# HG changeset patch
# User malbuquerque
# Date 1421434524 18000
# Node ID a81a91bfb789c3d9878daebd8318ec887559584c
# Parent ca4f8e80a36a6fd282920ce3804e9cbfa22dd3cf
Uploaded
diff -r ca4f8e80a36a -r a81a91bfb789 factera/factera.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/factera.xml Fri Jan 16 13:55:24 2015 -0500
@@ -0,0 +1,59 @@
+
+
+ Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm
+
+
+ package_samtools_0_1_19
+ package_blast_plus_2_2_26
+ package_ucsc_user_apps
+ perl
+ factera_1_4_3
+ FACTERA_DIR
+
+
+
+
+ #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
+
+
+ cat *fusions.txt > $outfile;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ This tool does Factera
+
+
diff -r ca4f8e80a36a -r a81a91bfb789 factera/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/tool_dependencies.xml Fri Jan 16 13:55:24 2015 -0500
@@ -0,0 +1,52 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0608.tar.gz
+ perl Makefile.PL PREFIX=$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
+
+
+
+
+
+
+