[Blends-commit] [Git][blends-team/med][master] 2 commits: More packages in list (even more to come later)
Andreas Tille
gitlab at salsa.debian.org
Thu Jul 16 13:36:04 BST 2020
Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
6f051a3a by Andreas Tille at 2020-07-16T14:30:57+02:00
More packages in list (even more to come later)
- - - - -
d1b8e269 by Andreas Tille at 2020-07-16T14:35:11+02:00
Revert "Update bio" - Steffen, please stop mass-degrading Recommends to Suggests. I've thought this is settled for the moment. Thank you.
This reverts commit 82fef035750880267dd6de6734c3dc4971a17dde.
- - - - -
2 changed files:
- covid-19_doc/bio_covid-19_dependencies_query
- tasks/bio
Changes:
=====================================
covid-19_doc/bio_covid-19_dependencies_query
=====================================
@@ -249,7 +249,11 @@ INSERT INTO covid19_packages VALUES
(DEFAULT,'wham-align'),
(DEFAULT,'yanagiba'),
(DEFAULT,'yanosim'),
+(DEFAULT,'libargs-dev'),
+(DEFAULT,'libatomicqueue-dev'),
(DEFAULT,'libatomicbitvector-dev'),
+(DEFAULT,'libconcurrentqueue-dev'),
+(DEFAULT,'tao-json'),
(DEFAULT,'python3-h5py'),
(DEFAULT,'python3-numpy'),
(DEFAULT,'python3-pandas'),
=====================================
tasks/bio
=====================================
@@ -6,41 +6,41 @@ Description: Debian Med bioinformatics packages
X-Begin-Category: Phylogenetic analysis
-Suggests: altree
+Recommends: altree
-Suggests: beast-mcmc, beast2-mcmc
+Recommends: beast-mcmc, beast2-mcmc
-Suggests: fastdnaml, njplot, tree-puzzle | tree-ppuzzle
+Recommends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle
-Suggests: probalign
+Recommends: probalign
-Suggests: treeviewx
+Recommends: treeviewx
-Suggests: figtree
+Recommends: figtree
-Suggests: hyphy-mpi | hyphy-pt
+Recommends: hyphy-mpi | hyphy-pt
-Suggests: spread-phy
+Recommends: spread-phy
-Suggests: omegamap
+Recommends: omegamap
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-Suggests: sweed
+Recommends: sweed
X-End-Category: Phylogenetic analysis
-Suggests: phylip
-Why: Phylogenetic analysis
+Recommends: phylip
+Why: Phylogenetic analysis (Non-free, thus only suggested).
X-Comment: treetool is removed from Debian because it is not maintained upstream since
1995 and cause the Xserver to freeze under Squeeze
-Suggests: fastlink, loki, plink, plink1.9, r-cran-qtl, r-cran-genabel, gemma, bolt-lmm
+Recommends: fastlink, loki, plink, plink1.9, r-cran-qtl, r-cran-genabel, gemma, bolt-lmm
Why: Genetics
X-Begin-Category: Sequence alignments and related programs.
-Suggests: amap-align
+Recommends: amap-align
Remark: Dead upstream
The homepage of this project vanished as well as the Download area. An
old unmaintained version remained at code.google.com. Please drop the
@@ -48,88 +48,88 @@ Remark: Dead upstream
Suggests: conda-package-handling
-Suggests: boxshade, gff2aplot, muscle, sim4, sibsim4, tabix, wise
+Recommends: boxshade, gff2aplot, muscle, sim4, sibsim4, tabix, wise
-Suggests: maqview
+Recommends: maqview
-Suggests: blasr
+Recommends: blasr
Recommends: daligner
Suggests: dascrubber
-Suggests: mhap
+Recommends: mhap
-Suggests: bwa
+Recommends: bwa
-Suggests: megahit
+Recommends: megahit
-Suggests: metabat
+Recommends: metabat
-Suggests: mummer, e-mem
+Recommends: mummer, e-mem
-Suggests: ncbi-blast+-legacy, plast
+Recommends: ncbi-blast+-legacy, plast
-Suggests: ncbi-blast+
+Recommends: ncbi-blast+
-Suggests: mafft
+Recommends: mafft
-Suggests: sra-toolkit
+Recommends: sra-toolkit
-Suggests: t-coffee
+Recommends: t-coffee
-Suggests: kalign
+Recommends: kalign
-Suggests: ghmm, hmmer
+Recommends: ghmm, hmmer
-Suggests: gramalign
+Recommends: gramalign
-Suggests: exonerate
+Recommends: exonerate
-Suggests: elph
+Recommends: elph
-Suggests: dialign
+Recommends: dialign
-Suggests: dialign-tx
+Recommends: dialign-tx
-Suggests: poa
+Recommends: poa
-Suggests: probcons
+Recommends: probcons
-Suggests: proda
+Recommends: proda
-Suggests: seaview
+Recommends: seaview
-Suggests: sigma-align
+Recommends: sigma-align
-Suggests: wham-align
+Recommends: wham-align
-Suggests: emboss
+Recommends: emboss
-Suggests: embassy-domalign, embassy-domainatrix, embassy-domsearch, embassy-phylip
+Recommends: embassy-domalign, embassy-domainatrix, embassy-domsearch, embassy-phylip
Suggests: emboss-explorer
Why: The EMBOSS sequence analysis suite and its galaxy.
