# HG changeset patch
# User yhoogstrate
# Date 1426921154 14400
# Node ID 267d0c2ebe56955505161faf5dc575dbd7417ec7
Uploaded
diff -r 000000000000 -r 267d0c2ebe56 fuma.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fuma.xml Sat Mar 21 02:59:14 2015 -0400
@@ -0,0 +1,69 @@
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+ FuMa (FusionMatcher) matches detected fusion genes based on gene name subset matching (designed in particular for RNA-Seq).
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+ fuma
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+ fuma --version
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+ #import pipes
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+ #set $gene_annotations = []
+ #set $samples = []
+ #set $links = []
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+ #for $i, $d in enumerate( $datasets )
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+ #set $sample_name = pipes.quote(str($d['sample'].name))
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+ #set $gene_annotations = $gene_annotations + [ "ga_" + str($i) + ":" + str($d['gene_annotation'].file_name) ]
+
+ #set $samples = $samples + [ $sample_name + ":" + str($d['format']) + ":" + str($d['sample'].file_name) ]
+ #set $links = $links + [ $sample_name + ":" + str("ga_") + str($i) ]
+ #end for
+
+ #set $gene_annotations_str = " ".join(gene_annotations)
+ #set $samples_str = " ".join(samples)
+ #set $links_str = " ".join(links)
+
+ fuma
+ -a
+ $gene_annotations_str
+ -s
+ $samples_str
+ -l
+ $links_str
+ -f 'list'
+ -o $fuma_overview
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diff -r 000000000000 -r 267d0c2ebe56 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Sat Mar 21 02:59:14 2015 -0400
@@ -0,0 +1,29 @@
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+ $INSTALL_DIR/lib/python
+ $INSTALL_DIR/lib64/python
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+ git clone https://github.com/yhoogstrate/fuma.git fuma &&
+ cd fuma &&
+ git reset --hard 7d22741f37549eb65b85136316ca0dd2cda529ec &&
+
+ export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &&
+ python setup.py build &&
+ python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin
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+ $INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python
+ $INSTALL_DIR/bin
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+ Downloads and installs Fuma; requires python pip and get to be installed.
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