

set -ex



augustus --version
aa2nonred.pl --help 2>&1 | grep "aa2nonred.pl" > /dev/null
autoAug.pl --help
autoAugPred.pl --help
autoAugTrain.pl --help 2>&1 | grep "autoAugTrain.pl" > /dev/null
bam2hints --help
bam2wig 2>&1 | grep "bam2wig" > /dev/null
bedgraph2wig.pl
blat2gbrowse.pl --help 2>&1 | grep "blat2gbrowse.pl" > /dev/null
blat2hints.pl
cegma2gff.pl 2>&1 | grep "cegma2gff.pl" > /dev/null
checkParamArchive.pl
cleanDOSfasta.pl
clusterAndSplitGenes.pl --help
compileSpliceCands 2>&1 | grep "compileSpliceCands" > /dev/null
computeFlankingRegion.pl 2>&1 | grep "computeFlankingRegion.pl" > /dev/null
createAugustusJoblist.pl
del_from_prfl.pl --help 2>&1 | grep "del_from_prfl.pl" > /dev/null
evalCGP.pl
eval_dualdecomp.pl --help
eval_multi_gtf.pl --help 2>&1 | grep "eval_multi_gtf.pl" > /dev/null
exonerate2hints.pl
filterBam --help 2>&1 | grep "filterBam" > /dev/null
filterGenesIn_mRNAname.pl
filterGenesIn.pl
filterGenesOut_mRNAname.pl
filterGenes.pl
filterInFrameStopCodons.pl
filterMaf.pl --help 2>&1 | grep "filterMaf.pl" > /dev/null
filterPSL.pl --help
filterShrimp.pl --help
filterSpliceHints.pl
findGffNamesInFasta.pl --help 2>&1 | grep "file" > /dev/null
gbrowseold2gff3.pl --help 2>&1 | grep "gbrowseold2gff3.pl" > /dev/null
gbSmallDNA2gff.pl 2>&1 | grep "gbSmallDNA2gff.pl" > /dev/null
getAnnoFasta.pl
getLinesMatching.pl 2>&1 | grep "getLinesMatching.pl" > /dev/null
gff2gbSmallDNA.pl 2>&1 | grep "gff2gbSmallDNA.pl" > /dev/null
gffGetmRNA.pl
gp2othergp.pl --help 2>&1 | grep "gp2othergp.pl" > /dev/null
gtf2aa.pl 2>&1 | grep "gtf2aa.pl" > /dev/null
gtf2bed.pl --help 2>&1 | grep "gtf2bed.pl" > /dev/null
gtf2gff.pl --help 2>&1 | grep "gtf2gff.pl" > /dev/null
gth2gtf.pl 2>&1 | grep "gth2gtf.pl" > /dev/null
hal2maf_split.pl --help 2>&1 | grep "hal2maf_split.pl" > /dev/null
homGeneMapping --help 2>&1 | grep "homGeneMapping" > /dev/null
intron2exex.pl --help 2>&1 | grep "intron2exex.pl" > /dev/null
join_mult_hints.pl --help 2>&1 | grep "join_mult_hints.pl" > /dev/null
joingenes --help 2>&1 | grep "joingenes" > /dev/null
joinPeptides.pl 2>&1 | grep "joinPeptides.pl" > /dev/null
maf2conswig.pl --help 2>&1 | grep "maf2conswig.pl" > /dev/null
makeMatchLists.pl --help 2>&1 | grep "help" > /dev/null
makeUtrTrainingSet.pl 2>&1 | grep "makeUtrTrainingSet.pl" > /dev/null
maskNregions.pl
moveParameters.pl
msa2prfl.pl --help
new_species.pl
optimize_augustus.pl
opt_init_and_term_probs.pl 2>&1 | grep "open" > /dev/null
parseSim4Output.pl 2>&1 | grep "parseSim4Output.pl" > /dev/null
partition_gtf2gb.pl --help 2>&1 | grep "parition_gtf2gb.pl" > /dev/null
pasapolyA2hints.pl 2>&1 | grep "pasapolyA2hints.pl" > /dev/null
peptides2alternatives.pl 2>&1 | grep "peptides2alternatives.pl" > /dev/null
peptides2hints.pl 2>&1 | grep "peptides2hints.pl" > /dev/null
polyA2hints.pl
pslMap.pl 2>&1 | grep "pslMap.pl" > /dev/null
randomSplit.pl
rmRedundantHints.pl 2>&1 | grep "rmRedundantHints.pl" > /dev/null
runAllSim4.pl --help 2>&1 | grep "runAllSim4.pl" > /dev/null
samMap.pl
scipiogff2gff.pl 2>&1 | grep "scipiogff2gff.pl" > /dev/null
setStopCodonFreqs.pl 2>&1 | grep "setStopCodonFreqs.pl" > /dev/null
simpleFastaHeaders.pl 2>&1 | grep "simpleFastaHeaders.pl" > /dev/null
simplifyFastaHeaders.pl 2>&1 | grep "simplifyFastaHeaders.pl" > /dev/null
splitMfasta.pl
split_wiggle.pl
summarizeACGTcontent.pl 2>&1 | grep "summarizeACGTcontent.pl" > /dev/null
transMap2hints.pl
uniquePeptides.pl 2>&1 | grep "uniquePeptides.pl" > /dev/null
utrgff2gbrowse.pl --help 2>&1 | grep "utrgff2gbrowse.pl" > /dev/null
utrrnaseq --help
weedMaf.pl --help 2>&1 | grep "weedMaf.pl" > /dev/null
wigchoose.pl --help
writeResultsPage.pl
yaml2gff.1.4.pl --help 2>&1 | grep "yaml2gff.pl" > /dev/null
getAnnoFastaFromJoingenes.py --help
bamToWig.py --help | grep -Fq 'bamToWig.py'
compare_masking.pl --help | grep -Fq 'compare_masking'
merge_masking.pl --help | grep -Fq 'merge_masking.pl'
fix_in_frame_stop_codon_genes.py --help | grep -Fq 'fix_in_frame_stop_codon_genes.py'
exit 0
