Author: plessy
Date: Mon Sep 22 06:32:43 2014
New Revision: 4059
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=4059
Log:
First draft of the cloud package.
Modified:
projects/med/trunk/debian-med/tasks/cloud
Modified: projects/med/trunk/debian-med/tasks/cloud
URL:
http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/cloud?rev=4059&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/cloud (original)
+++ projects/med/trunk/debian-med/tasks/cloud Mon Sep 22 06:32:43 2014
@@ -7,54 +7,73 @@
X-Begin-Category: Phylogenetic analysis
Depends:
- altree, fastdnaml, phyml, tree-puzzle | tree-ppuzzle
+ altree, clearcut, fastdnaml, fasttree, parsinsert, phyml, phyutility,
+ prime-phylo, mrbayes, tree-puzzle | tree-ppuzzle
X-End-Category: Phylogenetic analysis
-X-Begin-Category: Genetics
+X-Begin-Category: Genetics and genomics
Depends:
- alien-hunter, bagpipe, fastlink, loki, plink, r-cran-qtl,
- r-other-valdar-bagphenotype.library, r-other-mott-happy
+ alien-hunter, bagpipe, fastlink, loki, gasic, genometools, plink,
+ probabel, r-cran-qtl, r-other-valdar-bagphenotype.library,
r-other-mott-happy
X-End-Category: Genetics
X-Begin-Category: Sequence alignments and related programs.
Depends:
- amap-align, blast2, boxshade, dialign, dialign-tx, exonerate,
- fastx-toolkit, gff2aplot, glam2, gmap, hmmer, kalign, mafft, mummer,
- muscle, poa, probcons, proda, python-pynast, sibsim4, sigma-align,
- sim4, t-coffee, vcftools, wise
-Depends:
- clustalw | clustalw-mpi
-Comment: non-free
+ amap-align, blast2, biosquid, boxshade, cassiopee, cdbfasta, cd-hit,
+ clustalo, clustalw, conservation-code, dialign, dialign-tx,
+ emboss, embassy-domalign, embassy-domainatrix, embassy-domsearch,
+ embassy-phylip, exonerate, gff2aplot, gff2ps, glam2, gmap, hmmer,
+ jellyfish, kalign, mafft, mlv-smile, mummer, muscle, neobio, poa, prank,
+ probcons, proda, python-pynast, sibsim4, sigma-align, sim4, snap,
+ squizz, t-coffee, wise, zalign
X-End-Category: Sequence alignments and related programs.
-
-X-Begin-Category: EMBOSS
-Depends:
- emboss, embassy-domalign, embassy-domainatrix, embassy-domsearch,
- embassy-phylip
-X-End-Category: EMBOSS
X-Begin-Category: High throughput sequencing
Depends:
- bedtools, bwa, filo, last-align, maq, picard-tools, r-bioc-hilbertvis,
- samtools, ssake, tophat, velvet
+ bamtools, bedtools, fastx-toolkit, flexbar, picard-tools, samtools,
+ tabix, vcftools
+Comment: Processing
+Depends:
+ anfo, cufflinks, bowtie, bowtie2, bwa, last-align, maq, perm, tophat,
smalt
+ soapdenovo, soapdenovo2
+Comment: Aligners
+Depends:
+ abyss, mapsembler2, idba, minia, mira, ssake, velvet
+Comment: Assembly
+Depends:
+ ampliconnoise, arden, fastqc
+Comment: Filtering and QC
+Depends:
+ discosnp, dnaclust, fitgcp, giira, grinder, kissplice, macs, mothur,
+ r-bioc-hilbertvis, sra-sdk
+Comment: Other
X-End-Category: High throughput sequencing
X-Begin-Category: Analysis of RNA sequences.
Depends:
- infernal, rnahybrid
+ aragorn, infernal, rnahybrid, rtax
X-End-Category: Analysis of RNA sequences.
X-Begin-Category: Molecular modelling and molecular dynamics
Depends:
- gromacs, mustang, theseus
-Depends: autodock, raster3d
+ autodock, autodock-vina, autogrid, coils, concavity, dssp, freecontact,
+ gromacs, hhsuite, mustang, pdb2pqr, raster3d, theseus
Comment: non-free
X-End-Category: Molecular modelling and molecular dynamics
X-Begin-Category: Tools for the molecular biologist.
Depends:
- acedb-other, melting, mipe, ncbi-epcr, ncbi-tools-bin, ncoils, primer3,
+ melting, mipe, ncbi-epcr, primer3
+Comment: Oligonucleotides and PCR
+Depends:
+ acedb-other, disulfinder, ncbi-tools-bin, ncoils,
readseq, tigr-glimmer, seqan-apps, staden-io-libs-utils
Depends: python-cogent
Comment: non-free
X-End-Category: Tools for the molecular biologist.
+
+X-Begin-Category: Others
+Depends:
+ aevol, biomaj, bioperl, bioperl-run, cain, clonalframe, circos,
datamash, filo,
+ prodigal, python-biopython, python3-biopython, qiime, r-bioc-edger,
+ r-cran-pvclust, r-cran-vegan
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