[Blends-commit] [SCM] med branch, master, updated. 4a52ab0d229f69140efbba3d235a758257cf12be
Steffen Moeller
moeller at debian.org
Thu Sep 21 16:55:03 UTC 2017
The following commit has been merged in the master branch:
commit 4a52ab0d229f69140efbba3d235a758257cf12be
Author: Steffen Moeller <moeller at debian.org>
Date: Thu Sep 21 18:54:02 2017 +0200
Moved many packages from bio to bio-ngs.
diff --git a/tasks/bio b/tasks/bio
index d87bc7d..3fca599 100644
--- a/tasks/bio
+++ b/tasks/bio
@@ -41,9 +41,7 @@ Remark: Dead upstream
old unmaintained version remained at code.google.com. Please drop the
maintainer a note if you have any news of this project.
-Recommends: boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4, tabix, tophat, wise
-
-Recommends: maqview
+Recommends: boxshade, gff2aplot, muscle, sim4, sibsim4, tabix, wise
Recommends: blasr
@@ -63,8 +61,6 @@ Recommends: ncbi-blast+
Recommends: mafft
-Recommends: sra-toolkit
-
Recommends: t-coffee
Recommends: kalign
@@ -100,19 +96,10 @@ Recommends: clustalx, clustalo
Recommends: clustalw
-Recommends: mothur, bowtie, bowtie2
-
Recommends: transtermhp
X-End-Category: Sequence alignments and related programs.
-X-Begin-Category: high-throughput sequencing
-
-Recommends: last-align, maq, ssake, velvet | velvet-long
-
-Recommends: qiime
-
-X-End-Category: high-throughput sequencing
X-Begin-Category: Analysis of RNA sequences.
@@ -221,10 +208,6 @@ Recommends: r-other-mott-happy.hbrem
Recommends: seq-gen
-Recommends: snp-sites
-
-Recommends: mira-assembler
-
Recommends: alien-hunter
Recommends: seqan-apps
@@ -235,18 +218,12 @@ Recommends: gentle
Recommends: gmap
-Recommends: igv
-
-Recommends: picard-tools
-
Recommends: acedb-other-dotter, acedb-other-belvu, acedb-other
Recommends: python-cogent
Recommends: paml
-Recommends: velvetoptimiser
-
Recommends: ensembl
Pkg-URL: http://snapshot.debian.org/package/ensembl/63-1/
Remark: Ensembl was removed from Debian due #645487
@@ -277,14 +254,10 @@ Suggests: cain
Recommends: cd-hit
-Recommends: cufflinks
-
Recommends: r-bioc-cummerbund
Recommends: eigensoft
-Recommends: grinder
-
Recommends: jalview
Recommends: reprof
@@ -309,8 +282,6 @@ Recommends: hhsuite
Recommends: ffindex
-Recommends: flexbar
-
Recommends: blimps-utils
Recommends: sift
@@ -323,28 +294,16 @@ Recommends: ugene
Recommends: logol-bin
-Recommends: soapdenovo, soapdenovo2
-
-Recommends: microbiomeutil, chimeraslayer, nast-ier, wigeon
+Recommends: chimeraslayer, nast-ier
Recommends: minia
-Recommends: trimmomatic
-
Recommends: saint
-Recommends: rtax
-
Recommends: rate4site
-Recommends: rna-star
-
Recommends: topp, openms
-Recommends: scythe
-
-Recommends: sickle
-
Recommends: kmc
Recommends: king-probe
@@ -355,8 +314,6 @@ Recommends: tvc
Suggests: science-workflow
-Recommends: libvcflib-tools
-
Recommends: bppsuite, bppphyview
Suggests: getdata
@@ -373,10 +330,6 @@ Recommends: aegean
Recommends: andi
-Recommends: arden
-
-Recommends: artfastqgenerator, art-nextgen-simulation-tools
-
Recommends: augustus
Recommends: baitfisher
@@ -402,8 +355,6 @@ Recommends: fitgcp
Recommends: gasic
-Recommends: giira
-
Recommends: ipig
Recommends: aevol
@@ -413,8 +364,6 @@ Recommends: alter-sequence-alignment
Recommends: amos-assembler, hawkeye
