miga-base 1.2.17.0 → 1.2.17.1
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- checksums.yaml +4 -4
- data/lib/miga/version.rb +1 -1
- data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm +41964 -0
- data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm +32439 -0
- data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm +62056 -0
- data/utils/FastAAI/FastAAI +3659 -0
- data/utils/FastAAI/FastAAI-legacy/FastAAI +1336 -0
- data/utils/FastAAI/FastAAI-legacy/kAAI_v1.0_virus.py +1296 -0
- data/utils/FastAAI/README.md +84 -0
- data/utils/enveomics/Docs/recplot2.md +244 -0
- data/utils/enveomics/Examples/aai-matrix.bash +66 -0
- data/utils/enveomics/Examples/ani-matrix.bash +66 -0
- data/utils/enveomics/Examples/essential-phylogeny.bash +105 -0
- data/utils/enveomics/Examples/unus-genome-phylogeny.bash +100 -0
- data/utils/enveomics/LICENSE.txt +73 -0
- data/utils/enveomics/Makefile +52 -0
- data/utils/enveomics/Manifest/Tasks/aasubs.json +103 -0
- data/utils/enveomics/Manifest/Tasks/blasttab.json +790 -0
- data/utils/enveomics/Manifest/Tasks/distances.json +161 -0
- data/utils/enveomics/Manifest/Tasks/fasta.json +802 -0
- data/utils/enveomics/Manifest/Tasks/fastq.json +291 -0
- data/utils/enveomics/Manifest/Tasks/graphics.json +126 -0
- data/utils/enveomics/Manifest/Tasks/mapping.json +137 -0
- data/utils/enveomics/Manifest/Tasks/ogs.json +382 -0
- data/utils/enveomics/Manifest/Tasks/other.json +906 -0
- data/utils/enveomics/Manifest/Tasks/remote.json +355 -0
- data/utils/enveomics/Manifest/Tasks/sequence-identity.json +650 -0
- data/utils/enveomics/Manifest/Tasks/tables.json +308 -0
- data/utils/enveomics/Manifest/Tasks/trees.json +68 -0
- data/utils/enveomics/Manifest/Tasks/variants.json +111 -0
- data/utils/enveomics/Manifest/categories.json +165 -0
- data/utils/enveomics/Manifest/examples.json +162 -0
- data/utils/enveomics/Manifest/tasks.json +4 -0
- data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +69 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +1 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +1 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +1 -0
- data/utils/enveomics/Pipelines/assembly.pbs/README.md +189 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +112 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +23 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +44 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +50 -0
- data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +37 -0
- data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +68 -0
- data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +49 -0
- data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +80 -0
- data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +57 -0
- data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +63 -0
- data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +38 -0
- data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +73 -0
- data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +21 -0
- data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +72 -0
- data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +98 -0
- data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +1 -0
- data/utils/enveomics/Pipelines/blast.pbs/README.md +127 -0
- data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +109 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +128 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +16 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +22 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +26 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +89 -0
- data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +29 -0
- data/utils/enveomics/Pipelines/idba.pbs/README.md +49 -0
- data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +95 -0
- data/utils/enveomics/Pipelines/idba.pbs/run.pbs +56 -0
- data/utils/enveomics/Pipelines/trim.pbs/README.md +54 -0
- data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +70 -0
- data/utils/enveomics/Pipelines/trim.pbs/run.pbs +130 -0
- data/utils/enveomics/README.md +42 -0
- data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +171 -0
- data/utils/enveomics/Scripts/Aln.cat.rb +221 -0
- data/utils/enveomics/Scripts/Aln.convert.pl +35 -0
- data/utils/enveomics/Scripts/AlphaDiversity.pl +152 -0
- data/utils/enveomics/Scripts/BedGraph.tad.rb +93 -0
- data/utils/enveomics/Scripts/BedGraph.window.rb +71 -0
- data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +102 -0
- data/utils/enveomics/Scripts/BlastTab.addlen.rb +63 -0
- data/utils/enveomics/Scripts/BlastTab.advance.bash +48 -0
- data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +55 -0
- data/utils/enveomics/Scripts/BlastTab.catsbj.pl +104 -0
- data/utils/enveomics/Scripts/BlastTab.cogCat.rb +76 -0
- data/utils/enveomics/Scripts/BlastTab.filter.pl +47 -0
- data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +194 -0
- data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +104 -0
- data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +157 -0
- data/utils/enveomics/Scripts/BlastTab.recplot2.R +48 -0
- data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +86 -0
- data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +119 -0
- data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +86 -0
- data/utils/enveomics/Scripts/BlastTab.subsample.pl +47 -0
- data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +114 -0
- data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +90 -0
- data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +123 -0
- data/utils/enveomics/Scripts/Chao1.pl +97 -0
- data/utils/enveomics/Scripts/CharTable.classify.rb +234 -0
- data/utils/enveomics/Scripts/EBIseq2tax.rb +83 -0
- data/utils/enveomics/Scripts/FastA.N50.pl +60 -0
- data/utils/enveomics/Scripts/FastA.extract.rb +152 -0
- data/utils/enveomics/Scripts/FastA.filter.pl +52 -0
- data/utils/enveomics/Scripts/FastA.filterLen.pl +28 -0
- data/utils/enveomics/Scripts/FastA.filterN.pl +60 -0
- data/utils/enveomics/Scripts/FastA.fragment.rb +100 -0
- data/utils/enveomics/Scripts/FastA.gc.pl +42 -0
- data/utils/enveomics/Scripts/FastA.interpose.pl +93 -0
- data/utils/enveomics/Scripts/FastA.length.pl +38 -0
- data/utils/enveomics/Scripts/FastA.mask.rb +89 -0
- data/utils/enveomics/Scripts/FastA.per_file.pl +36 -0
- data/utils/enveomics/Scripts/FastA.qlen.pl +57 -0
- data/utils/enveomics/Scripts/FastA.rename.pl +65 -0
- data/utils/enveomics/Scripts/FastA.revcom.pl +23 -0
- data/utils/enveomics/Scripts/FastA.sample.rb +98 -0
- data/utils/enveomics/Scripts/FastA.slider.pl +85 -0
- data/utils/enveomics/Scripts/FastA.split.pl +55 -0
- data/utils/enveomics/Scripts/FastA.split.rb +79 -0
- data/utils/enveomics/Scripts/FastA.subsample.pl +131 -0
- data/utils/enveomics/Scripts/FastA.tag.rb +65 -0
- data/utils/enveomics/Scripts/FastA.toFastQ.rb +69 -0
- data/utils/enveomics/Scripts/FastA.wrap.rb +48 -0
- data/utils/enveomics/Scripts/FastQ.filter.pl +54 -0
- data/utils/enveomics/Scripts/FastQ.interpose.pl +90 -0
- data/utils/enveomics/Scripts/FastQ.maskQual.rb +89 -0
- data/utils/enveomics/Scripts/FastQ.offset.pl +90 -0
- data/utils/enveomics/Scripts/FastQ.split.pl +53 -0
- data/utils/enveomics/Scripts/FastQ.tag.rb +70 -0
- data/utils/enveomics/Scripts/FastQ.test-error.rb +81 -0
- data/utils/enveomics/Scripts/FastQ.toFastA.awk +24 -0
- data/utils/enveomics/Scripts/GFF.catsbj.pl +127 -0
