm-align
-Recommends: norsnet
+Suggests: norsnet
-Recommends: norsp
+Suggests: norsp
-Recommends: predictnls
+Suggests: predictnls
-Recommends: prime-phylo
+Suggests: prime-phylo
-Recommends: proftmb
+Suggests: proftmb
-Recommends: profbval
+Suggests: profbval
-Recommends: profisis
+Suggests: profisis
-Recommends: hhsuite
+Suggests: hhsuite
-Recommends: ffindex
+Suggests: ffindex
-Recommends: flexbar
+Suggests: flexbar
-Recommends: blimps-utils
+Suggests: blimps-utils
Recommends: sift
-Recommends: neobio
+Suggests: neobio
-Recommends: ray
+Suggests: ray
Recommends: ugene
-Recommends: logol
+Suggests: logol
-Recommends: soapdenovo, soapdenovo2, soapsnp, soapaligner
+Suggests: soapdenovo, soapdenovo2, soapsnp, soapaligner
-Recommends: microbiomeutil, chimeraslayer, nast-ier, wigeon
+Suggests: microbiomeutil, chimeraslayer, nast-ier, wigeon
-Recommends: minia
+Suggests: minia
-Recommends: trimmomatic, trim-galore
+Suggests: trimmomatic, trim-galore
-Recommends: saint
+Suggests: saint
-Recommends: rtax
+Suggests: rtax
-Recommends: rate4site
+Suggests: rate4site
-Recommends: rna-star
+Suggests: rna-star
-Recommends: sailfish
+Suggests: sailfish
-Recommends: topp, openms
+Suggests: topp, openms
-Recommends: scythe
+Suggests: scythe
-Recommends: sickle
+Suggests: sickle
-Recommends: skewer
+Suggests: skewer
-Recommends: kmc
+Suggests: kmc
-Recommends: king-probe
+Suggests: king-probe
-Recommends: ncl-tools
+Suggests: ncl-tools
-Recommends: tvc
+Suggests: tvc
Suggests: science-workflow
-Recommends: libvcflib-tools
+Suggests: libvcflib-tools
-Recommends: bppsuite, bppphyview
+Suggests: bppsuite, bppphyview
Suggests: getdata
@@ -419,243 +419,243 @@ X-Mark: Prospective packages are starting here
X-Mark: Packages in Vcs - Information about these is queried from UDD as well
-Recommends: acacia
+Suggests: acacia
-Recommends: adapterremoval
+Suggests: adapterremoval
-Recommends: aegean
+Suggests: aegean
-Recommends: andi
+Suggests: andi
-Recommends: arden
+Suggests: arden
-Recommends: artfastqgenerator, art-nextgen-simulation-tools
+Suggests: artfastqgenerator, art-nextgen-simulation-tools
-Recommends: assemblytics
+Suggests: assemblytics
-Recommends: ataqv
+Suggests: ataqv
-Recommends: augustus
+Suggests: augustus
-Recommends: baitfisher
+Suggests: baitfisher
-Recommends: bandage
+Suggests: bandage
-Recommends: beagle
+Suggests: beagle
-Recommends: bedops
+Suggests: bedops
-Recommends: biceps
+Suggests: biceps
Remark: Mentioned at http://www.renard.it/, developed in RKI
-Recommends: cnvkit
+Suggests: cnvkit
-Recommends: csb
+Suggests: csb
-Recommends: diamond-aligner
+Suggests: diamond-aligner
-Recommends: python3-emperor
+Suggests: python3-emperor
-Recommends: euler2, euler-sr
+Suggests: euler2, euler-sr
-Recommends: fitgcp
+Suggests: fitgcp
-Recommends: gasic
+Suggests: gasic
-Recommends: ipig
+Suggests: ipig
-Recommends: aevol
+Suggests: aevol
-Recommends: alter-sequence-alignment
+Suggests: alter-sequence-alignment
-Recommends: amos-assembler, hawkeye
+Suggests: amos-assembler, hawkeye
Language: Perl
-Recommends: anfo
+Suggests: anfo
Recommends: apollo
-Recommends: aragorn
+Suggests: aragorn
-Recommends: ariba
+Suggests: ariba
-Recommends: arvados
+Suggests: arvados
-Recommends: assembly-stats
+Suggests: assembly-stats
-Recommends: atac
+Suggests: atac
-Recommends: atropos
+Suggests: atropos
-Recommends: augur
+Suggests: augur
-Recommends: axe-demultiplexer
+Suggests: axe-demultiplexer
-Recommends: axparafit, axpcoords
+Suggests: axparafit, axpcoords
-Recommends: bali-phy
+Suggests: bali-phy
-Recommends: barrnap
+Suggests: barrnap
-Recommends: bamtools
+Suggests: bamtools
-Recommends: bagpipe
+Suggests: bagpipe
-Recommends: bax2bam
+Suggests: bax2bam
Recommends: bcbio
-Recommends: bcftools
+Suggests: bcftools
-Recommends: bigsdb
+Suggests: bigsdb
-Recommends: bio-eagle
+Suggests: bio-eagle
-Recommends: bio-tradis
+Suggests: bio-tradis
-Recommends: biobambam2
+Suggests: biobambam2
-Recommends: biosyntax
+Suggests: biosyntax
