Mercurial > repos > mzeidler > virana

changeset 26:0add6f5e9344 draft

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Uploaded
author mzeidler
date Mon, 23 Sep 2013 06:57:19 -0400
parents a352555788f9
children 27580103d50b
files tool_dependencies.xml
diffstat 1 files changed, 56 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Sep 23 06:37:27 2013 -0400
+++ b/tool_dependencies.xml	Mon Sep 23 06:57:19 2013 -0400
@@ -1,10 +1,4 @@
 <tool_dependency>
-    <package name="biopython" version="1.6.2">
-        <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
     <package name="virana_python" version="1.0">
         <install version="1.0">
             <actions>
@@ -14,6 +8,62 @@
             </actions>
         </install>
     </package>
+ <package name="numpy" version="1.7.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://pypi.python.org/packages/source/n/numpy/numpy-1.7.1.tar.gz</action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
+                <action type="set_environment">
+                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable name="PYTHONPATH_NUMPY" action="set_to">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+    </package>
+<package name="biopython" version="1.61">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
+                    export PATH=$PATH:$PATH_NUMPY &amp;&amp; 
+                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp; 
+                    python setup.py install --install-lib $INSTALL_DIR/lib/python
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="PYTHONPATH">$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_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
+                </action>
+            </actions>
+        </install>
+    </package>
+<package name="matplotlib" version="1.2.1">
+        <install version="1.0">
+            <actions>
+                <!-- first action is always downloading -->
+                <action type="download_by_url">http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.2.1/matplotlib-1.2.1.tar.gz</action>
+
+                             
+                <!-- install matplotlib -->
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY &amp;&amp;  
+                    python setup.py install --install-lib $INSTALL_DIR/lib/python --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>
+    </package>
  <package name="htseq" version="0.5.4">
         <install version="1.0">
             <actions>