- data/utils/enveomics/Scripts/GenBank.add_fields.rb +84 -0
- data/utils/enveomics/Scripts/HMM.essential.rb +351 -0
- data/utils/enveomics/Scripts/HMM.haai.rb +168 -0
- data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +83 -0
- data/utils/enveomics/Scripts/JPlace.distances.rb +88 -0
- data/utils/enveomics/Scripts/JPlace.to_iToL.rb +320 -0
- data/utils/enveomics/Scripts/M5nr.getSequences.rb +81 -0
- data/utils/enveomics/Scripts/MeTaxa.distribution.pl +198 -0
- data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +35 -0
- data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +49 -0
- data/utils/enveomics/Scripts/NCBIacc2tax.rb +92 -0
- data/utils/enveomics/Scripts/Newick.autoprune.R +27 -0
- data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +228 -0
- data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +32 -0
- data/utils/enveomics/Scripts/RefSeq.download.bash +48 -0
- data/utils/enveomics/Scripts/SRA.download.bash +55 -0
- data/utils/enveomics/Scripts/TRIBS.plot-test.R +36 -0
- data/utils/enveomics/Scripts/TRIBS.test.R +39 -0
- data/utils/enveomics/Scripts/Table.barplot.R +31 -0
- data/utils/enveomics/Scripts/Table.df2dist.R +30 -0
- data/utils/enveomics/Scripts/Table.filter.pl +61 -0
- data/utils/enveomics/Scripts/Table.merge.pl +77 -0
- data/utils/enveomics/Scripts/Table.prefScore.R +60 -0
- data/utils/enveomics/Scripts/Table.replace.rb +69 -0
- data/utils/enveomics/Scripts/Table.round.rb +63 -0
- data/utils/enveomics/Scripts/Table.split.pl +57 -0
- data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +227 -0
- data/utils/enveomics/Scripts/VCF.KaKs.rb +147 -0
- data/utils/enveomics/Scripts/VCF.SNPs.rb +88 -0
- data/utils/enveomics/Scripts/aai.rb +421 -0
- data/utils/enveomics/Scripts/ani.rb +362 -0
- data/utils/enveomics/Scripts/anir.rb +137 -0
- data/utils/enveomics/Scripts/clust.rand.rb +102 -0
- data/utils/enveomics/Scripts/gi2tax.rb +103 -0
- data/utils/enveomics/Scripts/in_silico_GA_GI.pl +96 -0
- data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
- data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
- data/utils/enveomics/Scripts/lib/enveomics.R +1 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/anir.rb +293 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb +175 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +24 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/errors.rb +17 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb +30 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +253 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/match.rb +88 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +182 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +49 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +74 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +237 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb +31 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb +152 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +3 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/utils.rb +74 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +135 -0
- data/utils/enveomics/Scripts/ogs.annotate.rb +88 -0
- data/utils/enveomics/Scripts/ogs.core-pan.rb +160 -0
- data/utils/enveomics/Scripts/ogs.extract.rb +125 -0
- data/utils/enveomics/Scripts/ogs.mcl.rb +186 -0
- data/utils/enveomics/Scripts/ogs.rb +104 -0
- data/utils/enveomics/Scripts/ogs.stats.rb +131 -0
- data/utils/enveomics/Scripts/rbm-legacy.rb +172 -0
- data/utils/enveomics/Scripts/rbm.rb +108 -0
- data/utils/enveomics/Scripts/sam.filter.rb +148 -0
- data/utils/enveomics/Tests/Makefile +10 -0
- data/utils/enveomics/Tests/Mgen_M2288.faa +3189 -0
- data/utils/enveomics/Tests/Mgen_M2288.fna +8282 -0
- data/utils/enveomics/Tests/Mgen_M2321.fna +8288 -0
- data/utils/enveomics/Tests/Nequ_Kin4M.faa +2970 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +7 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +17 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +137 -0
- data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +123 -0
- data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +200 -0
- data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +55 -0
- data/utils/enveomics/Tests/alkB.nwk +1 -0
- data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +13 -0
- data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +17 -0
- data/utils/enveomics/Tests/hiv1.faa +59 -0
- data/utils/enveomics/Tests/hiv1.fna +134 -0
- data/utils/enveomics/Tests/hiv2.faa +70 -0
- data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +233 -0
- data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +1 -0
- data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +233 -0
- data/utils/enveomics/Tests/phyla_counts.tsv +10 -0
- data/utils/enveomics/Tests/primate_lentivirus.ogs +11 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +9 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +8 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +6 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +9 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +6 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +6 -0
- data/utils/enveomics/build_enveomics_r.bash +45 -0
- data/utils/enveomics/enveomics.R/DESCRIPTION +31 -0
- data/utils/enveomics/enveomics.R/NAMESPACE +39 -0
- data/utils/enveomics/enveomics.R/R/autoprune.R +155 -0
- data/utils/enveomics/enveomics.R/R/barplot.R +184 -0
- data/utils/enveomics/enveomics.R/R/cliopts.R +135 -0
- data/utils/enveomics/enveomics.R/R/df2dist.R +154 -0
- data/utils/enveomics/enveomics.R/R/growthcurve.R +331 -0
- data/utils/enveomics/enveomics.R/R/prefscore.R +79 -0
- data/utils/enveomics/enveomics.R/R/recplot.R +354 -0
- data/utils/enveomics/enveomics.R/R/recplot2.R +1631 -0
- data/utils/enveomics/enveomics.R/R/tribs.R +583 -0
- data/utils/enveomics/enveomics.R/R/utils.R +80 -0
- data/utils/enveomics/enveomics.R/README.md +81 -0
- data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
- data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +16 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +16 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +16 -0
- data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +25 -0
- data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +46 -0
- data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +47 -0
- data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +40 -0
- data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +103 -0
- data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +67 -0
- data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +24 -0
- data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +45 -0
- data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +44 -0
- data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +47 -0
- data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +75 -0
- data/utils/enveomics/enveomics.R/man/enve.prefscore.Rd +50 -0
