# HG changeset patch
# User malbuquerque
# Date 1421364572 18000
# Node ID 97973e7ca771a8eedde8e2e203c06d670a2e9ad4
# Parent c2e36f5b53c7ad2be74ba068e77f5cea9b2fc6f2
Uploaded
diff -r c2e36f5b53c7 -r 97973e7ca771 factera/factera.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/factera.xml Thu Jan 15 18:29:32 2015 -0500
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+ Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm
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+ #if $cond.additionalOpt.value == "no"
+ perl $FACTERA_DIR/factera-v1.4.3.pl -o ./ $sortedBam $exonBed $genome2Bit
+ #else
+ perl $FACTERA_DIR/factera-v1.4.3.pl -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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+ cat *fusions.txt > $outfile;
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+ This tool does Factera
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diff -r c2e36f5b53c7 -r 97973e7ca771 factera/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/tool_dependencies.xml Thu Jan 15 18:29:32 2015 -0500
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+ http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0608.tar.gz
+ perl Makefile.PL PREFIX=$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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