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container.yaml
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container.yaml
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url: https://biocontainers.pro/tools/maker
maintainer: '@vsoch'
description: shpc-registry automated BioContainers addition for maker
latest:
3.01.03--pl5262h8f1cd36_2: sha256:6d9024749b96d7873fb095e64412e73978170ef180467107e96a8d5b445f99e3
tags:
3.01.03--pl5262h8f1cd36_2: sha256:6d9024749b96d7873fb095e64412e73978170ef180467107e96a8d5b445f99e3
2.31.11--pl5262hec0a270_1: sha256:284cd94bd1aa733082aa673a8fd892e76453b87d210d5f410c02ea611b364ef0
docker: quay.io/biocontainers/maker
aliases:
AED_cdf_generator.pl: /usr/local/bin/AED_cdf_generator.pl
DateRepeats: /usr/local/bin/DateRepeats
DupMasker: /usr/local/bin/DupMasker
EukHighConfidenceFilter: /usr/local/bin/EukHighConfidenceFilter
PF00225_full.blocks.txt: /usr/local/bin/PF00225_full.blocks.txt
PF00225_seed.blocks.txt: /usr/local/bin/PF00225_seed.blocks.txt
ProcessRepeats: /usr/local/bin/ProcessRepeats
RM2Bed.py: /usr/local/bin/RM2Bed.py
RepeatMasker: /usr/local/bin/RepeatMasker
RepeatProteinMask: /usr/local/bin/RepeatProteinMask
SplicedAlignment.pm: /usr/local/bin/SplicedAlignment.pm
aa2nonred.pl: /usr/local/bin/aa2nonred.pl
add_name_to_gff3.pl: /usr/local/bin/add_name_to_gff3.pl
aln2wig: /usr/local/bin/aln2wig
augustify.py: /usr/local/bin/augustify.py
augustus2browser.pl: /usr/local/bin/augustus2browser.pl
augustus2gbrowse.pl: /usr/local/bin/augustus2gbrowse.pl
autoAug.pl: /usr/local/bin/autoAug.pl
autoAugPred.pl: /usr/local/bin/autoAugPred.pl
autoAugTrain.pl: /usr/local/bin/autoAugTrain.pl
bam2wig: /usr/local/bin/bam2wig
bamToWig.py: /usr/local/bin/bamToWig.py
bedgraph2wig.pl: /usr/local/bin/bedgraph2wig.pl
blat2gbrowse.pl: /usr/local/bin/blat2gbrowse.pl
blat2hints.pl: /usr/local/bin/blat2hints.pl
block2prfl.pl: /usr/local/bin/block2prfl.pl
buildRMLibFromEMBL.pl: /usr/local/bin/buildRMLibFromEMBL.pl
buildSummary.pl: /usr/local/bin/buildSummary.pl
calcDivergenceFromAlign.pl: /usr/local/bin/calcDivergenceFromAlign.pl
cdbfasta: /usr/local/bin/cdbfasta
cdbyank: /usr/local/bin/cdbyank
cds-trainer.pl: /usr/local/bin/cds-trainer.pl
cegma2gff.pl: /usr/local/bin/cegma2gff.pl
cegma2zff: /usr/local/bin/cegma2zff
chado2gff3: /usr/local/bin/chado2gff3
checkParamArchive.pl: /usr/local/bin/checkParamArchive.pl
checkUTR: /usr/local/bin/checkUTR
cleanDOSfasta.pl: /usr/local/bin/cleanDOSfasta.pl
clusterAndSplitGenes.pl: /usr/local/bin/clusterAndSplitGenes.pl
compare_gff3_to_chado: /usr/local/bin/compare_gff3_to_chado
compare_masking.pl: /usr/local/bin/compare_masking.pl
compileSpliceCands: /usr/local/bin/compileSpliceCands
computeFlankingRegion.pl: /usr/local/bin/computeFlankingRegion.pl
covels-SE: /usr/local/bin/covels-SE
coves-SE: /usr/local/bin/coves-SE
createAugustusJoblist.pl: /usr/local/bin/createAugustusJoblist.pl
