Mercurial > repos > iuc > package_gemini_0_10_0

changeset 1:0a450b7b5bc3 draft

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Uploaded
author iuc
date Tue, 13 Jan 2015 10:34:06 -0500
parents 42c72725f879
children 7c5b37efe4e5
files tool_dependencies.xml
diffstat 1 files changed, 15 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Aug 25 17:15:52 2014 -0400
+++ b/tool_dependencies.xml	Tue Jan 13 10:34:06 2015 -0500
@@ -1,36 +1,39 @@
 <?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 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" />
+        <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" />
+        <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" />
+        <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" 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" />
+        <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 -->
+        <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 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">$INSTALL_DIR/anaconda/bin</environment_variable>
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/gemini/bin</environment_variable>
                     <environment_variable action="set_to" name="GEMINI_ROOT_DIR">$INSTALL_DIR</environment_variable>
                 </action>