Mercurial > repos > fubar > htseq_bams_to_count_matrix

changeset 24:48c66da0ef3a draft

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Uploaded
author fubar
date Thu, 13 Jun 2013 07:47:04 -0400
parents 617d402f4c32
children 8f425715f549
files htseq_bams_to_count_matrix/tool_dependencies.xml
diffstat 1 files changed, 4 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- a/htseq_bams_to_count_matrix/tool_dependencies.xml	Thu Jun 13 06:39:20 2013 -0400
+++ b/htseq_bams_to_count_matrix/tool_dependencies.xml	Thu Jun 13 07:47:04 2013 -0400
@@ -7,35 +7,7 @@
         <repository changeset_revision="4e54e357ac25" name="package_freetype_2_4" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="matplotlib" version="1.2.1">
-        <install version="1.0">
-            <actions>
-                <!-- first action is always downloading -->
-                <action type="download_by_url">http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.2.1/matplotlib-1.2.1.tar.gz</action>
-                <!-- populate the environment variables from the dependend repos -->
-                <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>
-                <!-- install matplotlib -->
-                <action type="make_directory">$INSTALL_DIR/lib/python</action>
-                 <action type="shell_command">echo "### PYTHONPATH = $PYTHONPATH, PYTHONPATH_NUMPY = $PYTHONPATH_NUMPY"</action>
-               <action type="shell_command">export PYTHONPATH=$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY:$PYTHONPATH &amp;&amp; 
-                    export CPLUS_INCLUDE_PATH=$FREETYPE_INCLUDE_DIR:$FREETYPE_INCLUDE_DIR/freetype2/:$CPLUS_INCLUDE_PATH &amp;&amp; 
-                    export LIBRARY_PATH=$FREETYPE_LIB_DIR:$LIBRARY_PATH &amp;&amp; 
-                    python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
-                <action type="set_environment">
-                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
-                    <environment_variable action="set_to" name="PYTHONPATH_MATPLOTLIB">$INSTALL_DIR/lib/python</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Compiling matplotlib requires a C compiler (typically gcc) and libpng.</readme>
+        <repository changeset_revision="6d12f6830132" name="package_matplotlib_lite" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="htseq" version="0.5.4p3">
         <install version="1.0">
@@ -50,6 +22,9 @@
                         <package name="freetype" toolshed="http://testtoolshed.g2.bx.psu.edu" version="2.4.11">
                             <repository name="package_freetype_2_4" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
                         </package>
+                        <package name="matplotlib" toolshed="http://testtoolshed.g2.bx.psu.edu" version="1.2.1">
+                            <repository name="package_matplotlib_lite" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+                        </package>
                 </action>
                 <action type="shell_command">export PYTHONPATH=$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">