Skip to content

Instantly share code, notes, and snippets.

View mmterpstra's full-sized avatar

mmterpstra

8 followers · 4 following
View GitHub Profile
@mmterpstra
mmterpstra / uikit-default.css
Created December 18, 2014 14:30
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;
}
@mmterpstra
mmterpstra / easybuild_test_report_easyconfigs_pr1741_20150024-UTC-15-00-47.md
Created June 24, 2015 15:00
EasyBuild test report for easyconfigs PR #1741

Test report for easybuilders/easybuild-easyconfigs#1741

Test result

Build succeeded for 1 out of 1 (1 easyconfigs in this PR)

Overview of tested easyconfigs (in order)

  • SUCCESS cramtools-v2.0-Java-1.7.0_80.eb

Time info

  • start: Wed, 24 Jun 2015 14:59:21 +0000 (UTC)
@mmterpstra
mmterpstra / easybuild_test_report_easyconfigs_pr1741_20152901-UTC-11-29-44.md
Created July 1, 2015 11:29
EasyBuild test report for easyconfigs PR #1741

Test report for easybuilders/easybuild-easyconfigs#1741

Test result

Build succeeded for 1 out of 1 (1 easyconfigs in this PR)

Overview of tested easyconfigs (in order)

  • SUCCESS cramtools-2.0-Java-1.7.0_80.eb

Time info

  • start: Wed, 01 Jul 2015 11:28:54 +0000 (UTC)
@mmterpstra
mmterpstra / easybuild_test_report_easyconfigs_pr1741_20152701-UTC-12-27-26.md
Created July 1, 2015 12:27
EasyBuild test report for easyconfigs PR #1741

Test report for easybuilders/easybuild-easyconfigs#1741

Test result

Build succeeded for 1 out of 1 (1 easyconfigs in this PR)

Overview of tested easyconfigs (in order)

  • SUCCESS cramtools-2.0-Java-1.7.0_80.eb

Time info

  • start: Wed, 01 Jul 2015 12:26:42 +0000 (UTC)
@mmterpstra
mmterpstra / parameters.molgenis.csv
Created September 1, 2015 09:08
Additional files
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
@mmterpstra
mmterpstra / RemoveDuplicatesCompute.pl
Last active October 28, 2016 12:28
molgenis-compute tools
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);
}
@mmterpstra
mmterpstra / CreateBurnDown.rscript
Last active February 18, 2023 22:10
Use R to generate your Burndown Charts
#!/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
@mmterpstra
mmterpstra / Samplesheet_nugene.csv
Created September 21, 2016 07:41
Basecall Recepies
We can make this file beautiful and searchable if this error is corrected: It looks like row 2 should actually have 1 column, instead of 2 in line 1.
[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
@mmterpstra
mmterpstra / splitfqbyCATG.md
Last active August 30, 2017 06:57
Split fastq by sequence. if you ligated different inserts to eachother them this script can split the reads into separate reads. tags: TLA DEEPSAGE SAGE HTS NGS

###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

@mmterpstra
mmterpstra / FluxToTab.pl
Created November 9, 2016 14:12
#!/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