-Suggests: arb
+Recommends: arb
Why: Sequence alignments and related programs (Non-free, thus only suggested).
-Suggests: clustalx, clustalo
+Recommends: clustalx, clustalo
-Suggests: clustalw
+Recommends: clustalw
-Suggests: mothur, bowtie, bowtie2
+Recommends: mothur, bowtie, bowtie2
-Suggests: transtermhp
+Recommends: transtermhp
X-End-Category: Sequence alignments and related programs.
X-Begin-Category: high-throughput sequencing
-Suggests: bustools
+Recommends: bustools
Suggests: dnapi
-Suggests: last-align, maq, ssake, velvet | velvet-long
+Recommends: last-align, maq, ssake, velvet | velvet-long
Recommends: qiime
@@ -158,12 +158,12 @@ Suggets: q2-taxa,
q2-quality-control,
q2-fragment-insertion
-Suggests: scoary
+Recommends: scoary
-Suggests: tophat,
+Recommends: tophat,
tophat-recondition
-Suggests: umap
+Recommends: umap
Suggests: python3-intake
@@ -179,9 +179,9 @@ X-End-Category: high-throughput sequencing
X-Begin-Category: Analysis of RNA sequences.
-Suggests: infernal
+Recommends: infernal
-Suggests: rnahybrid
+Recommends: rnahybrid
Suggests: python3-anndata
@@ -189,17 +189,17 @@ X-End-Category: Analysis of RNA sequences.
X-Begin-Category: Molecular modelling and molecular dynamics
-Suggests: adun-core
+Recommends: adun-core
Suggests: adun.app
-Suggests: avogadro, garlic, gamgi, gdpc, ghemical, jmol, pymol, r-cran-bio3d, msxpertsuite
+Recommends: avogadro, garlic, gamgi, gdpc, ghemical, jmol, pymol, r-cran-bio3d, msxpertsuite
-Suggests: gromacs
+Recommends: gromacs
-Suggests: rasmol, viewmol, qutemol
+Recommends: rasmol, viewmol, qutemol
-Suggests: modeller
+Recommends: 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
@@ -214,31 +214,31 @@ Remark: The package is created independently from Debian Med or Debian Science.
X-End-Category: Molecular modelling and molecular dynamics
-Suggests: plasmidomics
+Recommends: plasmidomics
Why: Presentation
X-Begin-Category: Tools for the molecular biologist.
-Suggests: gff2ps, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, readseq, tigr-glimmer
+Recommends: gff2ps, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, readseq, tigr-glimmer
-Suggests: melting
+Recommends: melting
-Suggests: mipe
+Recommends: mipe
-Suggests: primer3
+Recommends: primer3
X-End-Category: Tools for the molecular biologist.
X-Begin-Category: Genome Browser
-Suggests: artemis
+Recommends: artemis
-Suggests: gbrowse
+Recommends: gbrowse
X-Importance: Academic ones are really expensive for commercial use
X-End-Category: Genome Browser
-Suggests: python3-biomaj3-daemon
+Recommends: python3-biomaj3-daemon
Ignore: mozilla-biofox
Remark: biofox was removed from Debian (see #727689)
@@ -246,66 +246,66 @@ 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.
-Suggests: glam2
+Recommends: glam2
Why: Motif search
-Suggests: raster3d
+Recommends: raster3d
-Suggests: phyml
+Recommends: phyml
-Suggests: autodock
+Recommends: autodock
Why: Molecular modelling and molecular dynamics.
