Mercurial > repos > fubar > htseq_bams_to_count_matrix

changeset 6:a79c6da81745 draft

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Uploaded
author fubar
date Thu, 06 Jun 2013 20:32:33 -0400
parents 5008d3b420a7
children 1c69e32649cb
files htseq_bams_to_count_matrix/tool_dependencies.xml
diffstat 1 files changed, 38 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/htseq_bams_to_count_matrix/tool_dependencies.xml	Thu Jun 06 20:22:51 2013 -0400
+++ b/htseq_bams_to_count_matrix/tool_dependencies.xml	Thu Jun 06 20:32:33 2013 -0400
@@ -1,5 +1,43 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="package_numpy_1_7" version="1.7.1">
+        <repository changeset_revision="af9633757cf0" name="package_numpy_1_7" owner="blankenberg" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="freetype" version="2.4.11">
+        <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">
+                    <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>
+                </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; 
+                    export CPLUS_INCLUDE_PATH=$FREETYPE_INCLUDE_DIR:$FREETYPE_INCLUDE_DIR/freetype2/ &amp;&amp; 
+                    export LIBRARY_PATH=$FREETYPE_LIB_DIR &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>
+    </package>
     <package name="package_htseq_0_5_4" version="0.5.4p3">
         <install version="1.0">
             <actions>
@@ -17,10 +55,4 @@
             Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Numpy Python package.
         </readme>
     </package>
-    <package name="package_numpy_1_7" version="1.7.1">
-        <repository changeset_revision="af9633757cf0" name="package_numpy_1_7" owner="blankenberg" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="package_matplotlib_1_2" version="1.2">
-        <repository changeset_revision="c888aa8ed318" name="package_matplotlib_1_2" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
 </tool_dependency>