Mercurial > repos > devteam > package_cufflinks_2_2_1
changeset 0:899067a260d1 draft default tip
Uploaded
| author | devteam |
|---|---|
| date | Fri, 19 Dec 2014 11:53:32 -0500 |
| parents | |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 52 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Dec 19 11:53:32 2014 -0500 @@ -0,0 +1,52 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="cufflinks" version="2.2.1"> + <install version="1.0"> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + </actions> + <actions architecture="x86_64" os="darwin"> + <action type="download_by_url">http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.OSX_x86_64.tar.gz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + </actions> + <actions> + <package name="boost" version="1.53.0"> + <repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="0.1.18"> + <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="eigen" version="3.2.0"> + <repository changeset_revision="c6204ba02233" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <action type="download_by_url">http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.2.1.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="cee17eb9de41" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="boost" version="1.53.0" /> + </repository> + <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="samtools" version="0.1.18" /> + </repository> + <repository changeset_revision="c6204ba02233" name="package_eigen_3_2_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="eigen" version="3.2.0" /> + </repository> + </action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-boost=$BOOST_ROOT_DIR --with-bam=$BAM_ROOT --with-eigen=$EIGEN_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>