Mercurial > repos > rnateam > package_gemini_0_10_0_1

changeset 0:816cb6c1a983 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_gemini_0_10_0_1 commit 0568344062d931c58be6a017998cfb22e702a94e-dirty
author rnateam
date Tue, 08 Dec 2015 10:54:35 -0500
parents
children e532cf8a27ba
files tool_dependencies.xml
diffstat 1 files changed, 45 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Dec 08 10:54:35 2015 -0500
@@ -0,0 +1,45 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="zlib" version="1.2.8">
+        <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="grabix" version="0.1.3">
+        <repository changeset_revision="8a1184d30e64" 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="54f8b9bf9b6c" 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="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" 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" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="gemini" version="0.10.0.1">
+        <install version="1.0">
+            <actions>
+                <!-- first action is always downloading -->
+                <action type="download_file">https://raw.githubusercontent.com/arq5x/gemini/adf750301f9766c95654d1189381ca370df66bcd/gemini/scripts/gemini_install.py</action>
+
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="zlib" version="1.2.8" />
+                    </repository>
+                </action>
+
+                <action type="shell_command">
+                    export HOME=$INSTALL_DIR &amp;&amp; python gemini_install.py $INSTALL_DIR $INSTALL_DIR --nosudo --nodata --notools --gemini-version 0.10.0
+                </action>
+
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/anaconda/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/gemini/bin</environment_variable>
+                    <environment_variable action="set_to" name="GEMINI_ROOT_DIR">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="HOME">.</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling GEMINI requires a recent c++ compiler, usually gcc.</readme>
+    </package>
+</tool_dependency>