| Previous changeset 0:42c72725f879 (2014-08-25) Next changeset 2:7c5b37efe4e5 (2015-01-13) |
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modified:
tool_dependencies.xml |
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| diff -r 42c72725f879 -r 0a450b7b5bc3 tool_dependencies.xml --- a/tool_dependencies.xml Mon Aug 25 17:15:52 2014 -0400 +++ b/tool_dependencies.xml Tue Jan 13 10:34:06 2015 -0500 |
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| @@ -1,36 +1,39 @@ <?xml version="1.0"?> <tool_dependency> - <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 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="grabix" version="0.1.3"> - <repository changeset_revision="0714d88bd854" name="package_grabix_0_1_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="0714d88bd854" name="package_grabix_0_1_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="tabix" version="0.2.6"> - <repository changeset_revision="3d6beba7393e" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="3d6beba7393e" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.19"> - <repository changeset_revision="923adc89c666" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="bedtools" version="2.19.1"> - <repository changeset_revision="fb3a854c7104" name="package_bedtools_2_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="fb3a854c7104" name="package_bedtools_2_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="gemini" version="0.10.0"> - <install version="1.0"> - <actions> - <!-- first action is always downloading --> + <install version="1.0"> + <actions> + <!-- first action is always downloading --> <action type="download_file">https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py</action> + <!-- populate the environment variables from the dependend 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 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"> python gemini_install.py $INSTALL_DIR $INSTALL_DIR --nosudo --nodata --notools --gemini-version 0.10.0 </action> + <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/anaconda/bin</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/anaconda/bin</environment_variable> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/gemini/bin</environment_variable> <environment_variable action="set_to" name="GEMINI_ROOT_DIR">$INSTALL_DIR</environment_variable> </action> |