Mercurial > repos > yhoogstrate > package_flaimapper_1_2_1
annotate tool_dependencies.xml @ 3:4242d24c6033 draft default tip
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| author | yhoogstrate |
|---|---|
| date | Fri, 31 Jul 2015 05:43:49 -0400 |
| parents | 13df148b30ef |
| children |
| rev | line source |
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88696b8f774b
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_flaimapper_1_2_1 commit 18c2fff1b59feb43640d744444d8fb6193def183-dirty
yhoogstrate
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1 <?xml version="1.0"?> |
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88696b8f774b
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_flaimapper_1_2_1 commit 18c2fff1b59feb43640d744444d8fb6193def183-dirty
yhoogstrate
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2 <tool_dependency> |
| 1 | 3 <!-- |
| 4 pysam has had several internal changes in 0.7.*, 0.8.1, 0.8.2 & | |
| 5 0.8.3 and therefore FlaiMapper is not compatible with all of | |
| 6 them. For compatibility this package is provided with pysam | |
| 7 0.8.2.1 which was not originally in the toolshed. | |
| 8 --> | |
| 9 <package name="pysam" version="0.8.2.1"> | |
| 3 | 10 <repository changeset_revision="f8fecf1f6eba" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
| 1 | 11 </package> |
| 12 | |
| 13 <package name="flaimapper" version="1.2.1"> | |
| 14 <install version="1.0"> | |
| 15 <actions> | |
| 16 <action type="set_environment_for_install"> | |
| 3 | 17 <repository changeset_revision="f8fecf1f6eba" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu"> |
| 1 | 18 <package name="pysam" version="0.8.2.1" /> |
| 19 </repository> | |
| 20 </action> | |
| 21 | |
| 22 <action type="make_directory">$INSTALL_DIR/bin</action> | |
| 23 <action type="make_directory">$INSTALL_DIR/lib/python</action> | |
| 24 <action type="make_directory">$INSTALL_DIR/lib64/python</action> | |
| 25 | |
| 26 <action type="shell_command"> | |
| 27 git clone https://github.com/yhoogstrate/flaimapper flaimapper && | |
| 28 cd flaimapper && | |
| 29 git reset --hard d3cc32a10ba3d33fde4cb76e8013a51ec8bdf779 && | |
| 30 | |
| 31 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR && | |
| 32 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib/python" && | |
| 33 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib64/python" && | |
| 34 export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH && | |
| 35 export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib/python" && | |
| 36 export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib64/python" && | |
| 37 | |
| 38 cd src && | |
| 39 | |
| 40 python setup.py build && | |
| 2 | 41 python setup.py install \ |
| 42 --home $INSTALL_DIR \ | |
| 1 | 43 --install-scripts $INSTALL_DIR/bin |
| 44 </action> | |
| 45 | |
| 46 <action type="set_environment"> | |
| 47 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable> | |
| 48 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
| 49 </action> | |
| 50 </actions> | |
| 51 </install> | |
| 52 | |
| 53 <readme> | |
| 54 Downloads and installs FlaiMapper. | |
| 55 | |
| 56 Prerequisites: | |
| 57 - Python | |
| 58 - git | |
| 59 | |
| 60 Because I accidentally included too much large files within | |
| 61 the GitHub repository of FlaiMapper, it has become large. | |
| 62 This is the reason why installation takes a while. | |
| 63 </readme> | |
| 64 </package> | |
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0
88696b8f774b
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/package_flaimapper_1_2_1 commit 18c2fff1b59feb43640d744444d8fb6193def183-dirty
yhoogstrate
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65 </tool_dependency> |