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# Packager Package Revision Test
linuxbrew hello 1 test $(/brew/bin/hello -g 'Hello_World') = 'Hello_World'
linuxbrew base64 1 echo -n mulled | /brew/bin/base64 | grep 'bXVsbGVk'
linuxbrew coreutils 1 test $(/brew/bin/factor 15 | tr ' ' '_') = '15:_3_5'
linuxbrew sha2 1 test $(echo -n mulled | /brew/bin/sha2 -256 -q) = '950af197b83c2b315d43232ffb1e11118874fd02e4a4d1d2baf93cea419feb5d'
alpine go 1 go version | grep 'go version'
alpine irssi 1 irssi -v
alpine mksh 1 mksh -v
alpine task 1 /usr/bin/task --version
alpine jq 1 test $(/usr/bin/jq -M -n -c '[true, (4+3)]') = '[true,7]'
alpine postgresql 1 postgres -V
alpine mtr 1 /usr/sbin/mtr -v
alpine znc 1 /usr/bin/znc -v
alpine bc 1 test $(echo '2+3' | bc -q) = '5'
conda bedtools 2.25.0--2 bedtools
conda bowtie2 2.2.5--py35_2 bowtie2 --version
conda bowtie2 2.2.8--py35_2 bowtie2 --version
conda circos 0.69.2--0 circos -v
conda circexplorer 0.1--py35_1 CIRCexplorer.py --help
conda circexplorer 1.1.9--py35_0 CIRCexplorer.py --help
conda perl-bioperl 1.6.924--6 perl -e 'use Bio::Seq;'
conda lighter 1.1.1--1 lighter -h
conda tmux 1.9a--1 tmux -V
conda tmux 2.1--1 tmux -V
conda barrnap 0.7--1 barrnap --help 2>&1 | grep Options > /dev/null
conda eoulsan 2.0_beta4--1 eoulsan.sh --version
conda metilene 0.2.6--r3.2.2_0 metilene --help 2>&1 | grep VERSION
conda m4 1.4.17--0 test $(echo 'define(a, bbb)a' | m4) = 'bbb'
conda openmg 0.1--0 openmg -h 2>&1 | grep 'Optional Parameters'
conda samtools 1.3--1 samtools --version
conda samtools 1.0--0 samtools --version
conda pyrad 3.0.64--py27_0 pyrad -h
conda bwa 0.7.13--1 bwa 2>&1 | grep 'alignment via Burrows-Wheeler' > /dev/null
conda bamtools 2.4.0--3 bamtools --help
conda stacks 1.37--0 cstacks 2>&1 | grep cstacks
conda stacks 1.40--0 cstacks 2>&1 | grep cstacks
conda stacks 1.40--1 cstacks 2>&1 | grep cstacks
conda r-vegan 2.3_4--r3.2.2_1 R -e 'library(''vegan'')'
conda cufflinks 2.2.1--py27_1 (cuffmerge --help 2>&1) | grep Options > /dev/null
conda tophat 2.1.0--py27_0 (tophat --version 2>&1) > /dev/null
conda curl 7.45.0--1 curl --fail icanhazip.com
conda bcftools 1.3--0 bcftools --version
conda deeptools 2.2.2--py27_0 bamCompare --version
conda deeptools 2.2.3--py27_0 bamCompare --version
conda bowtie 1.1.2--py35_1 (bowtie --version 2>&1) > /dev/null
conda metaphlan2 2.2.0--py27_1 metaphlan2.py -v
conda hifive 1.3.0--py27_0 python -c 'import hifive'
conda carna 1.3.1--3 carna --help
conda chemfp 1.1p1--py27_0 python -c 'import chemfp'
conda infernal 1.1.1--0 cmsearch -h
conda intarna 1.2.5--1 IntaRNA -h
conda locarna 1.8.9--2 locarna --version
conda rnacode 0.3--0 RNAcode --help
conda rnashapes 2.1.6--0 RNAshapes -h
conda rnastructure 5.7--1 refold -h
conda rnaz 2.1--1 RNAz -h
conda sortmerna 2.0--1 sortmerna --version
conda viennarna 2.2.5--2 RNAfold --version
conda mash 1.1--0 mash -h
conda rdkit 2015.09.2--py27_boost1.57_0 python -c 'import rdkit'
conda autodock-vina 1.1.2--0 vina --help
conda align_it 1.0.3--2 align-it --help
conda bamhash 1.0--0 bamhash_checksum_bam --version
conda hicexplorer 0.1--py27_0 hicBuildMatrix --version
