Mercurial > repos > iuc > package_gemini_0_9_1

changeset 0:18f4b4fe455c draft

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Uploaded
author iuc
date Wed, 06 Aug 2014 17:57:42 -0400
parents
children e516984ed2c5
files tool_dependencies.xml
diffstat 1 files changed, 54 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Aug 06 17:57:42 2014 -0400
@@ -0,0 +1,54 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="grabix" version="0.1.3">
+        <repository changeset_revision="ea8dd47bccea" name="package_grabix_0_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="tabix" version="0.2.6">
+        <repository changeset_revision="c1743e071a28" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bedtools" version="2.19.1">
+        <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pybedtools" version="0.6.6">
+        <repository changeset_revision="cc2ed79fc537" name="package_pybedtools_0_6_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="gemini" version="0.9.1">
+        <install version="1.0">
+            <actions>
+                <!-- first action is always downloading -->
+                <action type="download_by_url">https://github.com/arq5x/gemini/archive/v0.9.1.tar.gz</action>
+
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="c1743e071a28" name="package_tabix_0_2_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="tabix" version="0.2.6" />
+                    </repository>
+                    <repository changeset_revision="ea8dd47bccea" name="package_grabix_0_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="grabix" version="0.1.3" />
+                    </repository>
+                    <repository changeset_revision="cc2ed79fc537" name="package_pybedtools_0_6_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="pybedtools" version="0.6.6" />
+                    </repository>
+                </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 --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">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="PYTHONPATH_GEMINI">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="set_to" name="PATH_GEMINI">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="GEMINI_ROOT_DIR">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling GEMINI requires a recent c++ compiler, usually gcc.</readme>
+    </package>
+</tool_dependency>