createRepeatLandscape.pl: /usr/local/bin/createRepeatLandscape.pl
cufflinks2gff3: /usr/local/bin/cufflinks2gff3
del_from_prfl.pl: /usr/local/bin/del_from_prfl.pl
dupliconToSVG.pl: /usr/local/bin/dupliconToSVG.pl
esd2esi: /usr/local/bin/esd2esi
eufindtRNA: /usr/local/bin/eufindtRNA
evalCGP.pl: /usr/local/bin/evalCGP.pl
eval_dualdecomp.pl: /usr/local/bin/eval_dualdecomp.pl
eval_multi_gtf.pl: /usr/local/bin/eval_multi_gtf.pl
evaluator: /usr/local/bin/evaluator
evidence_modeler.pl: /usr/local/bin/evidence_modeler.pl
executeTestCGP.py: /usr/local/bin/executeTestCGP.py
exonerate: /usr/local/bin/exonerate
exonerate-server: /usr/local/bin/exonerate-server
exonerate2hints.pl: /usr/local/bin/exonerate2hints.pl
exoniphyDb2hints.pl: /usr/local/bin/exoniphyDb2hints.pl
exonpairs: /usr/local/bin/exonpairs
extractAnno.py: /usr/local/bin/extractAnno.py
extractTranscriptEnds.pl: /usr/local/bin/extractTranscriptEnds.pl
fasta2esd: /usr/local/bin/fasta2esd
fasta2gsi: /usr/local/bin/fasta2gsi
fasta2gsi.pl: /usr/local/bin/fasta2gsi.pl
fasta_merge: /usr/local/bin/fasta_merge
fasta_tool: /usr/local/bin/fasta_tool
fastaannotatecdna: /usr/local/bin/fastaannotatecdna
fastachecksum: /usr/local/bin/fastachecksum
fastaclean: /usr/local/bin/fastaclean
fastaclip: /usr/local/bin/fastaclip
fastacomposition: /usr/local/bin/fastacomposition
fastadiff: /usr/local/bin/fastadiff
fastaexplode: /usr/local/bin/fastaexplode
fastafetch: /usr/local/bin/fastafetch
fastahardmask: /usr/local/bin/fastahardmask
fastaindex: /usr/local/bin/fastaindex
fastalength: /usr/local/bin/fastalength
fastanrdb: /usr/local/bin/fastanrdb
fastaoverlap: /usr/local/bin/fastaoverlap
fastareformat: /usr/local/bin/fastareformat
fastaremove: /usr/local/bin/fastaremove
fastarevcomp: /usr/local/bin/fastarevcomp
fastasoftmask: /usr/local/bin/fastasoftmask
fastasort: /usr/local/bin/fastasort
fastasplit: /usr/local/bin/fastasplit
fastasubseq: /usr/local/bin/fastasubseq
fastatranslate: /usr/local/bin/fastatranslate
fastavalidcds: /usr/local/bin/fastavalidcds
fathom: /usr/local/bin/fathom
filter-ppx.pl: /usr/local/bin/filter-ppx.pl
filterGenes.pl: /usr/local/bin/filterGenes.pl
filterGenesIn.pl: /usr/local/bin/filterGenesIn.pl
filterGenesIn_mRNAname.pl: /usr/local/bin/filterGenesIn_mRNAname.pl
filterGenesOut_mRNAname.pl: /usr/local/bin/filterGenesOut_mRNAname.pl
filterInFrameStopCodons.pl: /usr/local/bin/filterInFrameStopCodons.pl
filterMaf.pl: /usr/local/bin/filterMaf.pl
filterPSL.pl: /usr/local/bin/filterPSL.pl
filterShrimp.pl: /usr/local/bin/filterShrimp.pl
filterSpliceHints.pl: /usr/local/bin/filterSpliceHints.pl
findGffNamesInFasta.pl: /usr/local/bin/findGffNamesInFasta.pl
fix_in_frame_stop_codon_genes.py: /usr/local/bin/fix_in_frame_stop_codon_genes.py
fix_joingenes_gtf.pl: /usr/local/bin/fix_joingenes_gtf.pl
forge: /usr/local/bin/forge
gbSmallDNA2gff.pl: /usr/local/bin/gbSmallDNA2gff.pl
gbrowse.conf: /usr/local/bin/gbrowse.conf
