Test report for easybuilders/easybuild-easyconfigs#1741
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
- SUCCESS cramtools-v2.0-Java-1.7.0_80.eb
- start: Wed, 24 Jun 2015 14:59:21 +0000 (UTC)
html { | |
font: normal 14px / 20px "Helvetica Neue", Helvetica, Arial, sans-serif; | |
-webkit-text-size-adjust: 100%; | |
-ms-text-size-adjust: 100%; | |
background: #ffffff; | |
color: #444444; | |
} | |
body { | |
margin: 0; | |
} |
Test report for easybuilders/easybuild-easyconfigs#1741
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
Test report for easybuilders/easybuild-easyconfigs#1741
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
Test report for easybuilders/easybuild-easyconfigs#1741
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
queue | mem | walltime | nodes | ppn | defaultInterpreter | stage | checkStage | WORKDIR | root | group | tmp | resDir | toolDir | projectDir | fastqcMod | bwaMod | picardMod | RMod | gatkMod | snpEffMod | varScanMod | samtoolsMod | vcfToolsMod | genomeLatSpecies | genomeSpecies | genomeBuild | genomeGrchBuild | ensemblVersion | onekgGenomeFasta | onekgGenomeFastaIdxBase | onekgGenomeFastaDict | goldStandardVcf | goldStandardVcfIdx | oneKgPhase1SnpsVcf | oneKgPhase1SnpsVcfIdx | oneKgPhase1IndelsVcf | oneKgPhase1IndelsVcfIdx | ${resDir}/${genomeBuild}/variants/1000G_Phase3/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf.gz | dbsnpVcf | dbsnpVcfIdx | exacVcf | exacVcfIdx | indelRealignmentTargets | snpEffStats | motifBin | nextProtBin | pwmsBin | regulation_CD4Bin | regulation_GM06990Bin | regulation_GM12878Bin | regulation_H1ESCBin | regulation_HeLaS3Bin | regulation_HepG2Bin | regulation_HMECBin | regulation_HSMMBin | regulation_HUVECBin | regulation_IMR90Bin | regulation_K562bBin | regulation_K562Bin | regulation_NHABin | regulation_NHEKBin | snpEffectPredictorBin | dbnsfp | dbnsfpTbi | oneKgP1wgsVcf | oneKgP1wgsVcfIdx | c |
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use warnings; | |
use strict; | |
use Data::Dumper; | |
main(); | |
sub main { | |
InfoMsg("Use 'perl $0 /Path/To/Compute/Jobs/*.sh'\n"); | |
InfoMsg("Commandline : $0 ".join(" ",@ARGV)."\n"); | |
DuplicateParameterRemoval(@ARGV); | |
} |
#!/usr/bin/env R | |
#maye add commandline to script | |
#Yeah, it is a little low I know. | |
scrum.points=4 | |
scrum.startdate="2016/10/24" | |
scrum.sprint="93" | |
scrum.days=19 |
[Header] | |
IEMFileVersion,4 | |
Investigator Name,JohnDoe | |
Experiment Name,Experiment1 | |
Date,01/01/2000 | |
Workflow,GenerateFASTQ | |
Application,FASTQ Only | |
Assay,TruSeq LT | |
Description,Nugene samples | |
Chemistry,Default |
###splitfqbyCATG.pl Splits reads by CA-TG Sequence. Due to PE difficulties writes to single file.
#Install
needs gzip
and perl
as prerequisites. On ubuntu installation is as easy as sudo apt install gzip perl && wget https://gist.githubusercontent.com/mmterpstra/2417200a96f841862c82220893490202/raw/b4172b5f907c46eb862c5387abca168fd6583388/splitfqbyCATG.pl
#Use perl splitfqbyCATG.pl [-q 0 ] reads_1.in.fq.gz reads.out.fq.gz [reads_2.in.fq.gz ]
###Example 1
#!/usr/bin/perl | |
use strict; | |
use warnings; | |
my $credits = "Written by Miente Martijn Terpstra from UMCG Department of Genetics subgroup oncogentics last modified [Thu Jul 4 16:35:29 CEST 2013]"; | |
my $exampleGTF = <<"END"; | |
chr1 HAVANA transcript 12010 13670 . + . transcript_id "ENST00000450305.2"; locus_id "chr1:11869-14412W"; gene_id "ENSG00000223972.4"; reads 0.000000; length 632; RPKM 0.000000 | |
chr1 HAVANA transcript 11869 14409 . + . transcript_id "ENST00000456328.2"; locus_id "chr1:11869-14412W"; gene_id "ENSG00000223972.4"; reads 232.000000; length 1657; RPKM 6.344208 |