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Commit message:
Uploaded |
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added:
tool_dependencies.xml |
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| diff -r 000000000000 -r 1e53d7d44ed6 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jun 24 11:44:44 2015 -0400 |
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| @@ -0,0 +1,33 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="sparsehash" version="2.0.2"> + <repository changeset_revision="2cc9627ae29c" name="package_sparsehash_2_0_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="stacks" version="1.32"> + <install version="1.0"> + <actions> + <!-- first action is always downloading --> + <action type="download_by_url">http://catchenlab.life.illinois.edu/stacks/source/stacks-1.32.tar.gz</action> + + <!-- populate the environment variables from the dependend repos --> + <action type="set_environment_for_install"> + <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="samtools" version="0.1.19" /> + </repository> + <repository changeset_revision="2cc9627ae29c" name="package_sparsehash_2_0_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="sparsehash" version="2.0.2" /> + </repository> + </action> + + <action type="autoconf">--enable-sparsehash --enable-bam --with-bam-include-path=${BAM_ROOT}/include --with-bam-lib-path=${BAM_LIB_PATH}</action> + + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + </package> +</tool_dependency> |