conda r-yaml 2.1.13--r3.2.2_0 Rscript -e 'library(''yaml'')'
conda bioconductor-gagedata 2.8.0--0 Rscript -e 'library(''gageData'')'
conda bioconductor-gage 2.21.1--0 Rscript -e 'library(''gage'')'
conda bioconductor-genefilter 1.52.1--r3.2.2_0 Rscript -e 'library(''genefilter'')'
conda bioconductor-affy 1.48.0--0 Rscript -e 'library(''affy'')'
conda bioconductor-deseq 1.22.1--r3.2.2_0 Rscript -e 'library(''DESeq'')'
conda bioconductor-limma 3.26.9--0 Rscript -e 'library(''limma'')'
conda age-metasv 2015.01.29.3--0 age_align
conda abyss 1.9.0--0 ABYSS --version
conda amos 3.1.0--py35_3 Minimo -h > /dev/null
conda bioconductor-gosemsim 1.28.2--0 Rscript -e 'library(''GOSemSim'')'
conda last 719--py27_1 lastal -V &> /dev/null
conda biobambam 2.0.42--0 bamsormadup --help
conda khmer 2.0--py27_1 python -c 'import khmer'
conda kid 0.9.6--py27_1 python -c 'import kid'
conda kraken 0.10.6_eaf8fb68--2 kraken --version 2>&1 > /dev/null
conda bioblend 0.7.0--py27_0 python -c 'import bioblend'
conda impute2 2.3.2--0 impute2 2>&1 | grep IMPUTE
conda keepalive 0.5--py27_0 python -c 'import keepalive'
conda abricate 0.2--0 abricate --help 2>&1 | grep ResFinder > /dev/null
conda bioconductor-go.db 3.2.2--0 Rscript -e 'library(''GO.db'')'
conda fiji 20141125--3 fiji --help
conda art 3.19.15--1 art_illumina -sam -i test.fasta -l 150 -ss MS -f 10 -o illumina_test
conda lastz 1.0.2--0 lastz --version 2>&1 | grep 1.02.00 > /dev/null
conda kallisto 0.42.4--2 kallisto | grep Usage > /dev/null
conda cancerit-allelecount 2.1.2--1 alleleCounter -h
conda julia 0.4.5--1 test $(julia -e "print(2+3)") = "5"
conda ccat 3.0--1 CCAT --help
conda cdbtools 0.99--1 cdbfasta -v
conda ceas 1.0.2--py27_0 ceas --version > /dev/null
conda chanjo 3.3.0--py27_0 chanjo --help
conda cnvkit 0.7.11--py27_0 cnvkit.py -h
conda cobra 0.4.0--py27_0 python -c 'import cobra'
conda crossmap 0.2.2--py27_2 CrossMap.py
conda cyvcf2 0.3.0--py27_0 python -c 'import cyvcf2'
conda sambamba 0.6.1--0 sambamba view
conda star 2.5.1b--0 STAR --version
conda theta2 0.7--py27_0 RunTHetA.py -h
conda opsin 2.1.0--1 opsin --help
conda ddocent 2.1--0 dDocent --help
conda peptide-shaker 1.1.3--1 peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI
conda searchgui 2.1.4--1 searchgui eu.isas.searchgui.cmd.FastaCLI
conda mothur 1.36.1--boost1.60_2 mothur '#help()'
conda macs2 2.1.1--r3.2.2_0 macs2 --version 2>&1 > /dev/null
conda sam 3.5--0 buildmodel -v
conda qiime 1.9.1--py27_0 python -c 'import qiime'
conda biom-format 2.1.5--py35_3 python -c 'import biom'
conda ucsc-addcols 324--0 which addCols
conda ucsc-axttomaf 324--0 which axtToMaf
conda ucsc-axttopsl 324--0 which axtToPsl
conda ucsc-bedclip 324--0 which bedClip
conda ucsc-bedcommonregions 324--0 which bedCommonRegions
conda ucsc-bedcoverage 324--0 which bedCoverage
conda ucsc-bedextendranges 324--0 which bedExtendRanges
conda ucsc-bedgeneparts 324--0 which bedGeneParts
conda ucsc-bedgraphpack 324--0 which bedGraphPack
conda ucsc-bedgraphtobigwig 324--0 which bedGraphToBigWig
conda ucsc-bedintersect 324--0 which bedIntersect
conda ucsc-beditemoverlapcount 324--0 which bedItemOverlapCount