- data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +44 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +139 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +45 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +24 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +77 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +25 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +21 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +47 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +29 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +18 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +45 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +36 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +27 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +52 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +17 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +51 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +43 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +82 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +59 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +27 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +36 -0
- data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +68 -0
- data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +28 -0
- data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +27 -0
- data/utils/enveomics/enveomics.R/man/growth.curves.Rd +14 -0
- data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +13 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +78 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +46 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +45 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +125 -0
- data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +19 -0
- data/utils/enveomics/globals.mk +8 -0
- data/utils/enveomics/manifest.json +9 -0
- data/utils/multitrim/Multitrim How-To.pdf +0 -0
- data/utils/multitrim/README.md +67 -0
- data/utils/multitrim/multitrim.py +1555 -0
- data/utils/multitrim/multitrim.yml +13 -0
- metadata +301 -5
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@author: Luis Miguel Rodriguez-R <lmrodriguezr at gmail dot com>
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@update: Feb-20-2014
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@license: artistic 2.0
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@status: auto
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@pbs: yes
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# IMPORTANT
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This pipeline was developed for the [PACE cluster](http://pace.gatech.edu/). You
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are free to use it in other platforms with adequate adjustments.
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# PURPOSE
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Simplifies submitting and tracking large BLAST jobs in cluster.
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# HELP
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1. Files preparation:
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1.1. Obtain the enveomics package in the cluster. You can use: `git clone https://github.com/lmrodriguezr/enveomics.git`
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1.2. Prepare the query sequences and the database.
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1.3. Copy the file `CONFIG.mock.bash` to `CONFIG.<name>.bash`, where `<name>` is a
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short name for your project (avoid characters other than alphanumeric).
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1.4. Change the variables in `CONFIG.<name>.bash`. The **Queue and resources** and the
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**Pipeline** variables are very standard, and can be kept unchanged. The **Paths**
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variables indicate where your input files are and where the output files are to
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be created, so check them carefully. Finally, the **FUNCTIONS** define the core
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functionality of the pipeline, and should also be reviewed. By default, the
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Pipeline simply runs BLAST+, with default parameters and tabular output with two
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extra columns (qlen and slen). However, additional functionality can easily be
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incorporated via these functions, such as BLAST filtering, concatenation, sorting,
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or even execution of other programs instead of BLAST, such as BLAT, etc. Note that
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the output MUST be BLAST-like tabular, because this is the only format supported
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to check completeness and recover incomplete runs.
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2. Pipeline execution:
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2.1. To initialize a run, execute: `./RUNME.bash <name> run`.
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2.2. To check the status of a job, execute: `./RUNME.bash <name> check`.
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2.3. To pause a run, execute: `./RUNME.bash <name> pause` (see 2.1 to resume).
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2.4. To check if your CONFIG defines all required parameters, execute: `./RUNME.bash <name> dry`.
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2.5. To review all the e/o files in the run, execute: `./RUNME.bash <name> eo`.
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3. Finalizing:
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3.1. `./RUNME.bash <name> check` will inform you if a project finished. If it finished successfully,
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you can review your (split) results in $SCRATCH/results. If you concatenated the results in the
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`END` function, you should have a file with all the results in $SCRATCH/<name>.blast.
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3.2. Usually, checking the e/o files at the end is a good idea (`./RUNME.bash <name> eo`). However,
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bear in mind that this Pipeline can overcome several errors and is robust to most failures, so
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don't be alarmed at the first sight of errors.
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# Comments
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* Some scripts contained in this package are actually symlinks to files in the
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_Scripts_ folder. Check the existance of these files when copied to
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the cluster.
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# Troubleshooting
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1. Do I really have to change directory (`cd`) to the pipeline's folder everytime I want to execute
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something?
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No. Not really. For simplicity, this file tells you to execute `./RUNME.bash`. However, you don't
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really have to be there, you can execute it from any location. For example, if you saved enveomics in
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your home directory, you can just execute `~/enveomics/blast.pbs/RUNME.bash` insted from any location
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in the head node.
