Mercurial > repos > yhoogstrate > package_segmentation_fold_1_6_5

annotate tool_dependencies.xml @ 3:1c7d6b167510 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit fb0bbb26638c0185ef16efa2e0ac3952d671b711-dirty
author yhoogstrate
date Thu, 19 May 2016 03:29:32 -0400
parents bf60a5f98e16
children e3ef4c5b6f19
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1 <?xml version="1.0"?>
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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2 <tool_dependency>
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3 <package name="boost" version="1.57">
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4 <repository changeset_revision="bd65814f17c5" name="package_boost_1_57" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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5 </package>
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6
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7 <package name="cmake" version="3.2.3">
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8 <repository changeset_revision="2da7b99cb1a1" name="package_cmake_3_2_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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9 </package>
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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10
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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11 <package name="python" version="2.7.10">
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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12 <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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13 </package>
3
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14 <package name="numpy" version="1.9">
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15 <repository changeset_revision="fe0870696ca7" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
1c7d6b167510 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit fb0bbb26638c0185ef16efa2e0ac3952d671b711-dirty
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16 </package>
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17 <package name="pysam" version="0.8.2.1">
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18 <repository changeset_revision="e6c1f548397a" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
1c7d6b167510 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit fb0bbb26638c0185ef16efa2e0ac3952d671b711-dirty
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19 </package>
0
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20
1
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21 <package name="setuptools" version="19.0">
fca872e2150a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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22 <repository changeset_revision="c0a6821af233" name="package_setuptools_19_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
fca872e2150a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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23 </package>
fca872e2150a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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24
0
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25 <package name="segmentation-fold" version="1.6.5">
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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26 <install version="1.0">
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27 <actions>
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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28 <action sha256sum="f7dfbc70313aa2502dd35692f33bf06ef32c17594a526ea054cf369837aad794" type="download_by_url">https://github.com/yhoogstrate/segmentation-fold/archive/3cce35ab2265caf186c492764afb5a71ae55d80d.tar.gz</action>
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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29
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30 <action type="set_environment_for_install">
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31 <repository changeset_revision="bd65814f17c5" name="package_boost_1_57" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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32 <package name="boost" version="1.57" />
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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33 </repository>
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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34 </action>
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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35
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36 <action type="set_environment_for_install">
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37 <repository changeset_revision="2da7b99cb1a1" name="package_cmake_3_2_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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38 <package name="cmake" version="3.2.3" />
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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39 </repository>
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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40 </action>
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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41
1
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42 <action type="set_environment_for_install">
fca872e2150a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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43 <repository changeset_revision="c0a6821af233" name="package_setuptools_19_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
fca872e2150a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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44 <package name="setuptools" version="19.0" />
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45 </repository>
fca872e2150a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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46 </action>
fca872e2150a planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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47
0
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48 <action type="shell_command">
2
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49 ls
0
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50 </action>
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51
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52 <!-- Also install the python utils -->
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53 <action type="set_environment_for_install">
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54 <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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55 <package name="python" version="2.7.10" />
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56 </repository>
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57 </action>
3
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58
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59 <action type="set_environment_for_install">
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60 <repository changeset_revision="fe0870696ca7" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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61 <package name="numpy" version="1.9" />
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62 </repository>
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63 </action>
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64
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65 <action type="set_environment_for_install">
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66 <repository changeset_revision="e6c1f548397a" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu">
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67 <package name="pysam" version="0.8.2.1" />
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68 </repository>
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69 </action>
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70
0
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71 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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72 <action type="make_directory">$INSTALL_DIR/lib64/python</action>
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73 <action type="shell_command">
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74 export PYTHONPATH="$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python" &amp;&amp;
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75 cd scripts/energy-estimation-utility &amp;&amp;
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76 python setup.py install --home "$INSTALL_DIR" --install-scripts "$INSTALL_DIR/bin"
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77 </action>
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78
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79 <action type="set_environment">
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80 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
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81 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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82 <environment_variable action="set_to" name="SEGMENTATION_FOLD_DEFAULT_XML">$INSTALL_DIR/share/segmentation-fold/segments.xml</environment_variable>
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83 </action>
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84 </actions>
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85 </install>
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86 <readme>
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87 Installation of segmentation-fold requires:
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88 - libboost (via toolshed)
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89 - CMake (via toolshed)
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90 - Python (for energy utils) (via toolshed)
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91 - c++11 compliant compiler: g++ or clang
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92 </readme>
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93 </package>
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94 </tool_dependency>