Mercurial > repos > fubar > htseq_bams_to_count_matrix

changeset 19:2ab11896fd22 draft

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Uploaded
author fubar
date Thu, 13 Jun 2013 03:37:30 -0400
parents 8c5184649b23
children 9aa25eb1365b
files htseq_bams_to_count_matrix/generatetest.sh htseq_bams_to_count_matrix/tool_dependencies.xml
diffstat 2 files changed, 5 insertions(+), 0 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/htseq_bams_to_count_matrix/generatetest.sh	Thu Jun 13 03:37:30 2013 -0400
@@ -0,0 +1,1 @@
+python ../htseqsams2mx.py -g rn4_chr20_100k.gtf -o test.xls --samf "'rn4chr20test1.bam','col1'" --samf "'rn4chr20test2.bam','col2'"
--- a/htseq_bams_to_count_matrix/tool_dependencies.xml	Fri Jun 07 07:35:11 2013 -0400
+++ b/htseq_bams_to_count_matrix/tool_dependencies.xml	Thu Jun 13 03:37:30 2013 -0400
@@ -22,6 +22,10 @@
                 </action>
                 <!-- install matplotlib -->
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                 <action type="shell_command">echo "ls $FREETYPE_INCLUDE_DIR =:"  </action>
+                 <action type="shell_command">`ls $FREETYPE_INCLUDE_DIR` </action>
+                 <action type="shell_command">echo "ls $FREETYPE_INCLUDE_DIR/freetype2/ =:"  </action>
+                 <action type="shell_command">`ls $FREETYPE_INCLUDE_DIR/freetype2/` </action>
                 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY &amp;&amp; 
                     export CPLUS_INCLUDE_PATH=$FREETYPE_INCLUDE_DIR:$FREETYPE_INCLUDE_DIR/freetype2/ &amp;&amp; 
                     export LIBRARY_PATH=$FREETYPE_LIB_DIR &amp;&amp;