-Suggests: autogrid
+Recommends: autogrid
-Suggests: autodock-vina
+Recommends: autodock-vina
-Suggests: mustang
+Recommends: mustang
-Suggests: probabel
+Recommends: probabel
-Suggests: theseus
+Recommends: theseus
-Suggests: staden-io-lib-utils
+Recommends: staden-io-lib-utils
-Suggests: samtools, bedtools, datamash
+Recommends: samtools, bedtools, datamash
-Suggests: gassst
+Recommends: gassst
-Suggests: hinge
+Recommends: hinge
-Suggests: r-bioc-hilbertvis
+Recommends: r-bioc-hilbertvis
Remark: It would be interesting to package HilbertVisGUI as well.
-Suggests: r-other-mott-happy.hbrem
+Recommends: r-other-mott-happy.hbrem
-Suggests: seq-gen
+Recommends: seq-gen
-Suggests: snp-sites
+Recommends: snp-sites
-Suggests: mira-assembler
+Recommends: mira-assembler
-Suggests: alien-hunter
+Recommends: alien-hunter
-Suggests: seqan-apps
+Recommends: seqan-apps
-Suggests: ncoils
+Recommends: ncoils
-Suggests: gentle
+Recommends: gentle
-Suggests: gmap
+Recommends: gmap
Recommends: igv
-Suggests: picard-tools
+Recommends: picard-tools
-Suggests: acedb-other
+Recommends: acedb-other
-Suggests: blixem, dotter, belvu
+Recommends: blixem, dotter, belvu
-Suggests: paml
+Recommends: paml
-Suggests: velvetoptimiser
+Recommends: velvetoptimiser
Recommends: ensembl
Pkg-URL: http://snapshot.debian.org/package/ensembl/63-1/
@@ -313,113 +313,113 @@ 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
-Suggests: mrbayes
+Recommends: mrbayes
-Suggests: pdb2pqr
+Recommends: pdb2pqr
-Suggests: squizz
+Recommends: squizz
-Suggests: clonalframe, clonalframeml
+Recommends: clonalframe, clonalframeml
-Suggests: dssp
+Recommends: dssp
-Suggests: jellyfish, jellyfish1
+Recommends: jellyfish, jellyfish1
-Suggests: ballview
+Recommends: ballview
-Suggests: pynast
+Recommends: pynast
-Suggests: pizzly
+Recommends: pizzly
-Suggests: raxml
+Recommends: raxml
-Suggests: mlv-smile
+Recommends: mlv-smile
-Suggests: cd-hit
+Recommends: cd-hit
-Suggests: cufflinks
+Recommends: cufflinks
-Suggests: eigensoft
+Recommends: eigensoft
-Suggests: grinder
+Recommends: grinder
Recommends: jalview
-Suggests: reprof
+Recommends: reprof
-Suggests: tm-align
+Recommends: tm-align
-Suggests: norsnet
+Recommends: norsnet
-Suggests: norsp
+Recommends: norsp
-Suggests: predictnls
+Recommends: predictnls
-Suggests: prime-phylo
+Recommends: prime-phylo
-Suggests: proftmb
+Recommends: proftmb
-Suggests: profbval
+Recommends: profbval
-Suggests: profisis
+Recommends: profisis
-Suggests: hhsuite
+Recommends: hhsuite
-Suggests: ffindex
+Recommends: ffindex
-Suggests: flexbar
+Recommends: flexbar
-Suggests: blimps-utils
+Recommends: blimps-utils
Recommends: sift
-Suggests: neobio
+Recommends: neobio
-Suggests: ray
+Recommends: ray
Recommends: ugene
-Suggests: logol
+Recommends: logol
-Suggests: soapdenovo, soapdenovo2, soapsnp, soapaligner
+Recommends: soapdenovo, soapdenovo2, soapsnp, soapaligner
-Suggests: microbiomeutil, chimeraslayer, nast-ier, wigeon
+Recommends: microbiomeutil, chimeraslayer, nast-ier, wigeon
-Suggests: minia
+Recommends: minia
-Suggests: trimmomatic, trim-galore
+Recommends: trimmomatic, trim-galore
-Suggests: saint
+Recommends: saint
-Suggests: rtax
+Recommends: rtax
-Suggests: rate4site
+Recommends: rate4site
-Suggests: rna-star
+Recommends: rna-star
-Suggests: sailfish
+Recommends: sailfish
-Suggests: topp, openms
+Recommends: topp, openms
-Suggests: scythe
+Recommends: scythe
-Suggests: sickle
+Recommends: sickle
-Suggests: skewer
+Recommends: skewer
-Suggests: kmc
+Recommends: kmc
