Mercurial > repos > fubar > htseq_bams_to_count_matrix

changeset 22:fd07a014d2e7 draft

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Uploaded
author fubar
date Thu, 13 Jun 2013 06:32:03 -0400
parents 349261fef17b
children 617d402f4c32
files htseq_bams_to_count_matrix/tool_dependencies.xml
diffstat 1 files changed, 9 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/htseq_bams_to_count_matrix/tool_dependencies.xml	Thu Jun 13 06:23:54 2013 -0400
+++ b/htseq_bams_to_count_matrix/tool_dependencies.xml	Thu Jun 13 06:32:03 2013 -0400
@@ -23,7 +23,7 @@
                 <!-- install matplotlib -->
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">export PYTHONPATH=$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY:$PYTHONPATH &amp;&amp; 
-                    export CPLUS_INCLUDE_PATH=$FREETYPE_INCLUDE_DIR:$FREETYPE_INCLUDE_DIR/freetype2/$CPLUS_INCLUDE_PATH &amp;&amp; 
+                    export CPLUS_INCLUDE_PATH=$FREETYPE_INCLUDE_DIR:$FREETYPE_INCLUDE_DIR/freetype2/:$CPLUS_INCLUDE_PATH &amp;&amp; 
                     export LIBRARY_PATH=$FREETYPE_LIB_DIR:$LIBRARY_PATH &amp;&amp; 
                     python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
                 <action type="set_environment">
@@ -42,6 +42,14 @@
                 <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
                 <action type="make_directory">$INSTALL_DIR/lib64/python</action> <!-- Not sure why these must be made apriori, but install fails otherwise -->
+                <action type="set_environment_for_install">
+                        <package name="numpy" toolshed="http://testtoolshed.g2.bx.psu.edu" version="1.7.1">
+                            <repository name="package_numpy_1_7" owner="blankenberg" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+                        </package>
+                        <package name="freetype" toolshed="http://testtoolshed.g2.bx.psu.edu" version="2.4.11">
+                            <repository name="package_freetype_2_4" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+                        </package>
+                </action>
                 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
                 <action type="set_environment">
                     <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>