[Blends-commit] [SCM] med branch, master, updated. fd524fa961ee64a0168f3b4c67963f65d1a423eb
Andreas Tille
tille at debian.org
Fri Sep 22 14:42:22 UTC 2017
The following commit has been merged in the master branch:
commit fd524fa961ee64a0168f3b4c67963f65d1a423eb
Author: Andreas Tille <tille at debian.org>
Date: Fri Sep 22 16:41:57 2017 +0200
Restore old bio task
diff --git a/tasks/bio b/tasks/bio
index 3fca599..d87bc7d 100644
--- a/tasks/bio
+++ b/tasks/bio
@@ -41,7 +41,9 @@ 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, gff2aplot, muscle, sim4, sibsim4, tabix, wise
+Recommends: boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4, tabix, tophat, wise
+
+Recommends: maqview
Recommends: blasr
@@ -61,6 +63,8 @@ Recommends: ncbi-blast+
Recommends: mafft
+Recommends: sra-toolkit
+
Recommends: t-coffee
Recommends: kalign
@@ -96,10 +100,19 @@ 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.
@@ -208,6 +221,10 @@ Recommends: r-other-mott-happy.hbrem
Recommends: seq-gen
+Recommends: snp-sites
+
+Recommends: mira-assembler
+
Recommends: alien-hunter
Recommends: seqan-apps
@@ -218,12 +235,18 @@ 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
@@ -254,10 +277,14 @@ Suggests: cain
Recommends: cd-hit
+Recommends: cufflinks
+
Recommends: r-bioc-cummerbund
Recommends: eigensoft
+Recommends: grinder
+
Recommends: jalview
Recommends: reprof
@@ -282,6 +309,8 @@ Recommends: hhsuite
Recommends: ffindex
+Recommends: flexbar
+
Recommends: blimps-utils
Recommends: sift
@@ -294,16 +323,28 @@ Recommends: ugene
Recommends: logol-bin
-Recommends: chimeraslayer, nast-ier
+Recommends: soapdenovo, soapdenovo2
+
+Recommends: microbiomeutil, chimeraslayer, nast-ier, wigeon
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
@@ -314,6 +355,8 @@ Recommends: tvc
Suggests: science-workflow
+Recommends: libvcflib-tools
+
Recommends: bppsuite, bppphyview
Suggests: getdata
@@ -330,6 +373,10 @@ Recommends: aegean
Recommends: andi
+Recommends: arden
+
+Recommends: artfastqgenerator, art-nextgen-simulation-tools
+
Recommends: augustus
Recommends: baitfisher
@@ -355,6 +402,8 @@ Recommends: fitgcp
Recommends: gasic
+Recommends: giira
+
Recommends: ipig
Recommends: aevol
@@ -364,6 +413,8 @@ Recommends: alter-sequence-alignment
Recommends: amos-assembler, hawkeye
Language: Perl
+Recommends: anfo
+
Recommends: apollo
Recommends: aragorn
@@ -378,8 +429,13 @@ Recommends: axparafit, axpcoords
Recommends: barrnap
+Recommends: bamtools
+
Recommends: bagpipe
+Recommends: bcftools
+WNPP: 804007
+
Recommends: bigsdb
Recommends: bio-eagle
@@ -392,6 +448,8 @@ Recommends: blat
Recommends: blobology
+Recommends: bio-rainbow
+
Recommends: card-rgi
Recommends: cassiopee
@@ -419,11 +477,15 @@ Recommends: condetri
Recommends: contrafold
+Recommends: crac
+
Recommends: crossbow
X-Category: Sequencing
Recommends: crux-toolkit
+Recommends: cutadapt
+
Recommends: cytoscape
Recommends: dawg
@@ -432,6 +494,16 @@ 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
@@ -444,6 +516,8 @@ Recommends: examl, raxml-ng
Recommends: exabayes
+Recommends: berkeley-express
+
Recommends: falcon
Recommends: fasta3
@@ -452,14 +526,20 @@ 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
@@ -480,6 +560,8 @@ 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
@@ -500,6 +582,10 @@ 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
@@ -508,10 +594,14 @@ 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
@@ -523,6 +613,10 @@ Recommends: kempbasu
Recommends: kineticstools
WNPP: 797676
+Recommends: kissplice
+
+Recommends: kraken
+
Recommends: lagan
X-Category: Comparative genomics
@@ -538,6 +632,8 @@ Recommends: logomat-m
Recommends: kclust
+Recommends: khmer
+
Recommends: kmer
Recommends: radiant
@@ -546,6 +642,8 @@ Recommends: lefse
Recommends: mach-haplotyper
+Recommends: macs
+
Recommends: macsyfinder
Recommends: maffilter
@@ -556,6 +654,8 @@ Recommends: malt
Recommends: manta
+Recommends: mapdamage
+
Recommends: martj
Recommends: mash
@@ -604,6 +704,8 @@ Recommends: nanocall
Recommends: nanook
+Recommends: nanopolish
+
Recommends: ncbi-entrez-direct
WNPP: 810949
@@ -625,6 +727,8 @@ Recommends: r-other-apmswapp
Recommends: pal2nal
+Recommends: paleomix
+
Recommends: paraclu
Recommends: parsinsert
@@ -640,8 +744,15 @@ Language: Java
Recommends: pbalign, pbbarcode, pbdagcon
+Recommends: pbsuite
+WNPP: 807802
+
Recommends: pbgenomicconsensus
+Recommends: pbjelly, pbhoney
+
+Recommends: pbh5tools
+
Recommends: pbsim
Recommends: pcma
@@ -678,10 +789,16 @@ Recommends: pipasic, inspect, tide
Recommends: physamp
+Recommends: pirs
+
+Recommends: placnet
+
Recommends: plato
Recommends: plip
+Recommends: poretools
+
Recommends: prank
Recommends: predictprotein
@@ -712,21 +829,25 @@ 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-dnacopy, r-bioc-geneplotter
+Recommends: r-bioc-deseq2, r-bioc-dnacopy, r-bioc-geneplotter
Recommends: r-bioc-mergeomics
-Recommends: r-bioc-phyloseq
+Recommends: r-bioc-metagenomeseq, r-bioc-phyloseq
Recommends: r-bioc-ebseq
@@ -784,18 +905,28 @@ 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
@@ -812,17 +943,38 @@ 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
@@ -832,11 +984,17 @@ Recommends: sspace
Recommends: staden
+Recommends: stacks
+
Recommends: strap, strap-base
Language: Java
+Recommends: subread
+
Recommends: suitename
+Recommends: sumatra, sumaclust
+
Recommends: sumtrees
Recommends: surankco
@@ -857,6 +1015,8 @@ Recommends: tnseq-transit
Recommends: tn-seqexplorer
+Recommends: transrate-tools
+
Recommends: treeview
X-Category: Visualisation
@@ -864,6 +1024,11 @@ 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
@@ -875,11 +1040,20 @@ 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
@@ -2518,6 +2692,8 @@ Recommends: librg-utils-perl
Recommends: snap
+Recommends: vcftools
+
Suggests: mobyle, mobyle-programs, mobyle-tutorials
Recommends: hilbertvisgui
--
Debian Med metapackages
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