conda ucsc-bedpileups 324--0 which bedPileUps
conda ucsc-bedremoveoverlap 324--0 which bedRemoveOverlap
conda ucsc-chainprenet 324--0 which chainPreNet
conda ucsc-chainsort 324--0 which chainSort
conda ucsc-chainsplit 324--0 which chainSplit
conda ucsc-chainstitchid 324--0 which chainStitchId
conda ucsc-chainswap 324--0 which chainSwap
conda ucsc-chaintoaxt 324--0 which chainToAxt
conda ucsc-chaintopsl 324--0 which chainToPsl
conda ucsc-chaintopslbasic 324--0 which chainToPslBasic
conda ucsc-crtreeindexbed 324--0 which crTreeIndexBed
conda ucsc-crtreesearchbed 324--0 which crTreeSearchBed
conda ucsc-fatotwobit 324--0 which faToTwoBit
conda ucsc-fetchchromsizes 324--0 which fetchChromSizes
conda ucsc-genepredtobed 324--0 which genePredToBed
conda ucsc-genepredtofakepsl 324--0 which genePredToFakePsl
conda ucsc-twobitinfo 324--0 which twoBitInfo
conda ucsc-twobitmask 324--0 which twoBitMask
conda ucsc-twobittofa 324--0 which twoBitToFa
conda ucsc-validatefiles 324--0 which validateFiles
conda ucsc-validatemanifest 324--0 which validateManifest
conda ucsc-wigcorrelate 324--0 which wigCorrelate
conda ucsc-wigtobigwig 324--0 which wigToBigWig
conda ucsc-wordline 324--0 which wordLine
conda ucsc-xmlcat 324--0 which xmlCat
conda ucsc-xmltosql 324--0 which xmlToSql
conda ucsc-splitfile 324--0 which splitFile
conda ucsc-splitfilebycolumn 324--0 which splitFileByColumn
conda ucsc-sqltoxml 324--0 which sqlToXml
conda ucsc-stringify 324--0 which stringify
conda ucsc-subchar 324--0 which subChar
conda ucsc-subcolumn 324--0 which subColumn
conda ucsc-taillines 324--0 which tailLines
conda ucsc-tdbquery 324--0 which tdbQuery
conda ucsc-texthistogram 324--0 which textHistogram
conda ucsc-ticktodate 324--0 which tickToDate
conda ucsc-tolower 324--0 which toLower
conda ucsc-toupper 324--0 which toUpper
conda ucsc-trfbig 324--0 which trfBig
conda ucsc-twobitdup 324--0 which twoBitDup
conda ucsc-mafsinregion 324--0 which mafsInRegion
conda ucsc-mafspecieslist 324--0 which mafSpeciesList
conda ucsc-mafspeciessubset 324--0 which mafSpeciesSubset
conda ucsc-mafsplit 324--0 which mafSplit
conda ucsc-mafsplitpos 324--0 which mafSplitPos
conda ucsc-maftoaxt 324--0 which mafToAxt
conda ucsc-maftopsl 324--0 which mafToPsl
conda ucsc-maftosnpbed 324--0 which mafToSnpBed
conda ucsc-netchainsubset 324--0 which netChainSubset
conda ucsc-nettobed 324--0 which netToBed
conda ucsc-pslcat 324--0 which pslCat
conda ucsc-pslcdnafilter 324--0 which pslCDnaFilter
conda ucsc-pslcheck 324--0 which pslCheck
conda ucsc-psldropoverlap 324--0 which pslDropOverlap
conda ucsc-maffetch 324--0 which mafFetch
conda ucsc-maffilter 324--0 which mafFilter
conda ucsc-maffrag 324--0 which mafFrag
conda ucsc-maffrags 324--0 which mafFrags
conda ucsc-mafgene 324--0 which mafGene
conda ucsc-mafmefirst 324--0 which mafMeFirst
conda ucsc-maforder 324--0 which mafOrder
conda ucsc-mafranges 324--0 which mafRanges
conda ucsc-genepredtomafframes 324--0 which genePredToMafFrames
conda ucsc-gtftogenepred 324--0 which gtfToGenePred
conda ucsc-hgloadbed 324--0 which hgLoadBed
conda ucsc-hgloadchain 324--0 which hgLoadChain
conda ucsc-hgloadmaf 324--0 which hgLoadMaf