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2. When I check a project, few sub-jobs are Active for much longer than the others. How do I know if those
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sub-jobs are really active?
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Lets review an example of a problematic run. When you run `./RUNME.bash <name> check`, you see the
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following in the "Active jobs" section:
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````
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Idle: 155829.shared-sched.pace.gatech.edu: 02: 00: Mon Mar 17 14:10:28 EDT 2014
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Sub-jobs:500 Active:4 ( 0.8% ) Eligible:0 ( 0.0% ) Blocked:0 ( 0.0% ) Completed:496 ( 99.2% )
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Idle: 155830.shared-sched.pace.gatech.edu: 02: 00: Mon Mar 17 14:10:28 EDT 2014
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Running jobs: 0.
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Idle jobs: 2.
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````
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That means that the job "155829.shared-sched.pace.gatech.edu" has four Active jobs, while all the others are Completed. This is
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a sign of something problematic. You can see the complete status of each array using
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`checkjob -v <JOB_NAME>`. In our example above, you would run `checkjob -v 155829`. In the output
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of checkjob, most jobs should report "Completed". In this example, there are four jobs that are not
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complete:
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````
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...
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387 : 155829[387] : Completed
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388 : 155829[388] : Running
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389 : 155829[389] : Running
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390 : 155829[390] : Running
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391 : 155829[391] : Running
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392 : 155829[392] : Completed
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...
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````
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So you can simply check these sub-jobs in more detail. For example, if I run `checkjob -v 155829[388]`,
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I see that the job is running in the machine `iw-k30-12.pace.gatech.edu` (Task Distribution), so I can try
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to login to that machine to check if the job is actually running, using `top -u $(whoami)`. However, when
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I run `ssh iw-k30-12`, I got a "Connection closed" error, which means that the machine hung up. At this point,
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you might want to try one of the following solutions:
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2.1. Pause the project using `./RUNME.bash <name> pause`, wait a few minutes, and resume using
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`./RUNME.bash <name> run`. If you tried this a couple of times and you still have sub-jobs hanging, try:
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2.2. Check if your sub-jobs finished. Sometimes sub-jobs die too soon to return a success code, but they actually
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finished. Just run the following command: `ls <SCRATCH>/<name>/success/02.* | wc -l`, where `<SCRATCH>` is the
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value you set for the `SCRATCH` variable in the CONFIG file, and `<name>` is the name of your project. If the
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output of that command is a number, and that number is exactly six times the number of jobs (`MAX_JOBS` in the
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CONFIG file, typically 500), then your step 2 actually finished. In my case, I have 500 jobs, and the output
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was 3000, so my job finished successfully, but the pipeline didn't notice. You can manually tell the pipeline
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to go on running: `touch <SCRATCH>/<name>/success/02`, and pausing/resuming the project (see 2.1 above). If
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the output is not the expected number (in my case, 3000, which is 6*500), DON'T RUN `touch`, just try the
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solution 2.1 above once again.
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#!/bin/bash
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##################### VARIABLES
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# Find the directory of the pipeline
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if [[ "$PDIR" == "" ]] ; then PDIR=$(dirname $(readlink -f $0)); fi ;
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CWD=$(pwd)
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# Load config
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if [[ "$PROJ" == "" ]] ; then PROJ="$1" ; fi
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if [[ "$TASK" == "" ]] ; then TASK="$2" ; fi
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if [[ "$TASK" == "" ]] ; then TASK="check" ; fi
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NAMES=$(ls $PDIR/CONFIG.*.bash | sed -e 's/.*CONFIG\./ o /' | sed -e 's/\.bash//');
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if [[ "$PROJ" == "" ]] ; then
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if [[ "$HELP" == "" ]] ; then
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echo "
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Usage:
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$0 name task
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name The name of the run. CONFIG.name.bash must exist.
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task The action to perform. One of:
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o run: Executes the BLAST.
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o check: Indicates the progress of the task (default).
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o pause: Cancels running jobs (resume using run).
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o dry: Checks that the parameters are correct, but doesn't run.
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o eo: Review all eo files produced in the project.
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See $PDIR/README.md for more information.