Language: Perl
-Recommends: anfo
-
Recommends: apollo
Recommends: aragorn
@@ -429,13 +378,8 @@ Recommends: axparafit, axpcoords
Recommends: barrnap
-Recommends: bamtools
-
Recommends: bagpipe
-Recommends: bcftools
-WNPP: 804007
-
Recommends: bigsdb
Recommends: bio-eagle
@@ -448,8 +392,6 @@ Recommends: blat
Recommends: blobology
-Recommends: bio-rainbow
-
Recommends: card-rgi
Recommends: cassiopee
@@ -477,15 +419,11 @@ Recommends: condetri
Recommends: contrafold
-Recommends: crac
-
Recommends: crossbow
X-Category: Sequencing
Recommends: crux-toolkit
-Recommends: cutadapt
-
Recommends: cytoscape
Recommends: dawg
@@ -494,16 +432,6 @@ Recommends: dazzdb
Recommends: dazzle
-Recommends: deepnano
-Remark: There is no intend to keep continue the existing packaging since
- the program nanocall seems to serve the intended purpose better
-
-Recommends: dindel
-
-Recommends: dwgsim
-
-Recommends: ea-utils
-
Recommends: ecell
Recommends: ecopcr
@@ -516,8 +444,6 @@ Recommends: examl, raxml-ng
Recommends: exabayes
-Recommends: berkeley-express
-
Recommends: falcon
Recommends: fasta3
@@ -526,20 +452,14 @@ Recommends: fasttree
Recommends: fastahack
-Recommends: fastaq
-
Recommends: fastml
-Recommends: fastqc
-
Recommends: fastqtl
Recommends: ffp
Recommends: unc-fish
-Recommends: fml-asm
-
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
@@ -560,8 +480,6 @@ 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
-
Recommends: garli
Recommends: gatk
@@ -582,10 +500,6 @@ Recommends: haploview
Recommends: harvest-tools
-Recommends: hilive
-
-Recommends: hisat2
-
Recommends: hmmer2
Remark: This older version of HMMER is used in some applications
While Debian has HMMER 3 since some time there are users of
@@ -594,14 +508,10 @@ Remark: This older version of HMMER is used in some applications
Recommends: htqc
-Recommends: idba
-
Recommends: indelible
Recommends: iqtree
-Recommends: iva
-
Recommends: jaligner
Recommends: jbrowse
@@ -613,10 +523,6 @@ Recommends: kempbasu
Recommends: kineticstools
WNPP: 797676
-Recommends: kissplice
-
-Recommends: kraken
-
Recommends: lagan
X-Category: Comparative genomics
@@ -632,8 +538,6 @@ Recommends: logomat-m
Recommends: kclust
-Recommends: khmer
-
Recommends: kmer
Recommends: radiant
@@ -642,8 +546,6 @@ Recommends: lefse
Recommends: mach-haplotyper
-Recommends: macs
-
Recommends: macsyfinder
Recommends: maffilter
@@ -654,8 +556,6 @@ Recommends: malt
Recommends: manta
-Recommends: mapdamage
-
Recommends: martj
Recommends: mash
@@ -704,8 +604,6 @@ Recommends: nanocall
Recommends: nanook
-Recommends: nanopolish
-
Recommends: ncbi-entrez-direct
WNPP: 810949
@@ -727,8 +625,6 @@ Recommends: r-other-apmswapp
Recommends: pal2nal
-Recommends: paleomix
-
Recommends: paraclu
Recommends: parsinsert
@@ -744,15 +640,8 @@ Language: Java
Recommends: pbalign, pbbarcode, pbdagcon
-Recommends: pbsuite
-WNPP: 807802
-
Recommends: pbgenomicconsensus
-Recommends: pbjelly, pbhoney
-
-Recommends: pbh5tools
-
Recommends: pbsim
Recommends: pcma
@@ -789,16 +678,10 @@ Recommends: pipasic, inspect, tide
Recommends: physamp
-Recommends: pirs
-
-Recommends: placnet
-
Recommends: plato
Recommends: plip
-Recommends: poretools
-
Recommends: prank
Recommends: predictprotein
