Mercurial > repos > iuc > package_rdkit_2012_12
annotate tool_dependencies.xml @ 2:842dd2fa4ace draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rdkit_2012_12 commit 710c0d73202078bd43efd595c28526ba26c8fa50-dirty
| author | iuc |
|---|---|
| date | Sun, 01 Nov 2015 11:33:32 -0500 |
| parents | 2ab9cdc5cd14 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 3 <package name="numpy" version="1.7.1"> | |
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842dd2fa4ace
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rdkit_2012_12 commit 710c0d73202078bd43efd595c28526ba26c8fa50-dirty
iuc
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changeset
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4 <repository changeset_revision="300877695495" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
| 0 | 5 </package> |
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842dd2fa4ace
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rdkit_2012_12 commit 710c0d73202078bd43efd595c28526ba26c8fa50-dirty
iuc
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1
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changeset
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6 <package name="boost" version="1.55.0"> |
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842dd2fa4ace
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rdkit_2012_12 commit 710c0d73202078bd43efd595c28526ba26c8fa50-dirty
iuc
parents:
1
diff
changeset
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7 <repository changeset_revision="f0da948c5302" name="package_boost_1_55" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
| 0 | 8 </package> |
| 9 | |
| 10 <package name="rdkit" version="2012_12_1"> | |
| 11 <install version="1.0"> | |
| 12 <actions> | |
| 13 <!-- first action is always downloading --> | |
| 14 <action type="download_by_url">http://downloads.sourceforge.net/project/rdkit/rdkit/Q4_2012/RDKit_2012_12_1.tgz</action> | |
| 15 | |
| 16 <!-- populate the environment variables from the dependend repos --> | |
| 17 <action type="set_environment_for_install"> | |
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842dd2fa4ace
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rdkit_2012_12 commit 710c0d73202078bd43efd595c28526ba26c8fa50-dirty
iuc
parents:
1
diff
changeset
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18 <repository changeset_revision="300877695495" name="package_numpy_1_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
| 0 | 19 <package name="numpy" version="1.7.1" /> |
| 20 </repository> | |
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842dd2fa4ace
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rdkit_2012_12 commit 710c0d73202078bd43efd595c28526ba26c8fa50-dirty
iuc
parents:
1
diff
changeset
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21 <repository changeset_revision="f0da948c5302" name="package_boost_1_55" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
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842dd2fa4ace
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rdkit_2012_12 commit 710c0d73202078bd43efd595c28526ba26c8fa50-dirty
iuc
parents:
1
diff
changeset
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22 <package name="boost" version="1.55.0" /> |
| 0 | 23 </repository> |
| 24 </action> | |
| 25 | |
| 26 <!-- PYTHONPATH_NUMPY is set in the numpy package --> | |
| 27 <action type="shell_command">export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`pwd`/lib/ && | |
| 28 export PYTHONPATH=$PYTHONPATH:`pwd`/ && | |
| 29 mkdir build && | |
| 30 cd build && | |
| 31 cmake .. -DBOOST_ROOT=$BOOST_ROOT_DIR -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/rdkit/ -DRDK_INSTALL_INTREE=OFF -DPYTHON_NUMPY_INCLUDE_PATH=$PYTHONPATH_NUMPY/numpy/core/include/</action> | |
| 32 <action type="shell_command">cd ./build && make </action> | |
| 33 <action type="shell_command">cd ./build && make install</action> | |
| 34 | |
| 35 <action type="set_environment"> | |
| 36 <environment_variable action="set_to" name="RDBASE">$INSTALL_DIR/rdkit</environment_variable> | |
| 37 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/rdkit/lib/</environment_variable> | |
| 38 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/rdkit/bin</environment_variable> | |
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2ab9cdc5cd14
In Addition to lib, export also lib64 (not matter it it exists or not), to satisfy the Fedora installation process.
bgruening
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39 <!-- on fedora everything is installed under lib64 --> |
| 0 | 40 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/rdkit/lib/python2.7/site-packages/</environment_variable> |
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2ab9cdc5cd14
In Addition to lib, export also lib64 (not matter it it exists or not), to satisfy the Fedora installation process.
bgruening
parents:
0
diff
changeset
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41 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/rdkit/lib64/python2.7/site-packages/</environment_variable> |
| 0 | 42 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> |
| 43 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[BOOST_ROOT_DIR]/lib/</environment_variable> | |
| 44 </action> | |
| 45 </actions> | |
| 46 </install> | |
| 47 <readme>Compiling rdkit requires cmake, python headers, sqlite3, flex and bison.</readme> | |
| 48 </package> | |
| 49 </tool_dependency> |