Mercurial > repos > jjohnson > package_cistrome_2014_09_29
changeset 0:b9b48eb563d1 draft default tip
Imported from capsule None
| author | jjohnson |
|---|---|
| date | Tue, 14 Oct 2014 10:06:50 -0400 |
| parents | |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 55 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 14 10:06:50 2014 -0400 @@ -0,0 +1,55 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="numpy" version="1.7.1"> + <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="cython" version="0.20.1"> + <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="cistrome" version="2014-09-29"> + <install version="1.0"> + <actions> + <action type="shell_command">hg clone https://bitbucket.org/jjohnson/cistrome-applications-harvard cistrome</action> + <action type="shell_command">hg update -d 2014-09-29</action> + <action type="shell_command">cd cistrome-extra-apps && python setup.py install --home=$INSTALL_DIR</action> + <action type="shell_command">cd published-packages/CEAS && python setup.py install --home=$INSTALL_DIR</action> + <action type="shell_command">cd published-packages/MA2C && python setup.py install --home=$INSTALL_DIR</action> + <!-- needs numpy --> + <action type="set_environment_for_install"> + <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="numpy" version="1.7.1" /> + </repository> + </action> + <action type="shell_command">cd published-packages/MACS && python setup.py install --home=$INSTALL_DIR</action> + <action type="shell_command">cd published-packages/MAT && python setup.py install --home=$INSTALL_DIR</action> + <action type="shell_command">cd published-packages/NPS && python setup.py install --home=$INSTALL_DIR</action> + <!-- needs numpy Cython --> + <action type="set_environment_for_install"> + <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="cython" version="0.20.1" /> + </repository> + </action> + <action type="shell_command"> + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + cd mdseqpos && + sed "s#/data/static_libraries/assembly/#$INSTALL_DIR/assembly/#" lib/settings.py.example > lib/settings.py && + sed -i".tmp" "s#NUMPY_PATH = numpy#global NUMPY_PATH; NUMPY_PATH = numpy#" setup.py && + python setup.py install --home=$INSTALL_DIR + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + <!-- this includes CistromeAP --> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib64/python</environment_variable> + </action> + </actions> + </install> + <readme> +Installs the cistrome applications code from https://bitbucket.org/cistrome/cistrome-applications-harvard + ( branch for genome_dir option to override settings.py https://bitbucket.org/jjohnson/cistrome-applications-harvard ) +Runtime dependencies: bx-python, biopython, PIL, jinja2, MySQLdb + </readme> + </package> +</tool_dependency>