# HG changeset patch
# User fubar
# Date 1370565538 14400
# Node ID ba2ee6c83fe5dbbbdd2f60177dde7e40da5c3098
# Parent  1c69e32649cb3a5a5b20f499561198e513e78e97
Uploaded

diff -r 1c69e32649cb -r ba2ee6c83fe5 htseq_bams_to_count_matrix/htseqsams2mx.xml
--- a/htseq_bams_to_count_matrix/htseqsams2mx.xml	Thu Jun 06 20:35:40 2013 -0400
+++ b/htseq_bams_to_count_matrix/htseqsams2mx.xml	Thu Jun 06 20:38:58 2013 -0400
@@ -4,7 +4,7 @@
       <requirement type="package" version="2.4.11">freetype</requirement>
       <requirement type="package" version="0.5.4p3">package_htseq_0_5_4</requirement>
       <requirement type="package" version="1.7.1">package_numpy_1_7</requirement>
-      <requirement type="package" version="1.2_1">matplotlib</requirement>
+      <requirement type="package" version="1.2.1">matplotlib</requirement>
     </requirements>
     <command interpreter="python">
     htseqsams2mx.py -g "$gfffile" -o "$outfile" -m "$model" --id_attribute "$id_attr" --feature_type "$feature_type"
diff -r 1c69e32649cb -r ba2ee6c83fe5 htseq_bams_to_count_matrix/tool_dependencies.xml
--- a/htseq_bams_to_count_matrix/tool_dependencies.xml	Thu Jun 06 20:35:40 2013 -0400
+++ b/htseq_bams_to_count_matrix/tool_dependencies.xml	Thu Jun 06 20:38:58 2013 -0400
@@ -14,14 +14,13 @@
 
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="ad6ebe2c75ef" name="package_numpy_1_7" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-                        <package name="numpy" version="1.7.1" />
-                    </repository>
-                    <repository changeset_revision="4e54e357ac25" name="package_freetype_2_4" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-                        <package name="freetype" version="2.4.11" />
-                    </repository>
+                        <package name="package_numpy_1_7" toolshed="http://testtoolshed.g2.bx.psu.edu" version="1.7.1">
+                            <repository name="package_numpy_1_7" owner="blankenberg" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                        </package>
+                        <package name="freetype" toolshed="http://testtoolshed.g2.bx.psu.edu" version="2.4.11">
+                            <repository name="package_freetype_2_4" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+                        </package>
                 </action>
-
                 <!-- install matplotlib -->
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY &amp;&amp;