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comparison 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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0:6adb6e16b00f 1:1fea05cdc1a1
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="mosaik" version="2.2.26"> 3 <package name="zlib" version="1.2.8">
4 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="mosaik" version="2.2.28">
4 <install version="1.0"> 7 <install version="1.0">
5 <actions> 8 <actions>
6 <action type="shell_command">git clone https://github.com/wanpinglee/MOSAIK.git mosaik</action> 9 <action type="shell_command">git clone https://github.com/wanpinglee/MOSAIK.git mosaik</action>
7 <action type="shell_command">git reset --hard e04c806bb1410cf1dbd1534991c46d696aec6723</action> 10 <action type="shell_command">git reset --hard 24cf066048228a729c79f1de06b403ad8b0bc920</action>
8 <action type="shell_command">sed -i 's/ -static//g' src/includes/linux.inc</action> 11 <action type="shell_command">sed -i 's/ -static//g' src/includes/linux.inc</action>
12 <!-- populate the environment variables from the dependent repos -->
13 <action type="set_environment_for_install">
14 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
15 <package name="zlib" version="1.2.8" />
16 </repository>
17 </action>
9 <action type="shell_command">make -C src/</action> 18 <action type="shell_command">make -C src/</action>
10 <action type="move_directory_files"> 19 <action type="move_directory_files">
11 <source_directory>bin</source_directory> 20 <source_directory>bin</source_directory>
12 <destination_directory>$INSTALL_DIR/bin</destination_directory> 21 <destination_directory>$INSTALL_DIR/bin</destination_directory>
13 </action> 22 </action>
14 <action type="move_directory_files"> 23 <action type="move_directory_files">
15 <source_directory>src/networkFile</source_directory> 24 <source_directory>src/networkFile</source_directory>
16 <destination_directory>$INSTALL_DIR/networkFile</destination_directory> 25 <destination_directory>$INSTALL_DIR/networkFile</destination_directory>
17 </action> 26 </action>
18 <action type="set_environment"> 27 <action type="set_environment">
19 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 28 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
20 </action> 29 </action>
21 <action type="set_environment"> 30 <action type="set_environment">
22 <environment_variable name="MOSAIK_NETWORK_DIR" action="set_to">$INSTALL_DIR/networkFile</environment_variable> 31 <environment_variable action="set_to" name="MOSAIK_NETWORK_DIR">$INSTALL_DIR/networkFile</environment_variable>
23 </action> 32 </action>
24 </actions> 33 </actions>
25 </install> 34 </install>
26 </package> 35 </package>
27 <!-- <package name="samtools" version="0.1.19"> 36 <package name="samtools" version="0.1.19">
28 <repository name="package_samtools_0_1_19" owner="devteam" /> 37 <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
29 </package>--> 38 </package>
30 </tool_dependency> 39 </tool_dependency>