# HG changeset patch
# User malbuquerque
# Date 1421436155 18000
# Node ID 14853655737f17c5c4d53d2d5d2e787cf45b6f0d
# Parent 0831d918fce120229d903a711e88cfe84290c31b
Uploaded
diff -r 0831d918fce1 -r 14853655737f factera/factera.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/factera.xml Fri Jan 16 14:22:35 2015 -0500
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+ Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm
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+ package_samtools_0_1_19
+ package_blast_plus_2_2_26
+ package_ucsc_user_apps
+ perl
+ factera_1_4_3
+ FACTERA_DIR
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+ #if $cond.additionalOpt == "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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+ if [ -f "*fusions.txt" ]; then cat *fusions.txt > $outfile ; else echo "No Fusions" > $outfile ; fi
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+ This tool does Factera
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diff -r 0831d918fce1 -r 14853655737f factera/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/tool_dependencies.xml Fri Jan 16 14:22:35 2015 -0500
@@ -0,0 +1,45 @@
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+ http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0608.tar.gz
+ perl Makefile.PL PREFIX=$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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