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Available names are:
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$NAMES
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" >&2
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else
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echo "$HELP
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Available names are:
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$NAMES
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" >&2
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fi
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exit 1
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fi
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if [[ ! -e "$PDIR/CONFIG.$PROJ.bash" ]] ; then
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echo "$0: Error: Impossible to find $PDIR/CONFIG.$PROJ.bash, available names are:
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$NAMES" >&2
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exit 1
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fi
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source "$PDIR/CONFIG.$PROJ.bash" ;
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SCRATCH="$SCRATCH_DIR/$PROJ" ;
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MINVARS="PDIR=$PDIR,SCRATCH=$SCRATCH,PROJ=$PROJ" ;
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case $QUEUE in
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bioforce-6)
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MAX_H=120 ;;
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iw-shared-6)
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MAX_H=12 ;;
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micro-largedata)
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MAX_H=120 ;;
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biocluster-6 | biohimem-6 | microcluster)
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MAX_H=240 ;;
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*)
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echo "Unrecognized queue: $QUEUE." >&2 ;
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exit 1 ;;
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esac ;
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##################### FUNCTIONS
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function REGISTER_JOB {
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local STEP=$1
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local SUBSTEP=$2
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local MESSAGE=$3
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local JOBID=$4
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if [[ "$JOBID" != "" ]] ; then
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MESSAGE="$MESSAGE [$JOBID]" ;
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echo "$STEP: $SUBSTEP: $(date)" >> "$SCRATCH/log/active/$JOBID" ;
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fi
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echo "$MESSAGE." >> "$SCRATCH/log/status/$STEP" ;
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}
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function LAUNCH_JOB {
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local STEP=$1
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local SUBSTEP=$2
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local MESSAGE=$3
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local BASHFILE=$4
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cd "$SCRATCH/log/eo" ;
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date >> "$SCRATCH/etc/trials" ;
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source "$BASHFILE" || exit 1 ;
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cd $CWD ;
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if [[ "$SENTINEL_JOBID" != "" ]] ; then
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REGISTER_JOB "$STEP" "$SUBSTEP" "Guarding job $NEW_JOBID" "$SENTINEL_JOBID" ;
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fi ;
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REGISTER_JOB "$STEP" "$SUBSTEP" "$MESSAGE" "$NEW_JOBID" ;
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echo $NEW_JOBID ;
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}
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function JOB_DONE {
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STEP=$1
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echo "Done." >> "$SCRATCH/log/status/$STEP" ;
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touch "$SCRATCH/success/$STEP" ;
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echo -n '# ' > "$SCRATCH/etc/trials" ;
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}
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##################### RUN
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# Execute task
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if [[ ! -e "$PDIR/TASK.$TASK.bash" ]] ; then
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echo "Unrecognized task: $TASK." >&2 ;
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exit 1 ;
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else
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source "$PDIR/TASK.$TASK.bash"
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fi
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#!/bin/bash
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##################### RUN
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# Check if it was sourced from RUNME.bash
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if [[ "$PDIR" == "" ]] ; then
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echo "$0: Error: This file is not stand-alone." >&2
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echo " Execute RUNME.bash as described in the README.txt file" >&2
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exit 1
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fi
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# Check if the project exists
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if [[ ! -d "$SCRATCH" ]] ; then
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echo "The project $PROJ doesn't exist at $SCRATCH_DIR." >&2
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echo " Execute '$PDIR/RUNME.bash $PROJ run' first." >&2
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exit 1
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fi
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# Get log:
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echo "==[ Running tasks ]=="
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for i in $(ls $SCRATCH/log/status/* 2>/dev/null) ; do
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echo " $(basename $i): $(tail -n 1 $i)"
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done
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echo ""
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# Get active jobs:
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echo "==[ Active jobs ]=="
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job_r=0
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job_i=0
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job_c=0
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for i in $(ls $SCRATCH/log/active/* 2>/dev/null) ; do
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jid=$(basename $i)
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stat=$(qstat -f1 $jid 2>&1)
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state=$(echo "$stat" | grep '^ *job_state = ' | sed -e 's/.*job_state = //')
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case $state in
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C)
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code=$(echo "$stat" | grep '^ *exit_status = ' | sed -e 's/.*exit_status = //')
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if [[ "$code" == "0" ]] ; then
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mv "$i" "$SCRATCH/log/done/"
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let job_c=$job_c+1
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else
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echo "Warning: Job $jid ($(cat $i|tr -d '\n')) failed with code $code." >&2
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echo " see errors at: $(echo "$stat" | grep '^ *Error_Path = ' | sed -e 's/.*Error_Path = //')"
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mv "$i" "$SCRATCH/log/failed/"
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fi ;;
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R)
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echo " Running: $jid: $(cat "$i")"
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let job_r=$job_r+1 ;;
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[HQW])
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echo " Idle: $jid: $(cat "$i")"
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let job_i=$job_i+1 ;;
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E)
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echo " Canceling: $jid: $(cat "$i")" ;;
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*)
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tmp_err=$(echo "$stat" | grep ERROR)
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if [[ "$tmp_err" == "" ]] ; then
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echo "Warning: Unrecognized state: $jid: $state." >&2
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echo " Please report this problem." >&2
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else
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echo " Error: $jid: $tmp_err"
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fi ;;
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esac
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#subjobs=$(echo "$stat" | grep 'Sub-jobs:' | sed -e 's/.*: *//')
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#if [[ "$subjobs" -gt 0 ]] ; then
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# echo "$stat" | grep '^ *\(Sub-jobs\|Active\|Eligible\|Blocked\|Completed\):' | sed -e 's/^ *//' | sed -e 's/ *//' | tr '\n' ' ' | sed -e 's/^/ /'
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# echo
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#fi
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done
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if [[ $job_c -gt 0 ]] ; then
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echo ""
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echo " Completed since last check: $job_c."
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fi
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if [[ $job_r -gt 0 || $job_i -gt 0 ]] ; then
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echo ""
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echo " Running jobs: $job_r."
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echo " Idle jobs: $job_i."
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fi
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echo ""
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# Auto-trials
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echo "==[ Auto-trials ]=="
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if [[ -e "$SCRATCH/etc/trials" ]] ; then
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trials=$(cat "$SCRATCH/etc/trials" | wc -l | sed -e 's/ //g')
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if [[ $trials -gt 1 ]] ; then
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echo " $trials trials attempted:"
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else
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echo " No recent failures in the current step, job launched:"
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fi
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cat "$SCRATCH/etc/trials" | sed -e 's/^/ o /' | sed -e 's/# $/No active trials\n/g'
|
89
|
+
fi
|
90
|
+
echo ""
|
91
|
+
|
92
|
+
# Step-specific checks:
|
93
|
+
echo "==[ Step summary ]=="
|
94
|
+
todo=1
|
95
|
+
if [[ -e "$SCRATCH/success/00" ]] ; then
|
96
|
+
echo " Successful project initialization."
|
97
|
+
if [[ -e "$SCRATCH/success/01" ]] ; then
|
98
|
+
echo " Successful input preparation."
|
99
|
+
if [[ -e "$SCRATCH/success/02" ]] ; then
|
100
|
+
echo " Successful BLAST execution."
|
101
|
+
if [[ -e "$SCRATCH/success/02" ]] ; then
|
102
|
+
echo " Successful concatenation."
|
103
|
+
echo " Project finished successfully!"
