# HG changeset patch
# User malbuquerque
# Date 1421448004 18000
# Node ID c793d9c3f26b6e2eeb4a6013f935e55019c925e2
# Parent 8ca27ecc9f7d54f9c7342637619f96cccf79fbfb
Uploaded
diff -r 8ca27ecc9f7d -r c793d9c3f26b factera/factera.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/factera.xml Fri Jan 16 17:40:04 2015 -0500
@@ -0,0 +1,60 @@
+
+
+ Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm
+
+
+ samtools
+ blast+
+ ucsc_user_apps
+ perl
+ factera
+ perl_descriptive_statistics
+ FACTERA_DIR
+
+
+
+
+ #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
+
+
+ if [ -f "*fusions.txt" ]; then cat *fusions.txt > $outfile ; else echo "No Fusions" > $outfile ; fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool does Factera
+
+
diff -r 8ca27ecc9f7d -r c793d9c3f26b factera/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/tool_dependencies.xml Fri Jan 16 17:40:04 2015 -0500
@@ -0,0 +1,45 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0608.tar.gz
+ perl Makefile.PL PREFIX=$INSTALL_DIR
+ make
+ make install
+
+ $INSTALL_DIR/lib/perl5/site_perl
+
+
+
+
+
+
+
+
+ http://factera.stanford.edu/files/factera-v1.4.3.pl
+
+ .
+ $INSTALL_DIR
+
+
+ $INSTALL_DIR
+
+
+
+
+
+