Mercurial > repos > biomonika > linkyx

annotate run_snp_analysis.sh @ 0:05c27700e5ca

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author biomonika <biomonika@psu.edu>
date Thu, 04 Sep 2014 18:24:19 -0400
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biomonika <biomonika@psu.edu>
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1 #!/bin/bash
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2
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3 shopt -s extglob;
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4 #turns on extended globbing features ('!' can then be used to exclude file names)
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6 #entering SCRATCHDIR used for computation on Metacentrum nodes
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7 cd $SCRATCHDIR;
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8
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9 #copying input files
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10 cp -r /storage/brno2/home/nicki/linkyx/* .
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12 #logfile
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13 echo "Copying of the input data finished." `date` >/storage/brno2/home/nicki/linkyx/log;
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15 #adding needed modules
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16 module add trinity;
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17 module add bwa-0.6.2;
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18 module add bowtie-0.12.8;
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19 module add ics.muni.cz jdk-1.6.0; #initialization of the specific JAVA version
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20 module add samtools-0.1.18alt #samtools recompiled with -fPIC parameter
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21 module add picard-1.80;
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22 module add fastx-0.0.13;
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24 #export of perl modules
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25 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:;
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27 #execution of the linkYX pipeline
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28 ./runLinkYX.sh michalovova.monika@gmail.com misa
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30 echo "Copying of the output data started." `date` >>/storage/brno2/home/nicki/linkyx/log;
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32 #copying output files
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33 cp -ar * /storage/brno2/home/nicki/linkyx_out;
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34 #cleaning
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35 rm -rf $SCRATCHDIR
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36 trap "rm -rf $SCRATCHDIR" SIGTERM
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