Mercurial > repos > iuc > package_gemini_0_9_1

changeset 4:a10ebb5a71bb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Sun, 17 Aug 2014 07:44:39 -0400
parents 610ebefc0db1
children 9383ac88d426
files tool_dependencies.xml
diffstat 1 files changed, 17 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Sat Aug 16 09:22:06 2014 -0400
+++ b/tool_dependencies.xml	Sun Aug 17 07:44:39 2014 -0400
@@ -3,21 +3,36 @@
     <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="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" 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="0.9.1">
         <install version="1.0">
             <actions>
                 <!-- first action is always downloading -->
-                <action type="download_by_url">https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py</action>
+                <action type="download_by_url">https://raw.github.com/bgruening/gemini-versioned-install/master/gemini_install_0.9.1.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>
+                    <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="bedtools" version="2.19.1" />
+                    </repository>
                 </action>
 
                 <action type="shell_command">
-                    python gemini_install.py $INSTALL_DIR $INSTALL_DIR --nosudo --nodata
+                    python gemini_install.py $INSTALL_DIR $INSTALL_DIR --nosudo --nodata --notools
                 </action>
 
                 <action type="set_environment">