Mercurial > repos > yhoogstrate > package_segmentation_fold_1_6_5

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 6545dbf0edf3a0f9afda8d5a27a646253c8f7115
author yhoogstrate
date Thu, 26 May 2016 06:51:29 -0400
parents f4043c6a367a
children
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1 <?xml version="1.0"?>
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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" />
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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" />
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9 </package>
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10
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11 <package name="python" version="2.7.10">
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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" />
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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" />
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19 </package>
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20 <package name="htseq" version="0.6.1">
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21 <repository changeset_revision="25da74c1ff6d" name="package_htseq_0_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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22 </package>
0
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23
1
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24 <package name="setuptools" version="19.0">
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25 <repository changeset_revision="c0a6821af233" name="package_setuptools_19_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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26 </package>
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27
0
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28 <package name="segmentation-fold" version="1.6.5">
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29 <install version="1.0">
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30 <actions>
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31 <action sha256sum="f7d2307f5234c133ad9807c6e5e68312866888ffa993e96ccdbb0f9b7ab5ff62" type="download_by_url">https://github.com/yhoogstrate/segmentation-fold/archive/0ce5f9901e7dcb5d78d750b4df63ab6e03165edb.tar.gz</action>
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33 <action type="set_environment_for_install">
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34 <repository changeset_revision="bd65814f17c5" name="package_boost_1_57" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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35 <package name="boost" version="1.57" />
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36 </repository>
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37
0
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38 <repository changeset_revision="2da7b99cb1a1" name="package_cmake_3_2_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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39 <package name="cmake" version="3.2.3" />
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40 </repository>
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41 </action>
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42
5ca5075b1f49 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 879dad538d7c2fa8b7e7f3e9460ff88874797d2c-dirty
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43 <action type="shell_command">
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44 cmake -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR . &amp;&amp;
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45 make &amp;&amp;
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46 make check &amp;&amp;
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47 make install
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48 </action>
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49
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50 <action type="set_environment">
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51 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
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52 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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53 <environment_variable action="set_to" name="SEGMENTATION_FOLD_DEFAULT_XML">$INSTALL_DIR/share/segmentation-fold/segments.xml</environment_variable>
0
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54 </action>
5
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55 </actions>
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56 </install>
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57 <readme>
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58 Installation of segmentation-fold requires:
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59 - libboost (via toolshed)
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60 - CMake (via toolshed)
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61 - c++11 compliant compiler: g++ or clang
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62 </readme>
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63 </package>
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64
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65 <package name="segmentation-fold-utils" version="2.0.0">
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66 <install version="1.0">
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67 <actions>
14
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68 <action sha256sum="f7d2307f5234c133ad9807c6e5e68312866888ffa993e96ccdbb0f9b7ab5ff62" type="download_by_url">https://github.com/yhoogstrate/segmentation-fold/archive/0ce5f9901e7dcb5d78d750b4df63ab6e03165edb.tar.gz</action>
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70 <!-- Also install the python utils -->
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71 <action type="set_environment_for_install">
7
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72 <repository changeset_revision="c0a6821af233" name="package_setuptools_19_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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73 <package name="setuptools" version="19.0" />
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74 </repository>
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75
0
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76 <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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77 <package name="python" version="2.7.10" />
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78 </repository>
11
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79
3
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80 <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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81 <package name="numpy" version="1.9" />
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82 </repository>
11
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83
3
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84 <repository changeset_revision="e6c1f548397a" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu">
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85 <package name="pysam" version="0.8.2.1" />
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86 </repository>
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87
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88 <repository changeset_revision="25da74c1ff6d" name="package_htseq_0_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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89 <package name="htseq" version="0.6.1" />
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90 </repository>
15
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91
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92 <package sha256sum="cc6a19da8ebff6e7074f731447ef7e112bd23adf3de5c597cf9989f2fd8defe9">https://pypi.python.org/packages/7a/00/c14926d8232b36b08218067bcd5853caefb4737cda3f0a47437151344792/click-6.6.tar.gz</package>
3
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93 </action>
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94
0
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95 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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96 <action type="make_directory">$INSTALL_DIR/lib64/python</action>
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97 <action type="shell_command">
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98 export PYTHONPATH="$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python" &amp;&amp;
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99 cd scripts/energy-estimation-utility &amp;&amp;
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100 echo "---------------------------------------------------------------------------" &amp;&amp;
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101 head -n 161 segmentation_fold_utils/XMLFile.py | tail -n 11 &amp;&amp;
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102 echo "---------------------------------------------------------------------------" &amp;&amp;
0
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103 python setup.py install --home "$INSTALL_DIR" --install-scripts "$INSTALL_DIR/bin"
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104 </action>
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105
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106 <action type="set_environment">
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107 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
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108 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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109 </action>
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110 </actions>
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111 </install>
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112 <readme>
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113 Installation of segmentation-fold-utils requires:
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114 - Python (via toolshed)
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115 - numpy (via toolshed)
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116 - pysam (via toolshed)
0
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117 </readme>
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118 </package>
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119 </tool_dependency>