Mercurial > repos > iuc > package_khmer_2_0

diff tool_dependencies.xml @ 4:30fef72bb5ea draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be26d5871e25cedbc642669993e64439715c7a24
author iuc
date Thu, 12 Nov 2015 02:52:56 -0500
parents 6e27d4c40bf6
children 80f3e4a906b1
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Nov 11 10:33:36 2015 -0500
+++ b/tool_dependencies.xml	Thu Nov 12 02:52:56 2015 -0500
@@ -1,18 +1,22 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="python" version="2.7.10">
-        <repository changeset_revision="2f32acbaf21a" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="bz2file" version="0.98">
+        <repository changeset_revision="f504007348bb" name="package_bz2file_0_98" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="screed" version="0.9">
+        <repository changeset_revision="09145f96007c" name="package_screed_0_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="khmer" version="2.0">
         <install version="1.0">
             <actions>
-                <action type="setup_python_environment">
-                    <repository changeset_revision="2f32acbaf21a" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="python" version="2.7.10" />
-                    </repository>
-                    <package md5sum="27d6f711ae0db6cfd1eb37f95621dfb5">https://pypi.python.org/packages/source/b/bz2file/bz2file-0.98.tar.gz</package>
-                    <package md5sum="611dd11105489e4153265e055f13debd">https://pypi.python.org/packages/source/s/screed/screed-0.9.tar.gz</package>
-                    <package md5sum="1f610abd021254e21b082179a100cd39">https://pypi.python.org/packages/source/k/khmer/khmer-2.0.tar.gz</package>
+                <action md5sum="1f610abd021254e21b082179a100cd39" type="download_by_url">https://pypi.python.org/packages/source/k/khmer/khmer-2.0.tar.gz</action>
+                <action type="shell_command">
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
+                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions>
         </install>