-Recommends: bismark
+Suggests: bismark
-Recommends: bitseq
+Suggests: bitseq
-Recommends: blat
+Suggests: blat
-Recommends: blobology
+Suggests: blobology
-Recommends: bio-rainbow
+Suggests: bio-rainbow
-Recommends: braker
+Suggests: braker
-Recommends: busco
+Suggests: busco
-Recommends: card-rgi
+Suggests: card-rgi
-Recommends: cassiopee
+Suggests: cassiopee
-Recommends: cat-bat
+Suggests: cat-bat
-Recommends: ccs
+Suggests: ccs
-Recommends: cdbfasta
+Suggests: cdbfasta
-Recommends: centrifuge
+Suggests: centrifuge
-Recommends: cellprofiler
+Suggests: cellprofiler
-Recommends: chromhmm
+Suggests: chromhmm
-Recommends: cgview, brig, cct
+Suggests: cgview, brig, cct
-Recommends: cinema
+Suggests: cinema
Language: Java
-Recommends: circlator
+Suggests: circlator
-Recommends: clearcut
+Suggests: clearcut
-Recommends: clonalorigin
+Suggests: clonalorigin
-Recommends: cluster3
+Suggests: cluster3
-Recommends: chromimpute
+Suggests: chromimpute
-Recommends: codonw
+Suggests: codonw
-Recommends: condetri
+Suggests: condetri
-Recommends: contrafold
+Suggests: contrafold
-Recommends: covtobed
+Suggests: covtobed
-Recommends: crac
+Suggests: crac
-Recommends: crossbow
+Suggests: crossbow
X-Category: Sequencing
-Recommends: crux-toolkit
+Suggests: crux-toolkit
-Recommends: cutadapt
+Suggests: cutadapt
Recommends: cytoscape
-Recommends: dawg
+Suggests: dawg
-Recommends: dazzdb
+Suggests: dazzdb
-Recommends: dazzle
+Suggests: dazzle
-Recommends: deepbinner
+Suggests: deepbinner
-Recommends: delly
+Suggests: delly
-Recommends: deepnano
+Suggests: deepnano
Remark: There is no intend to keep continue the existing packaging since
the program nanocall seems to serve the intended purpose better
-Recommends: dendroscope
+Suggests: dendroscope
-Recommends: dindel
+Suggests: dindel
-Recommends: drop-seq-tools
+Suggests: drop-seq-tools
-Recommends: dwgsim
+Suggests: dwgsim
-Recommends: ea-utils
+Suggests: ea-utils
-Recommends: ecell
+Suggests: ecell
-Recommends: ecopcr
+Suggests: ecopcr
-Recommends: edtsurf
+Suggests: edtsurf
-Recommends: emmax
+Suggests: emmax
-Recommends: ensembl-vep
+Suggests: ensembl-vep
-Recommends: examl, raxml-ng
+Suggests: examl, raxml-ng
-Recommends: exabayes
+Suggests: exabayes
-Recommends: berkeley-express
+Suggests: berkeley-express
-Recommends: falcon
+Suggests: falcon
-Recommends: fasta3
+Suggests: fasta3
-Recommends: fasttree
+Suggests: fasttree
-Recommends: fastahack
+Suggests: fastahack
-Recommends: fastaq
+Suggests: fastaq
-Recommends: fastml
+Suggests: fastml
-Recommends: fastp
+Suggests: fastp
-Recommends: fastqc
+Suggests: fastqc
-Recommends: fastqtl
+Suggests: fastqtl
-Recommends: flappie
+Suggests: flappie
-Recommends: flash
+Suggests: flash
-Recommends: flye
+Suggests: flye
-Recommends: ffp
+Suggests: ffp
-Recommends: fieldbioinformatics
+Suggests: fieldbioinformatics
-Recommends: filtlong
+Suggests: filtlong
-Recommends: unc-fish
+Suggests: unc-fish
-Recommends: fml-asm
+Suggests: fml-asm
-Recommends: forester
+Suggests: forester
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-amd64
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
BioLinux was following the upstream name change to archaeopteryx and thus the
@@ -663,11 +663,11 @@ Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
.
The binary package is full of JARs without source.
-Recommends: freecontact
+Suggests: freecontact
-Recommends: freebayes
+Suggests: freebayes
-Recommends: fsa
+Suggests: fsa
Enhances: t-coffee
Remark: Precondition for T-Coffee
see http://wiki.debian.org/DebianMed/TCoffee
@@ -675,9 +675,9 @@ Remark: Precondition for T-Coffee
Upstream address bounced when contacting about segfaults so it seems to be
dead upstream and no good code quality.
-Recommends: fsm-lite
+Suggests: fsm-lite
-Recommends: garli
+Suggests: garli
Recommends: gatb-core
View it on GitLab: https://salsa.debian.org/blends-team/med/-/commit/82fef035750880267dd6de6734c3dc4971a17dde
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