conda ucsc-hgloadwiggle 324--0 which hgLoadWiggle
conda ucsc-lavtopsl 324--0 which lavToPsl
conda ucsc-liftover 324--0 which liftOver
conda ucsc-liftup 324--0 which liftUp
conda ucsc-mafaddirows 324--0 which mafAddIRows
conda ucsc-mafaddqrows 324--0 which mafAddQRows
conda ucsc-mafcoverage 324--0 which mafCoverage
conda ucsc-bedrestricttopositions 324--0 which bedRestrictToPositions
conda ucsc-bedsort 324--0 which bedSort
conda ucsc-bedtobigbed 324--0 which bedToBigBed
conda ucsc-bedtogenepred 324--0 which bedToGenePred
conda ucsc-bedtopsl 324--0 which bedToPsl
conda ucsc-bedweedoverlapping 324--0 which bedWeedOverlapping
conda ucsc-bigbedinfo 324--0 which bigBedInfo
conda ucsc-bigbednameditems 324--0 which bigBedNamedItems
conda ucsc-bigbedsummary 324--0 which bigBedSummary
conda ucsc-pslswap 324--0 which pslSwap
conda ucsc-psltobed 324--0 which pslToBed
conda ucsc-psltobigpsl 324--0 which pslToBigPsl
conda ucsc-psltochain 324--0 which pslToChain
conda ucsc-psltopslx 324--0 which pslToPslx
conda ucsc-pslxtofa 324--0 which pslxToFa
conda ucsc-qactowig 324--0 which qacToWig
conda ucsc-qatoqac 324--0 which qaToQac
conda ucsc-randomlines 324--0 which randomLines
conda ucsc-rasqlquery 324--0 which raSqlQuery
conda ucsc-ratolines 324--0 which raToLines
conda ucsc-ratotab 324--0 which raToTab
conda ucsc-rmfadups 324--0 which rmFaDups
conda ucsc-rowstocols 324--0 which rowsToCols
conda ucsc-spacedtotab 324--0 which spacedToTab
conda ucsc-bigbedtobed 324--0 which bigBedToBed
conda ucsc-bigwigaverageoverbed 324--0 which bigWigAverageOverBed
conda ucsc-bigwigcat 324--0 which bigWigCat
conda ucsc-bigwigcluster 324--0 which bigWigCluster
conda ucsc-bigwigcorrelate 324--0 which bigWigCorrelate
conda ucsc-bigwiginfo 324--0 which bigWigInfo
conda ucsc-bigwigmerge 324--0 which bigWigMerge
conda ucsc-bigwigsummary 324--0 which bigWigSummary
conda ucsc-bigwigtobedgraph 324--0 which bigWigToBedGraph
conda ucsc-bigwigtowig 324--0 which bigWigToWig
conda ucsc-blasttopsl 324--0 which blastToPsl
conda ucsc-chainantirepeat 324--0 which chainAntiRepeat
conda ucsc-chainfilter 324--0 which chainFilter
conda ucsc-chainmergesort 324--0 which chainMergeSort
conda ucsc-chainnet 324--0 which chainNet
conda ucsc-pslreps 324--0 which pslReps
conda ucsc-pslscore 324--0 which pslScore
conda ucsc-pslselect 324--0 which pslSelect
conda ucsc-pslsort 324--0 which pslSort
conda ucsc-pslstats 324--0 which pslStats
conda ucsc-pslpostarget 324--0 which pslPosTarget
conda ucsc-pslpretty 324--0 which pslPretty
conda ucsc-pslrecalcmatch 324--0 which pslRecalcMatch
conda ucsc-pslfilter 324--0 which pslFilter
conda ucsc-pslhisto 324--0 which pslHisto
conda ucsc-pslliftsubrangeblat 324--0 which pslLiftSubrangeBlat
conda ucsc-pslmap 324--0 which pslMap
conda ucsc-pslmrnacover 324--0 which pslMrnaCover
conda ucsc-pslpairs 324--0 which pslPairs
conda ucsc-pslpartition 324--0 which pslPartition
conda variant-effect-predictor 83--4 variant_effect_predictor.pl --help
conda t_coffee 11.0.8--py35_1 t_coffee --help
conda piranha 1.2.1--gsl1.16_0 Piranha
conda piranha 1.2.1--gsl1.16_2 Piranha
conda trimmomatic 0.36--3 trimmomatic --help