|
104
|
+
todo=0
|
105
|
+
else
|
106
|
+
echo " Concatenating results."
|
107
|
+
fi
|
108
|
+
else
|
109
|
+
echo " Running BLAST."
|
110
|
+
fi
|
111
|
+
else
|
112
|
+
echo " Preparing input."
|
113
|
+
fi
|
114
|
+
else
|
115
|
+
echo " Initializing project."
|
116
|
+
fi
|
117
|
+
|
118
|
+
if [[ "$todo" -eq 1 && $job_r -eq 0 && $job_i -eq 0 ]] ; then
|
119
|
+
echo " Job currently paused. To resume, execute:"
|
120
|
+
echo " $PDIR/RUNME.bash $PROJ run"
|
121
|
+
fi
|
122
|
+
echo
|
123
|
+
|
124
|
+
# Entire log
|
125
|
+
echo "==[ Complete log ]=="
|
126
|
+
for i in $(ls $SCRATCH/log/status/* 2>/dev/null) ; do
|
127
|
+
cat "$i" | sed -e "s/^/ $(basename $i): /"
|
128
|
+
done
|
@@ -0,0 +1,16 @@
|
|
1
|
+
|
2
|
+
[[ "$QUEUE" == "" ]] && echo "Undefined QUEUE" >&2 && exit 1;
|
3
|
+
[[ "$MAX_JOBS" == "" ]] && echo "Undefined MAX_JOBS" >&2 && exit 1;
|
4
|
+
[[ "$PPN" == "" ]] && echo "Undefined PPN" >&2 && exit 1;
|
5
|
+
[[ "$RAM" == "" ]] && echo "Undefined RAM" >&2 && exit 1;
|
6
|
+
[[ "$SCRATCH_DIR" == "" ]] && echo "Undefined SCRATCH_DIR" >&2 && exit 1;
|
7
|
+
[[ "$INPUT" == "" ]] && echo "Undefined INPUT" >&2 && exit 1;
|
8
|
+
[[ "$DB" == "" ]] && echo "Undefined DB" >&2 && exit 1;
|
9
|
+
[[ "$PROGRAM" == "" ]] && echo "Undefined PROGRAM" >&2 && exit 1;
|
10
|
+
[[ "$MAX_TRIALS" == "" ]] && echo "Undefined MAX_TRIALS" >&2 && exit 1;
|
11
|
+
[[ "$(type -t BEGIN)" == "function" ]] || ( echo "Undefined function BEGIN" && exit 1 ) ;
|
12
|
+
[[ "$(type -t BEFORE_BLAST)" == "function" ]] || ( echo "Undefined function BEFORE_BLAST" && exit 1 ) ;
|
13
|
+
[[ "$(type -t RUN_BLAST)" == "function" ]] || ( echo "Undefined function RUN_BLAST" && exit 1 ) ;
|
14
|
+
[[ "$(type -t AFTER_BLAST)" == "function" ]] || ( echo "Undefined function AFTER_BLAST" && exit 1 ) ;
|
15
|
+
[[ "$(type -t END)" == "function" ]] || ( echo "Undefined function END" && exit 1 ) ;
|
16
|
+
|
@@ -0,0 +1,22 @@
|
|
1
|
+
#!/bin/bash
|
2
|
+
|
3
|
+
##################### RUN
|
4
|
+
# Check if it was sourced from RUNME.bash
|
5
|
+
if [[ "$PDIR" == "" ]] ; then
|
6
|
+
echo "$0: Error: This file is not stand-alone." >&2
|
7
|
+
echo " Execute RUNME.bash as described in the README.txt file" >&2 ;
|
8
|
+
exit 1 ;
|
9
|
+
fi ;
|
10
|
+
|
11
|
+
# Check if the project exists
|
12
|
+
if [[ ! -d "$SCRATCH" ]] ; then
|
13
|
+
echo "The project $PROJ doesn't exist at $SCRATCH_DIR." >&2 ;
|
14
|
+
echo " Execute '$PDIR/RUNME.bash $PROJ run' first." >&2 ;
|
15
|
+
exit 1 ;
|
16
|
+
fi ;
|
17
|
+
|
18
|
+
# Review errors
|
19
|
+
(echo -e "==[ Last 10 lines of all e files ]==\nPress q to exit\n" ; tail -n 10 $SCRATCH/log/eo/*.e* ) | less
|
20
|
+
# Review output
|
21
|
+
(echo -e "==[ Last 100 lines of all o files ]==\nPress q to exit\n" ; tail -n 100 $SCRATCH/log/eo/*.o* ) | less
|
22
|
+
|
@@ -0,0 +1,26 @@
|
|
1
|
+
#!/bin/bash
|
2
|
+
|
3
|
+
##################### RUN
|
4
|
+
# Check if it was sourced from RUNME.bash
|
5
|
+
if [[ "$PDIR" == "" ]] ; then
|
6
|
+
echo "$0: Error: This file is not stand-alone." >&2
|
7
|
+
echo " Execute RUNME.bash as described in the README.txt file" >&2 ;
|
8
|
+
exit 1 ;
|
9
|
+
fi ;
|
10
|
+
|
11
|
+
# Get active jobs:
|
12
|
+
echo "======[ check ]======"
|
13
|
+
job_r=0;
|
14
|
+
job_i=0;
|
15
|
+
job_c=0;
|
16
|
+
|
17
|
+
echo "======[ pause ]======"
|
18
|
+
for i in $(ls $SCRATCH/log/active/* 2>/dev/null) ; do
|
19
|
+
echo " Pausing $jid." ;
|
20
|
+
jid=$(basename $i) ;
|
21
|
+
qdel $jid ;
|
22
|
+
done ;
|
23
|
+
|
24
|
+
