Mercurial > repos > iuc > package_gemini_0_10_0

changeset 0:42c72725f879 draft

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Imported from capsule None
author iuc
date Mon, 25 Aug 2014 17:15:52 -0400
parents
children 0a450b7b5bc3
files tool_dependencies.xml
diffstat 1 files changed, 41 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Aug 25 17:15:52 2014 -0400
@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="zlib" version="1.2.8">
+      <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="grabix" version="0.1.3">
+      <repository changeset_revision="0714d88bd854" name="package_grabix_0_1_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="tabix" version="0.2.6">
+      <repository changeset_revision="3d6beba7393e" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="0.1.19">
+      <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bedtools" version="2.19.1">
+      <repository changeset_revision="fb3a854c7104" name="package_bedtools_2_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="gemini" version="0.10.0">
+      <install version="1.0">
+          <actions>
+              <!-- first action is always downloading -->
+                <action type="download_file">https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py</action>
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="set_environment_for_install">
+                  <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                      <package name="zlib" version="1.2.8" />
+                    </repository>
+                </action>
+                <action type="shell_command">
+                    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>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling GEMINI requires a recent c++ compiler, usually gcc.</readme>
+    </package>
+</tool_dependency>