@@ -829,25 +712,21 @@ Recommends: python-reaper
Recommends: python-treetime
-Recommends: qcumber
-
Recommends: qtltools
Recommends: qualimap
-Recommends: quorum
-
Recommends: rambo-k
Recommends: rapmap
Recommends: 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
+Recommends: r-bioc-dnacopy, r-bioc-geneplotter
Recommends: r-bioc-mergeomics
-Recommends: r-bioc-metagenomeseq, r-bioc-phyloseq
+Recommends: r-bioc-phyloseq
Recommends: r-bioc-ebseq
@@ -905,28 +784,18 @@ Recommends: rsat
Recommends: rsem
-Recommends: sambamba
-
-Recommends: salmon
-
Recommends: sap
Remark: Precondition for T-Coffee
see http://wiki.debian.org/DebianMed/TCoffee
Recommends: scrm
-Recommends: sga
-
Recommends: seer
Recommends: segemehl
-Recommends: seqprep
-
Recommends: seqsero
-Recommends: seqtk
-
Recommends: sequenceconverter.app
Remark: Formerly part of Debian as biococoa.app but removed
The package was part of Debian under the name biococoa.app which is confusing
@@ -943,38 +812,17 @@ Recommends: situs
Recommends: sim4db
-Recommends: smalt
-Remark: This can be regarded as successor of ssaha2
- This program is from the same author as ssaha2 and according to its author
- faster and more precise than ssaha2 (except for sequences > 2000bp).
-
Recommends: smithwaterman
Recommends: ssw-align
-Recommends: smrtanalysis
-
Recommends: snpeff
-Recommends: snpomatic
-
-Recommends: sortmerna
-
-Recommends: snap-aligner
-
-Recommends: sniffles
-
Recommends: spaced
WNPP: 815672
-Recommends: spades
-
Recommends: sparta
-Recommends: sprai
-
-Recommends: srst2
-
Recommends: ssaha
Remark: Successor for ssaha2 available: smalt
The program smalt is from the same author is according to its author
@@ -984,17 +832,11 @@ Recommends: sspace
Recommends: staden
-Recommends: stacks
-
Recommends: strap, strap-base
Language: Java
-Recommends: subread
-
Recommends: suitename
-Recommends: sumatra, sumaclust
-
Recommends: sumtrees
Recommends: surankco
@@ -1015,8 +857,6 @@ Recommends: tnseq-transit
Recommends: tn-seqexplorer
-Recommends: transrate-tools
-
Recommends: treeview
X-Category: Visualisation
@@ -1024,11 +864,6 @@ 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
-
-Recommends: uc-echo
-X-Category: NGS
-
Recommends: varna
Recommends: varmatch
@@ -1040,20 +875,11 @@ X-Category: Secondary structure of nucleic acids
Recommends: vmd
-Recommends: vsearch
-
-Recommends: canu
-Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-
Recommends: zalign
Recommends: zodiac-zeden
Language: C, C++
-Recommends: discosnp, mapsembler2
-
-Recommends: dnaclust
-
X-Mark: The information below needs to be checked whether it can be obtained from Vcs or needs to stay here
Recommends: copycat
@@ -2692,8 +2518,6 @@ Recommends: librg-utils-perl
Recommends: snap
-Recommends: vcftools
-
Suggests: mobyle, mobyle-programs, mobyle-tutorials
Recommends: hilbertvisgui
diff --git a/tasks/bio-ngs b/tasks/bio-ngs
index 6b721d0..2f9f6da 100644
--- a/tasks/bio-ngs
+++ b/tasks/bio-ngs
@@ -1,11 +1,8 @@
Task: Next Generation Sequencing
Metapackage: false
Description: Debian Med bioinformatics applications usable in Next Generation Sequencing
- It aims at gettting packages which specializes in alignment of
- sequences produced by next generation sequencing.