-Suggests: king-probe
+Recommends: king-probe
-Suggests: ncl-tools
+Recommends: ncl-tools
-Suggests: tvc
+Recommends: tvc
Suggests: science-workflow
-Suggests: libvcflib-tools
+Recommends: libvcflib-tools
-Suggests: bppsuite, bppphyview
+Recommends: bppsuite, bppphyview
Suggests: getdata
@@ -427,251 +427,251 @@ X-Mark: Prospective packages are starting here
X-Mark: Packages in Vcs - Information about these is queried from UDD as well
-Suggests: acacia
+Recommends: acacia
-Suggests: adapterremoval
+Recommends: adapterremoval
-Suggests: aegean
+Recommends: aegean
-Suggests: andi
+Recommends: andi
-Suggests: arden
+Recommends: arden
-Suggests: artfastqgenerator, art-nextgen-simulation-tools
+Recommends: artfastqgenerator, art-nextgen-simulation-tools
-Suggests: assemblytics
+Recommends: assemblytics
-Suggests: ataqv
+Recommends: ataqv
-Suggests: augustus
+Recommends: augustus
-Suggests: baitfisher
+Recommends: baitfisher
-Suggests: bandage
+Recommends: bandage
-Suggests: bbmap
+Recommends: bbmap
-Suggests: bcalm
+Recommends: bcalm
-Suggests: beagle
+Recommends: beagle
-Suggests: bedops
+Recommends: bedops
-Suggests: biceps
+Recommends: biceps
Remark: Mentioned at http://www.renard.it/, developed in RKI
-Suggests: cnvkit
+Recommends: cnvkit
-Suggests: csb
+Recommends: csb
-Suggests: diamond-aligner
+Recommends: diamond-aligner
-Suggests: python3-emperor
+Recommends: python3-emperor
-Suggests: euler2, euler-sr
+Recommends: euler2, euler-sr
-Suggests: fitgcp
+Recommends: fitgcp
-Suggests: gasic
+Recommends: gasic
-Suggests: ipig
+Recommends: ipig
-Suggests: aevol
+Recommends: aevol
-Suggests: alter-sequence-alignment
+Recommends: alter-sequence-alignment
-Suggests: amos-assembler, hawkeye
+Recommends: amos-assembler, hawkeye
Language: Perl
-Suggests: anfo
+Recommends: anfo
Recommends: apollo
-Suggests: aragorn
+Recommends: aragorn
-Suggests: ariba
+Recommends: ariba
-Suggests: arvados
+Recommends: arvados
-Suggests: assembly-stats
+Recommends: assembly-stats
-Suggests: atac
+Recommends: atac
-Suggests: atropos
+Recommends: atropos
-Suggests: augur
+Recommends: augur
-Suggests: axe-demultiplexer
+Recommends: axe-demultiplexer
-Suggests: axparafit, axpcoords
+Recommends: axparafit, axpcoords
-Suggests: bali-phy
+Recommends: bali-phy
-Suggests: barrnap
+Recommends: barrnap
-Suggests: bamtools
+Recommends: bamtools
-Suggests: bagpipe
+Recommends: bagpipe
-Suggests: bax2bam
+Recommends: bax2bam
Recommends: bcbio
-Suggests: bcftools
+Recommends: bcftools
-Suggests: bigsdb
+Recommends: bigsdb
-Suggests: bio-eagle
+Recommends: bio-eagle
-Suggests: bio-tradis
+Recommends: bio-tradis
-Suggests: biobambam2
+Recommends: biobambam2
-Suggests: biosyntax
+Recommends: biosyntax
-Suggests: bismark
+Recommends: bismark
-Suggests: bitseq
+Recommends: bitseq
-Suggests: blat
+Recommends: blat
-Suggests: blobology
+Recommends: blobology
-Suggests: bio-rainbow
+Recommends: bio-rainbow
-Suggests: braker
+Recommends: braker
-Suggests: busco
+Recommends: busco
-Suggests: card-rgi
+Recommends: card-rgi
-Suggests: cassiopee
+Recommends: cassiopee
-Suggests: cat-bat
+Recommends: cat-bat
-Suggests: ccs
+Recommends: ccs
-Suggests: cdbfasta
+Recommends: cdbfasta
-Suggests: centrifuge
+Recommends: centrifuge
-Suggests: cellprofiler
+Recommends: cellprofiler
-Suggests: chromhmm
+Recommends: chromhmm
-Suggests: cgview, brig, cct
+Recommends: cgview, brig, cct
-Suggests: cinema
+Recommends: cinema
Language: Java
-Suggests: circlator
+Recommends: circlator
-Suggests: clearcut
+Recommends: clearcut
