[Blends-commit] r4059 - /projects/med/trunk/debian-med/tasks/cloud

Mon Sep 22 06:32:43 UTC 2014

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


