pjbriggs

diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
index 3d28462..5c98da6 100755
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
@@ -81,7 +81,7 @@ class CompressedFile( object ):
         if self.file_type == 'zip':
             for zipped_file in self.getmembers():
                 filename = self.getname( zipped_file )
-                absolute_filepath = os.path.join( extraction_path, filename )
+                absolute_filepath = os.path.join( path, filename )

pjbriggs

#!/usr/bin/bash
#
packages="dplyr coloc readr tidyr stringr optparse"

export INSTALL_DIR=$(pwd)/R_LIBS/CRAFT-GP
if [ ! -d $INSTALL_DIR ] ; then
    mkdir -p $INSTALL_DIR
fi
export R_LIBS=$R_LIBS:$INSTALL_DIR
for package in $packages ; do

pjbriggs

#!/bin/bash
#
# Run example CRAFT-GP pipeline based on docs
#
# 0. Set up test data
if [ ! -d test-data ] ; then
    mkdir test-data
fi
cat >test-data/test_index_snps.in <<EOF
rs	chr	position

pjbriggs

#!/usr/bin/env perl
#
# Client JSV script from Mark Lundie for running cellranger
# pipeline
#
# Strips "-pe smp.pe 1" lines from job submission scripts
# (requests for >1 core will be kept unchanged)
#
# Include in qsub commands using -jsv PATH/TO/sge.strip_pe.pl