packages.tsv

# 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'
alpine	git	1	git --version
alpine	mc	1	mc --version
alpine	lftp	1	lftp --version
conda	segway	1.4--py27_0	segway --help
conda	emboss	6.5.7--2	needle --help
conda	cofold	2.0.4--1	CoFold --help
conda	repeatmasker	4.0.6--4	RepeatMasker | grep 'RepeatMasker - Mask repetitive DNA'
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	bedops	2.4.19--0	bedops --help
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	rgi	3.1.0--py27_1	rgi -h
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	tophat	2.1.1--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	gemini	0.19.0--py27_0	python -c 'import gemini'
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	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
conda	bwa	0.7.15--0	which bwa
conda	ribotaper	1.3.1--0	Ribotaper.sh 2>&1  | grep Usage > /dev/null
conda	viral-ngs	1.10.1--py35_2	illumina.py --help
conda	freebayes	1.0.2--0	which freebayes
conda r-pairadise 1.0.0 Rscript -e 'library(''PAIRADISE'')'