Mercurial > repos > crs4 > mosaik2
diff tool_dependencies.xml @ 1:1fea05cdc1a1 draft default tip
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 |
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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>