# Restart auto-trials
|
25
|
+
echo -n > "$SCRATCH/etc/trials" ;
|
26
|
+
|
@@ -0,0 +1,89 @@
|
|
1
|
+
#!/bin/bash
|
2
|
+
|
3
|
+
##################### RUN
|
4
|
+
# Check if it was sourced from RUNME.bash
|
5
|
+
if [[ "$PDIR" == "" ]] ; then
|
6
|
+
echo "$0: Error: This file is not stand-alone. Execute RUNME.bash as described in the README.txt file" >&2
|
7
|
+
exit 1
|
8
|
+
fi
|
9
|
+
|
10
|
+
# Check if too many auto-trials were attempted
|
11
|
+
trials=0 ;
|
12
|
+
if [[ -e "$SCRATCH/etc/trials" ]] ; then
|
13
|
+
trials=$(cat "$SCRATCH/etc/trials" | wc -l | sed -e 's/ //g');
|
14
|
+
if [[ $trials -ge $MAX_TRIALS ]] ; then
|
15
|
+
echo "The maximum number of trials was already attempted, halting." >&2 ;
|
16
|
+
exit 1 ;
|
17
|
+
fi ;
|
18
|
+
fi ;
|
19
|
+
|
20
|
+
# Create the scratch directory
|
21
|
+
if [[ ! -d "$SCRATCH" ]] ; then mkdir -p "$SCRATCH" || exit 1 ; fi;
|
22
|
+
|
23
|
+
if [[ ! -e "$SCRATCH/success/00" ]] ; then
|
24
|
+
# 00. Initialize the project
|
25
|
+
echo "00. Initializing project." >&2 ;
|
26
|
+
mkdir -p "$SCRATCH/tmp" "$SCRATCH/etc" "$SCRATCH/results" "$SCRATCH/success" || exit 1 ;
|
27
|
+
mkdir -p "$SCRATCH/log/active" "$SCRATCH/log/done" "$SCRATCH/log/failed" || exit 1 ;
|
28
|
+
mkdir -p "$SCRATCH/log/status" "$SCRATCH/log/eo" || exit 1 ;
|
29
|
+
echo "Preparing structure." >> "$SCRATCH/log/status/00" ;
|
30
|
+
# Build 01.bash
|
31
|
+
echo "NEW_JOBID=\$(qsub -q '$QUEUE' -l 'walltime=$MAX_H:00:00,mem=$RAM' -v '$MINVARS' -N '$PROJ-01' \\
|
32
|
+
'$PDIR/01.pbs.bash'|tr -d '\\n')" \
|
33
|
+
> "$SCRATCH/etc/01.bash" || exit 1 ;
|
34
|
+
echo "SENTINEL_JOBID=\$(qsub -q '$QUEUE' -l 'walltime=2:00:00' -W \"depend=afterany:\$NEW_JOBID\" \\
|
35
|
+
-v \"$MINVARS,STEP=01,AFTERJOB=\$NEW_JOBID\" -N '$PROJ-01-sentinel' '$PDIR/sentinel.pbs.bash'|tr -d '\\n')" \
|
36
|
+
>> "$SCRATCH/etc/01.bash" || exit 1 ;
|
37
|
+
# Build 02.bash
|
38
|
+
echo "NEW_JOBID=\$(qsub -q '$QUEUE' -l 'walltime=$MAX_H:00:00,mem=$RAM,nodes=1:ppn=$PPN' \\
|
39
|
+
-v '$MINVARS' -N '$PROJ-02' -t '1-$MAX_JOBS' '$PDIR/02.pbs.bash'|tr -d '\\n')" \
|
40
|
+
> "$SCRATCH/etc/02.bash" \
|
41
|
+
|| exit 1 ;
|
42
|
+
echo "SENTINEL_JOBID=\$(qsub -q '$QUEUE' -l 'walltime=2:00:00' -W \"depend=afteranyarray:\$NEW_JOBID\" \\
|
43
|
+
-v \"$MINVARS,STEP=02,AFTERJOB=\$NEW_JOBID\" -N '$PROJ-02-sentinel' '$PDIR/sentinel.pbs.bash'|tr -d '\\n')" \
|
44
|
+
>> "$SCRATCH/etc/02.bash" \
|
45
|
+
|| exit 1 ;
|
46
|
+
# Build 03.bash
|
47
|
+
echo "NEW_JOBID=\$(qsub -q '$QUEUE' -l 'walltime=$MAX_H:00:00,mem=$RAM' -v '$MINVARS' -N '$PROJ-03' \\
|
48
|
+
'$PDIR/03.pbs.bash'|tr -d '\\n')" \
|
49
|
+
> "$SCRATCH/etc/03.bash" || exit 1 ;
|
50
|
+
echo "SENTINEL_JOBID=\$(qsub -q '$QUEUE' -l 'walltime=2:00:00' -W \"depend=afterany:\$NEW_JOBID\" \\
|
51
|
+
-v \"$MINVARS,STEP=03,AFTERJOB=\$NEW_JOBID\" -N '$PROJ-03-sentinel' '$PDIR/sentinel.pbs.bash'|tr -d '\\n')" \
|
52
|
+
>> "$SCRATCH/etc/03.bash" || exit 1 ;
|
53
|
+
|
54
|
+
JOB_DONE "00" ;
|
55
|
+
fi ;
|
56
|
+
|
57
|
+
if [[ ! -e "$SCRATCH/success/01" ]] ; then
|
58
|
+
# 01. Preparing input
|
59
|
+
echo "01. Preparing input." >&2 ;
|
60
|
+
JOB01=$(LAUNCH_JOB "01" "00" "Preparing input files" "$SCRATCH/etc/01.bash") ;
|
61
|
+
echo " New job: $JOB01." >&2 ;
|
62
|
+
else
|
63
|
+
if [[ ! -e "$SCRATCH/success/02" ]] ; then
|
64
|
+
# 02. Launching BLAST
|
65
|
+
echo "02. Launching BLAST." >&2 ;
|
66
|
+
JOB02=$(LAUNCH_JOB "02" "00" "Running BLAST" "$SCRATCH/etc/02.bash") ;
|
67
|
+
echo " New job: $JOB02." >&2 ;
|
