diff run_snp_analysis.sh @ 0:1955f03f092e

initial commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_snp_analysis.sh	Tue Sep 02 14:16:04 2014 -0400
@@ -0,0 +1,37 @@
+#!/bin/bash
+
+shopt -s extglob; 
+#turns on extended globbing features ('!' can then be used to exclude file names)
+
+#entering SCRATCHDIR used for computation on Metacentrum nodes
+cd $SCRATCHDIR;
+
+#copying input files
+cp -r /storage/brno2/home/nicki/linkyx/* . 
+
+#logfile
+echo "Copying of the input data finished." `date` >/storage/brno2/home/nicki/linkyx/log;
+
+#adding needed modules
+module add trinity;
+module add bwa-0.6.2;
+module add bowtie-0.12.8;
+module add ics.muni.cz jdk-1.6.0; #initialization of the specific JAVA version
+module add samtools-0.1.18alt #samtools recompiled with -fPIC parameter
+module add picard-1.80;
+module add fastx-0.0.13;
+
+#export of perl modules
+export PERL5LIB=/storage/brno2/home/nicki/modules/File-Slurp-9999.19/lib:/storage/brno2/home/nicki/modules/Bio-SamTools-1.37/lib:/storage/brno2/home/nicki/modules/BioPerl-1.6.901:/storage/brno2/home/nicki/modules/Data-Dumper-2.139:/storage/brno2/home/nicki/modules/libwww-perl-6.04/lib:/storage/brno2/home/nicki/modules/URI-1.60:/storage/brno2/home/nicki/modules/UUID-Generator-PurePerl-0.04_02/lib:/storage/brno2/home/nicki/modules/UUID-Object-0.81:/storage/brno2/home/nicki/modules/UUID-Generator-PurePerl-0.04_02/lib/UUID/:Generator:/storage/brno2/home/nicki/modules/UUID-Object-0.81/lib:/home/nicki/lib:/storage/brno2/home/nicki/modules/bio_samtools_bin/local/lib/perl/5.10.0:/home/nicki/lib/x86_64-linux-gnu-thread-multi:/home/nicki/lib/man:/storage/brno2/home/nicki/modules/Data-GUID-0.046/lib:/home/nicki/perl/lib/perl5:/home/nicki/perl/lib/perl:/home/nicki/perl/share/perl:/home/nicki/perl/share/perl5:/home/nicki/lib/lib/perl5:/home/nicki/lib/lib/perl:/home/nicki/lib/share/perl:/home/nicki/lib/share/perl5:/home/nicki/lib/perl5/:/home/nicki/lib/perl5/site_perl:;
+
+#execution of the linkYX pipeline
+./runLinkYX.sh [e-mail] misa
+
+echo "Copying of the output data started." `date` >>/storage/brno2/home/nicki/linkyx/log;
+
+#copying output files
+cp -ar * /storage/brno2/home/nicki/linkyx_out;
+#cleaning
+rm -rf $SCRATCHDIR
+trap "rm -rf $SCRATCHDIR" SIGTERM
+