Task: Cloud
Description: Debian Med bioinformatics applications usable in cloud computing
 This metapackage will install Debian packages related to molecular biology,
 structural biology and bioinformatics for use in life sciences, that do not
 depend on graphical toolkits and therefore can fit on system images for use
 in cloud computing clusters, where space can be limited.

X-Begin-Category: Phylogenetic analysis
Depends: \
	altree, clearcut, fastdnaml, fasttree, parsinsert, phyml, phyutility,
	prime-phylo, mrbayes, tree-puzzle | tree-ppuzzle
X-End-Category: Phylogenetic analysis

X-Begin-Category: Genetics and genomics
Depends: \
	alien-hunter, bagpipe, fastlink, loki, gasic, genometools, plink,
	probabel, r-cran-qtl, r-other-valdar-bagphenotype.library, r-other-mott-happy.hbrem
X-End-Category: Genetics

X-Begin-Category: Sequence alignments and related programs.
Depends: \
	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, pynast, sibsim4, sigma-align, sim4, snap,
	squizz, t-coffee, wise, zalign
X-End-Category: Sequence alignments and related programs.

X-Begin-Category: High throughput sequencing
Depends: \
	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-assembler, ssake, velvet
Comment: Assembly

Depends: \
	ampliconnoise, arden, fastqc
Comment: Filtering and QC

Depends: \
	discosnp, dnaclust, fitgcp, giira, grinder, kissplice, macs, mothur,
	paraclu, r-bioc-hilbertvis, sra-toolkit
Comment: Other
X-End-Category: High throughput sequencing

X-Begin-Category: Analysis of RNA sequences.
Depends: \
	aragorn, infernal, rnahybrid, rtax
X-End-Category: Analysis of RNA sequences.

X-Begin-Category: Molecular modelling and molecular dynamics
Depends: \
	autodock, autodock-vina, autogrid, 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: \
	melting, mipe, ncbi-epcr, primer3
Comment: Oligonucleotides and PCR

Depends: \
	acedb-other, disulfinder, ncbi-tools-bin, ncoils, python-cogent,
	readseq, tigr-glimmer, seqan-apps, staden-io-lib-utils
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