-
-Comment: Do not build a metapackage because it is not clear in how far this set of
- packages is complete regarding NGS.
+ It aims at gettting packages which specialize in the processing or interpretation of
+ data generated with next- (and later-) generation high-thoughput sequencing technologies.
Recommends:
bedtools,
@@ -31,18 +28,198 @@ Recommends:
vcftools,
velvet
-Recommends: sprai
+Recommends: libvcflib-tools
+
+
+X-Begin -Category: metagenomics
Recommends: mothur
Recommends: qiime
+Recommends: microbiomeutil
+
+Recommends: r-bioc-metagenomeseq
+
+Recommends: rtax
+
+Recommends: sortmerna
+
+Recommends: srst2
+
+Recommends: stacks
+
+Recommends: subread
+
+Recommends: sumatra, sumaclust
+
+Recommends: vsearch
+
+Recommends: wigeon
+
+X-End-Category: metagenomics
+
+
+Recommends: anfo
+
+Recommends: arden
+
+Recommends: bowtie, bowtie2
+
+Recommends: artfastqgenerator, art-nextgen-simulation-tools
+
+Recommends: last-align, maq, ssake, velvet | velvet-long
+
+Recommends: bamtools
+
+Recommends: bcftools
+WNPP: 804007
+
+Recommends: berkeley-express
+
+Recommends: bio-rainbow
+
+Recommends: canu
+Remark: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Recommends: crac
+
Recommends: cufflinks
+Recommends: cutadapt
+
+Recommends: deepnano
+Remark: There is no intend to keep continue the existing packaging since
+ the program nanocall seems to serve the intended purpose better
+
+Recommends: dindel
+
+Recommends: discosnp
+
+Recommends: dnaclust
+
+Recommends: dwgsim
+
+Recommends: ea-utils
+
+Recommends: fastaq
+
+Recommends: fastqc
+
+Recommends: fastx-toolkit
+
+Recommends: flexbar
+
+Recommends: fml-asm
+
+Recommends: fsm-lite
+
+Recommends: grinder
+
+Recommends: giira
+
Recommends: hinge
+Recommends: hilive
+
+Recommends: hisat2
+
+Recommends: idba
+
+Recommends: igv
+
+Recommends: iva
+
+Recommends: khmer
+
+Recommends: kissplice
+
+Recommends: kraken
+
+Recommends: macs
+
+Recommends: mapdamage
+
+Recommends: maqview
+
Recommends: mira-assembler
+Recommends: mapsembler2
+
+Recommends: nanopolish
+
+Recommends: paleomix
+
+Recommends: pbsuite
+WNPP: 807802
+
+Recommends: pbh5tools
+
+Recommends: pbjelly, pbhoney
+
+Recommends: pirs
+
+Recommends: placnet
+
+Recommends: poretools
+
+Recommends: qcumber
+
+Recommends: quorum
+
+Recommends: r-bioc-deseq2
+
+Recommends: salmon
+
+Recommends: sambamba
+
+Recommends: scythe
+
+Recommends: seqprep
+
+Recommends: seqtk
+
+Recommends: sga
+
+Recommends: sickle
+
+Recommends: smalt
+Remark: This can be regarded as successor of ssaha2
+ This program is from the same author as ssaha2 and according to its author
+ faster and more precise than ssaha2 (except for sequences > 2000bp).
+
+Recommends: smrtanalysis
+
+Recommends: snap-aligner
+
+Recommends: sniffles
+
+Recommends: snp-sites
+
+Recommends: snpomatic
+
+Recommends: soapdenovo, soapdenovo2
+
+Recommends: spades
+
+Recommends: sprai
+
+Recommends: sra-toolkit
+
+Recommends: tophat
+
+Recommends: transrate-tools
+
+Recommends: trimmomatic
+
+Recommends: trinityrnaseq
+
+Recommends: uc-echo
+X-Category: NGS
+
+Recommends: velvetoptimiser
+
+
X-Mark: Prospective packages are starting here.
Recommends: kissplice
--
Debian Med metapackages
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