gbrowseold2gff3.pl: /usr/local/bin/gbrowseold2gff3.pl
gcc: /usr/local/bin/gcc
genbank2gsi.pl: /usr/local/bin/genbank2gsi.pl
genemark_gtf2gff3: /usr/local/bin/genemark_gtf2gff3
genpept2gsi.pl: /usr/local/bin/genpept2gsi.pl
getAnnoFasta.pl: /usr/local/bin/getAnnoFasta.pl
getAnnoFastaFromJoingenes.py: /usr/local/bin/getAnnoFastaFromJoingenes.py
getLinesMatching.pl: /usr/local/bin/getLinesMatching.pl
getRepeatMaskerBatch.pl: /usr/local/bin/getRepeatMaskerBatch.pl
getSeq: /usr/local/bin/getSeq
get_loci_from_gb.pl: /usr/local/bin/get_loci_from_gb.pl
gff2gbSmallDNA.pl: /usr/local/bin/gff2gbSmallDNA.pl
gff2ps_mycustom: /usr/local/bin/gff2ps_mycustom
gff3_merge: /usr/local/bin/gff3_merge
gffGetmRNA.pl: /usr/local/bin/gffGetmRNA.pl
gp2othergp.pl: /usr/local/bin/gp2othergp.pl
gtf2aa.pl: /usr/local/bin/gtf2aa.pl
gtf2gff.pl: /usr/local/bin/gtf2gff.pl
gth2gtf.pl: /usr/local/bin/gth2gtf.pl
hal2maf_split.pl: /usr/local/bin/hal2maf_split.pl
helpMod.pm: /usr/local/bin/helpMod.pm
hmm-assembler.pl: /usr/local/bin/hmm-assembler.pl
hmm-info: /usr/local/bin/hmm-info
ipcress: /usr/local/bin/ipcress
ipr_update_gff: /usr/local/bin/ipr_update_gff
iprscan2gff3: /usr/local/bin/iprscan2gff3
joinPeptides.pl: /usr/local/bin/joinPeptides.pl
join_aug_pred.pl: /usr/local/bin/join_aug_pred.pl
join_mult_hints.pl: /usr/local/bin/join_mult_hints.pl
load2sqlitedb: /usr/local/bin/load2sqlitedb
lp_solve: /usr/local/bin/lp_solve
maf2conswig.pl: /usr/local/bin/maf2conswig.pl
makeMatchLists.pl: /usr/local/bin/makeMatchLists.pl
makeUtrTrainingSet.pl: /usr/local/bin/makeUtrTrainingSet.pl
maker: /usr/local/bin/maker
maker2chado: /usr/local/bin/maker2chado
maker2eval_gtf: /usr/local/bin/maker2eval_gtf
maker2jbrowse: /usr/local/bin/maker2jbrowse
maker2wap: /usr/local/bin/maker2wap
maker2zff: /usr/local/bin/maker2zff
maker_functional_fasta: /usr/local/bin/maker_functional_fasta
maker_functional_gff: /usr/local/bin/maker_functional_gff
maker_map_ids: /usr/local/bin/maker_map_ids
map2assembly: /usr/local/bin/map2assembly
map_data_ids: /usr/local/bin/map_data_ids
map_fasta_ids: /usr/local/bin/map_fasta_ids
map_gff_ids: /usr/local/bin/map_gff_ids
maskFile.pl: /usr/local/bin/maskFile.pl
maskNregions.pl: /usr/local/bin/maskNregions.pl
match2gene.pl: /usr/local/bin/match2gene.pl
merge_masking.pl: /usr/local/bin/merge_masking.pl
moveParameters.pl: /usr/local/bin/moveParameters.pl
msa2prfl.pl: /usr/local/bin/msa2prfl.pl
new_species.pl: /usr/local/bin/new_species.pl
noncoding-trainer.pl: /usr/local/bin/noncoding-trainer.pl
opt_init_and_term_probs.pl: /usr/local/bin/opt_init_and_term_probs.pl
optimize_augustus.pl: /usr/local/bin/optimize_augustus.pl
parseSim4Output.pl: /usr/local/bin/parseSim4Output.pl
partition_gtf2gb.pl: /usr/local/bin/partition_gtf2gb.pl
pasapolyA2hints.pl: /usr/local/bin/pasapolyA2hints.pl
patch-hmm.pl: /usr/local/bin/patch-hmm.pl
peptides2alternatives.pl: /usr/local/bin/peptides2alternatives.pl
