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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
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