# HG changeset patch
# User malbuquerque
# Date 1421451164 18000
# Node ID a50dd32c32ccf30624dec2932d4e05ebd703d59e
# Parent a4af1a76fae3a74ff07a11794f43935ea54f9c36
Uploaded
diff -r a4af1a76fae3 -r a50dd32c32cc factera/factera.xml
--- a/factera/factera.xml Fri Jan 16 18:13:46 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
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- Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm
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- samtools
- blast+
- ucsc_user_apps
- perl
- factera
- perl_descriptive_statistics
- FACTERA_DIR
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- #if $cond.additionalOpt == "no"
- perl \$FACTERA_DIR/factera-v1.4.3.pl -F -o ./ $sortedBam $exonBed $genome2Bit;
- #else
- perl \$FACTERA_DIR/factera-v1.4.3.pl -F -r $cond.r -m $cond.m -x $cond.x -s $cond.s -f $cond.f -S $cond.S
- -k $cond.k -c $cond.c -b $cond.b -p $cond.p -a $cond.a -o ./ $sortedBam $exonBed $genome2Bit;
- #end if
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- if [ -e *fusions.txt ]; then cat *fusions.txt > $outfile ; else echo "No Fusions" > $outfile ; fi
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- This tool does Factera
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diff -r a4af1a76fae3 -r a50dd32c32cc factera/tool_dependencies.xml
--- a/factera/tool_dependencies.xml Fri Jan 16 18:13:46 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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- http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0608.tar.gz
- perl Makefile.PL PREFIX=$INSTALL_DIR
- make
- make install
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- $INSTALL_DIR/lib/perl5/site_perl
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- http://factera.stanford.edu/files/factera-v1.4.3.pl
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- .
- $INSTALL_DIR
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- $INSTALL_DIR
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