peptides2hints.pl: /usr/local/bin/peptides2hints.pl
phastconsDB2hints.pl: /usr/local/bin/phastconsDB2hints.pl
pir2gsi.pl: /usr/local/bin/pir2gsi.pl
polyA2hints.pl: /usr/local/bin/polyA2hints.pl
pp_simScore: /usr/local/bin/pp_simScore
prerapsearch: /usr/local/bin/prerapsearch
prints2prfl.pl: /usr/local/bin/prints2prfl.pl
pslMap.pl: /usr/local/bin/pslMap.pl
quality_filter.pl: /usr/local/bin/quality_filter.pl
randomSplit.pl: /usr/local/bin/randomSplit.pl
rapsearch: /usr/local/bin/rapsearch
retroDB2hints.pl: /usr/local/bin/retroDB2hints.pl
rmOut2Fasta.pl: /usr/local/bin/rmOut2Fasta.pl
rmOutToGFF3.pl: /usr/local/bin/rmOutToGFF3.pl
rmRedundantHints.pl: /usr/local/bin/rmRedundantHints.pl
rmToUCSCTables.pl: /usr/local/bin/rmToUCSCTables.pl
runAllSim4.pl: /usr/local/bin/runAllSim4.pl
samMap.pl: /usr/local/bin/samMap.pl
scipiogff2gff.pl: /usr/local/bin/scipiogff2gff.pl
setStopCodonFreqs.pl: /usr/local/bin/setStopCodonFreqs.pl
simpleFastaHeaders.pl: /usr/local/bin/simpleFastaHeaders.pl
simplifyFastaHeaders.pl: /usr/local/bin/simplifyFastaHeaders.pl
snap: /usr/local/bin/snap
snoscan: /usr/local/bin/snoscan
snoscanA: /usr/local/bin/snoscanA
snoscanH: /usr/local/bin/snoscanH
snoscanY: /usr/local/bin/snoscanY
sort-snos: /usr/local/bin/sort-snos
sort-snos.pl: /usr/local/bin/sort-snos.pl
splitMfasta.pl: /usr/local/bin/splitMfasta.pl
split_gff3: /usr/local/bin/split_gff3
split_wiggle.pl: /usr/local/bin/split_wiggle.pl
sstofa: /usr/local/bin/sstofa
stubmaker.pl: /usr/local/bin/stubmaker.pl
summarizeACGTcontent.pl: /usr/local/bin/summarizeACGTcontent.pl
swiss2gsi.pl: /usr/local/bin/swiss2gsi.pl
tRNAscan-SE: /usr/local/bin/tRNAscan-SE
tRNAscan-SE.conf: /usr/local/bin/tRNAscan-SE.conf
tophat2gff3: /usr/local/bin/tophat2gff3
train_augustus.pl: /usr/local/bin/train_augustus.pl
transMap2hints.pl: /usr/local/bin/transMap2hints.pl
trfMask: /usr/local/bin/trfMask
trnascan-1.4: /usr/local/bin/trnascan-1.4
uniquePeptides.pl: /usr/local/bin/uniquePeptides.pl
utrgff2gbrowse.pl: /usr/local/bin/utrgff2gbrowse.pl
utrrnaseq: /usr/local/bin/utrrnaseq
webserver-results.head: /usr/local/bin/webserver-results.head
webserver-results.tail: /usr/local/bin/webserver-results.tail
weedMaf.pl: /usr/local/bin/weedMaf.pl
wig2hints.pl: /usr/local/bin/wig2hints.pl
wigchoose.pl: /usr/local/bin/wigchoose.pl
writeResultsPage.pl: /usr/local/bin/writeResultsPage.pl
wublastToCrossmatch.pl: /usr/local/bin/wublastToCrossmatch.pl
yaml2gff.1.4.pl: /usr/local/bin/yaml2gff.1.4.pl
zff2genbank.pl: /usr/local/bin/zff2genbank.pl
zff2gff3.pl: /usr/local/bin/zff2gff3.pl
augustus: /usr/local/bin/augustus
bam2hints: /usr/local/bin/bam2hints
etraining: /usr/local/bin/etraining
fastBlockSearch: /usr/local/bin/fastBlockSearch
filterBam: /usr/local/bin/filterBam
gtf2bed.pl: /usr/local/bin/gtf2bed.pl
homGeneMapping: /usr/local/bin/homGeneMapping
joingenes: /usr/local/bin/joingenes
pg_amcheck: /usr/local/bin/pg_amcheck
prepareAlign: /usr/local/bin/prepareAlign