-Suggests: clonalorigin
+Recommends: clonalorigin
-Suggests: cluster3
+Recommends: cluster3
-Suggests: chromimpute
+Recommends: chromimpute
-Suggests: codonw
+Recommends: codonw
-Suggests: condetri
+Recommends: condetri
-Suggests: contrafold
+Recommends: contrafold
-Suggests: covtobed
+Recommends: covtobed
-Suggests: crac
+Recommends: crac
-Suggests: crossbow
+Recommends: crossbow
X-Category: Sequencing
-Suggests: crux-toolkit
+Recommends: crux-toolkit
-Suggests: cutadapt
+Recommends: cutadapt
Recommends: dextractor
Recommends: cytoscape
-Suggests: dawg
+Recommends: dawg
-Suggests: dazzdb
+Recommends: dazzdb
-Suggests: dazzle
+Recommends: dazzle
-Suggests: deepbinner
+Recommends: deepbinner
-Suggests: delly
+Recommends: delly
-Suggests: deepnano
+Recommends: deepnano
Remark: There is no intend to keep continue the existing packaging since
the program nanocall seems to serve the intended purpose better
-Suggests: dendroscope
+Recommends: dendroscope
-Suggests: dindel
+Recommends: dindel
-Suggests: drop-seq-tools
+Recommends: drop-seq-tools
-Suggests: dwgsim
+Recommends: dwgsim
-Suggests: ea-utils
+Recommends: ea-utils
-Suggests: ecell
+Recommends: ecell
-Suggests: ecopcr
+Recommends: ecopcr
-Suggests: edtsurf
+Recommends: edtsurf
-Suggests: emmax
+Recommends: emmax
-Suggests: ensembl-vep
+Recommends: ensembl-vep
Suggests: epigrass
-Suggests: examl, raxml-ng
+Recommends: examl, raxml-ng
-Suggests: exabayes
+Recommends: exabayes
-Suggests: berkeley-express
+Recommends: berkeley-express
-Suggests: falcon
+Recommends: falcon
-Suggests: fasta3
+Recommends: fasta3
-Suggests: fasttree
+Recommends: fasttree
-Suggests: fastahack
+Recommends: fastahack
-Suggests: fastaq
+Recommends: fastaq
-Suggests: fastml
+Recommends: fastml
-Suggests: fastp
+Recommends: fastp
-Suggests: fastqc
+Recommends: fastqc
-Suggests: fastqtl
+Recommends: fastqtl
-Suggests: flappie
+Recommends: flappie
-Suggests: flash
+Recommends: flash
-Suggests: flye
+Recommends: flye
-Suggests: ffp
+Recommends: ffp
-Suggests: fieldbioinformatics
+Recommends: fieldbioinformatics
-Suggests: filtlong
+Recommends: filtlong
-Suggests: unc-fish
+Recommends: unc-fish
-Suggests: fml-asm
+Recommends: fml-asm
-Suggests: forester
+Recommends: forester
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-amd64
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
BioLinux was following the upstream name change to archaeopteryx and thus the
@@ -679,11 +679,11 @@ Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
.
The binary package is full of JARs without source.
-Suggests: freecontact
+Recommends: freecontact
-Suggests: freebayes
+Recommends: freebayes
-Suggests: fsa
+Recommends: fsa
Enhances: t-coffee
Remark: Precondition for T-Coffee
see http://wiki.debian.org/DebianMed/TCoffee
@@ -691,9 +691,9 @@ Remark: Precondition for T-Coffee
Upstream address bounced when contacting about segfaults so it seems to be
dead upstream and no good code quality.
-Suggests: fsm-lite
+Recommends: fsm-lite
-Suggests: garli
+Recommends: garli
Recommends: gatb-core
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/26035fed5503e0529a0db0f406801059ee11b5f9...d1b8e269d50fa39ea231919aee15f0c8f495f5ad
--
View it on GitLab: https://salsa.debian.org/blends-team/med/-/compare/26035fed5503e0529a0db0f406801059ee11b5f9...d1b8e269d50fa39ea231919aee15f0c8f495f5ad
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/blends-commit/attachments/20200716/576627f6/attachment-0001.html>
More information about the Blends-commit
mailing list