Mercurial > repos > nml > package_python_3_4_pysam_0_8_3

changeset 0:085a17b297b1 draft default tip

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_pysam_0_8_3 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
author nml
date Thu, 07 Jul 2016 09:56:33 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 33 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jul 07 09:56:33 2016 -0400
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="python" version="3.4">
+      <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pysam" version="0.8.3">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://depot.galaxyproject.org/software/pysam/pysam_0.8.3_src_all.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="python" version="3.4" />
+                    </repository>
+                </action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
+                    python3 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">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="PYTHONPATH_PYSAM">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="set_to" name="PATH_PYSAM">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="PYSAM_ROOT_DIR">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Installation of pysam, pyrex and python are required. The installation can be accessed via PYSAM_PATH.
+        </readme>
+    </package>
+</tool_dependency>