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diff tool_dependencies.xml @ 1:1fea05cdc1a1 draft default tip

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Update Orione citation. Upgrade Mosaik dependency to v. 2.2.28 (2.2.30 is buggy, see https://github.com/wanpinglee/MOSAIK/issues/11 ). Use 2.1.78 neural networks. Add package_zlib_1_2_8 and package_samtools_0_1_19 dependencies. Add <citations>.
author crs4
date Thu, 06 Nov 2014 13:20:15 -0500
parents 6adb6e16b00f
children
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--- a/tool_dependencies.xml	Wed Apr 02 12:32:52 2014 -0400
+++ b/tool_dependencies.xml	Thu Nov 06 13:20:15 2014 -0500
@@ -1,11 +1,20 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="mosaik" version="2.2.26">
+  <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="mosaik" version="2.2.28">
     <install version="1.0">
       <actions>
         <action type="shell_command">git clone https://github.com/wanpinglee/MOSAIK.git mosaik</action>
-        <action type="shell_command">git reset --hard e04c806bb1410cf1dbd1534991c46d696aec6723</action>
+        <action type="shell_command">git reset --hard 24cf066048228a729c79f1de06b403ad8b0bc920</action>
         <action type="shell_command">sed -i 's/ -static//g' src/includes/linux.inc</action>
+        <!-- populate the environment variables from the dependent 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">make -C src/</action>
         <action type="move_directory_files">
           <source_directory>bin</source_directory>
@@ -16,15 +25,15 @@
           <destination_directory>$INSTALL_DIR/networkFile</destination_directory>
         </action>
         <action type="set_environment">
-          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
         </action>
         <action type="set_environment">
-          <environment_variable name="MOSAIK_NETWORK_DIR" action="set_to">$INSTALL_DIR/networkFile</environment_variable>
+          <environment_variable action="set_to" name="MOSAIK_NETWORK_DIR">$INSTALL_DIR/networkFile</environment_variable>
         </action>
       </actions>
     </install>
   </package>
-<!--  <package name="samtools" version="0.1.19">
-    <repository name="package_samtools_0_1_19" owner="devteam" />
-  </package>-->
+  <package name="samtools" version="0.1.19">
+    <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
 </tool_dependency>