68
|
+
# Clean on resubmission
|
69
|
+
cleaned=0
|
70
|
+
echo -n " Cleaning completed sub-jobs on $JOB02: " >&2 ;
|
71
|
+
for jobi in $(seq 1 $MAX_JOBS) ; do
|
72
|
+
if [[ -e "$SCRATCH/success/02.$jobi" ]] ; then
|
73
|
+
qdel "$JOB02""[$jobi]" &> /dev/null ;
|
74
|
+
let cleaned=$cleaned+1 ;
|
75
|
+
fi ;
|
76
|
+
done ;
|
77
|
+
echo "$cleaned sub-jobs completed." >&2 ;
|
78
|
+
else
|
79
|
+
if [[ ! -e "$SCRATCH/success/03" ]] ; then
|
80
|
+
# 03. Finalize
|
81
|
+
echo "03. Finalizing." >&2 ;
|
82
|
+
JOB03=$(LAUNCH_JOB "03" "00" "Concatenating results" "$SCRATCH/etc/03.bash") ;
|
83
|
+
echo " New job: $JOB03." >&2 ;
|
84
|
+
else
|
85
|
+
echo "Project complete, nothing to run." ;
|
86
|
+
fi ;
|
87
|
+
fi ;
|
88
|
+
fi ;
|
89
|
+
|
@@ -0,0 +1,29 @@
|
|
1
|
+
# blast.pbs pipeline
|
2
|
+
# Sentinel script
|
3
|
+
|
4
|
+
echo "Sentinel script after $AFTERJOB" ;
|
5
|
+
|
6
|
+
# Step-specific checks
|
7
|
+
if [[ "$STEP" == "02" ]] ; then
|
8
|
+
# Read configuration
|
9
|
+
cd $SCRATCH ;
|
10
|
+
TASK="dry" ;
|
11
|
+
source "$PDIR/RUNME.bash" ;
|
12
|
+
|
13
|
+
# Check tasks
|
14
|
+
INCOMPLETE=0;
|
15
|
+
for i in $(seq 1 $MAX_JOBS) ; do
|
16
|
+
if [[ ! -e "$SCRATCH/success/02.$i" ]] ; then
|
17
|
+
let INCOMPLETE=$INCOMPLETE+1 ;
|
18
|
+
fi ;
|
19
|
+
done
|
20
|
+
if [[ $INCOMPLETE -eq 0 ]] ; then
|
21
|
+
JOB_DONE "02" ;
|
22
|
+
else
|
23
|
+
echo "$INCOMPLETE incomplete jobs, re-launching step 02." ;
|
24
|
+
fi ;
|
25
|
+
fi
|
26
|
+
|
27
|
+
# Continue the workflow
|
28
|
+
"$PDIR/RUNME.bash" "$PROJ" run || exit 1 ;
|
29
|
+
|
@@ -0,0 +1,49 @@
|
|
1
|
+
@author: Luis Miguel Rodriguez-R <lmrodriguezr at gmail dot com>
|
2
|
+
|
3
|
+
@update: Feb-26-2015
|
4
|
+
|
5
|
+
@license: artistic 2.0
|
6
|
+
|
7
|
+
@status: auto
|
8
|
+
|
9
|
+
@pbs: yes
|
10
|
+
|
11
|
+
# IMPORTANT
|
12
|
+
|
13
|
+
This pipeline was developed for the [PACE cluster](http://pace.gatech.edu/). You
|
14
|
+
are free to use it in other platforms with adequate adjustments.
|
15
|
+
|
16
|
+
# PURPOSE
|
17
|
+
|
18
|
+
Performs assembly using IDBA-UD, designed for Single-Cell Genomics and Metagenomics.
|
19
|
+
|
20
|
+
# HELP
|
21
|
+
|
22
|
+
1. Files preparation:
|
23
|
+
|
24
|
+
1.1. Obtain the enveomics package in the cluster. You can use:
|
25
|
+
`git clone https://github.com/lmrodriguezr/enveomics.git`
|
26
|
+
|
27
|
+
1.2. Prepare the trimmed reads (e.g., use trim.bs) in interposed FastA format. Files
|
28
|
+
must be raw, not zipped or packaged. Filenames must conform the format:
|
29
|
+
<name>.CoupledReads.fa, where <name> is the name of the sample. Locate all the
|
30
|
+
files within a folder named 04.trimmed_fasta, within your project folder. If you
|
31
|
+
used trim.pbs, no further action is necessary.
|
32
|
+
|
33
|
+
2. Pipeline execution:
|
34
|
+
|
35
|
+
2.1. Simply execute `./RUNME.bash <dir> <data_type>`, where `<dir>` is the folder containing
|
36
|
+
the 04.trimmed_fasta folder, and `<data_type>` is a supported type of data (see help
|
37
|
+
message running `./RUNME.bash` without arguments).
|
38
|
+
|
39
|
+
3. What to expect:
|
40
|
+
|
41
|
+
By the end of the run, you should find the folder *05.assembly*, including the following
|
42
|
+
files for each dataset:
|
43
|
+
|
44
|
+
3.1. `<dataset>`: The IDBA output folder.
|
45
|
+
|
46
|
+
3.2. `<dataset>.AllContigs.fna`: All contigs longer than 200bp in FastA format.
|
47
|
+
|
48
|
+
3.2. `<dataset>.LargeContigs.fna`: Contigs longer than 500bp in FastA format.
|
49
|
+
|