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Commit message:
Imported from capsule None |
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added:
tool_dependencies.xml |
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| diff -r 000000000000 -r 8549fd545473 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 27 09:24:58 2014 -0500 |
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| @@ -0,0 +1,38 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="tophat2" version="2.0.9"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/tophat/tophat-2.0.9.Linux_x86_64.tar.gz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + </actions> + <actions architecture="x86_64" os="darwin"> + <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/tophat/tophat-2.0.9.OSX_x86_64.tar.gz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + </actions> + <actions> + <package name="samtools" version="0.1.18"> + <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <action type="download_by_url">http://tophat.cbcb.umd.edu/downloads/tophat-2.0.9.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-bam=$BAM_ROOT</action> + <action type="shell_command">make && make install</action> + </actions> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions_group> + </install> + <readme /> + </package> +</tool_dependency> |