# HG changeset patch
# User malbuquerque
# Date 1421447849 18000
# Node ID 9770263a050c92627e83c76cb68f5113cdffda20
# Parent 5749b96804c326227425a828afeaff8c7bc96ba4
Uploaded
diff -r 5749b96804c3 -r 9770263a050c factera/factera.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/factera.xml Fri Jan 16 17:37:29 2015 -0500
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+ Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm
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+ samtools
+ blast+
+ ucsc_user_apps
+ perl
+ factera
+ FACTERA_DIR
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+ #if $cond.additionalOpt == "no"
+ perl \$FACTERA_DIR/factera-v1.4.3.pl -o -F ./ $sortedBam $exonBed $genome2Bit;
+ #else
+ perl \$FACTERA_DIR/factera-v1.4.3.pl -r -F $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 [ -f "*fusions.txt" ]; then cat *fusions.txt > $outfile ; else echo "No Fusions" > $outfile ; fi
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+ This tool does Factera
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diff -r 5749b96804c3 -r 9770263a050c factera/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/tool_dependencies.xml Fri Jan 16 17:37:29 2015 -0500
@@ -0,0 +1,45 @@
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+ http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0608.tar.gz
+ perl Makefile.PL PREFIX=$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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