Mercurial > repos > yhoogstrate > package_flaimapper_1_2_1
changeset 1:6262f77f889a draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Fri, 31 Jul 2015 05:07:08 -0400 |
| parents | 88696b8f774b |
| children | 13df148b30ef |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 62 insertions(+), 57 deletions(-) [+] |
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--- a/tool_dependencies.xml Wed Jun 03 07:56:49 2015 -0400 +++ b/tool_dependencies.xml Fri Jul 31 05:07:08 2015 -0400 @@ -1,60 +1,65 @@ <?xml version="1.0"?> <tool_dependency> - <!-- - pysam has had several internal changes in 0.7.*, 0.8.1, 0.8.2 & - 0.8.3 and therefore FlaiMapper is not compatible with all of - them. For compatibility this package is provided with pysam - 0.8.2.1 which was not originally in the toolshed. - --> - <package name="pysam" version="0.8.2.1"> - <repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - - <package name="flaimapper" version="1.2.1"> - <install version="1.0"> - <actions> - <action type="set_environment_for_install"> - <repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="pysam" version="0.8.2.1" /> - </repository> - </action> - - <action type="make_directory">$INSTALL_DIR/bin</action> - <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="make_directory">$INSTALL_DIR/lib64/python</action> - - <action type="shell_command"> - git clone https://github.com/yhoogstrate/flaimapper flaimapper && - cd flaimapper && - git reset --hard d3cc32a10ba3d33fde4cb76e8013a51ec8bdf779 && - - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR && - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib/python" && - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib64/python" && - export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH && - export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib/python" && - export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib64/python" && - - cd src && - - python setup.py build && - python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin - </action> - - <action type="set_environment"> - <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - - <readme> - Downloads and installs FlaiMapper. Prerequisites: - - git - - Because I accidentally included too much large files within - the GitHub repository of FlaiMapper it has become large. - This explains why installation takes a while. - </readme> - </package> + <!-- + pysam has had several internal changes in 0.7.*, 0.8.1, 0.8.2 & + 0.8.3 and therefore FlaiMapper is not compatible with all of + them. For compatibility this package is provided with pysam + 0.8.2.1 which was not originally in the toolshed. + --> + <package name="pysam" version="0.8.2.1"> + <repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="flaimapper" version="1.2.1"> + <install version="1.0"> + <actions> + <action type="set_environment_for_install"> + <repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="pysam" version="0.8.2.1" /> + </repository> + </action> + + <action type="make_directory">$INSTALL_DIR/bin</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="make_directory">$INSTALL_DIR/lib64/python</action> + + <action type="shell_command"> + git clone https://github.com/yhoogstrate/flaimapper flaimapper && + cd flaimapper && + git reset --hard d3cc32a10ba3d33fde4cb76e8013a51ec8bdf779 && + + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR && + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib/python" && + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib64/python" && + export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH && + export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib/python" && + export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib64/python" && + + cd src && + + python setup.py build && + python setup.py install + --home $INSTALL_DIR + --install-scripts $INSTALL_DIR/bin + </action> + + <action type="set_environment"> + <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + + <readme> + Downloads and installs FlaiMapper. + + Prerequisites: + - Python + - git + + Because I accidentally included too much large files within + the GitHub repository of FlaiMapper, it has become large. + This is the reason why installation takes a while. + </readme> + </package> </tool_dependency>