Mercurial > repos > pjbriggs > ceas

annotate tool_dependencies.xml @ 6:55ed5e1b7a07 draft

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Get R 3.1.2 dependency from toolshed.
author pjbriggs
date Tue, 18 Oct 2016 07:36:43 -0400
parents 4e2883bb058d
children 7ed66f11cdcc
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <!-- R 3.1.2 from main/test toolshed -->
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4 <package name="R" version="3.1.2">
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5 <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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6 </package>
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7 <!-- Python mysqldb package -->
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8 <package name="python_mysqldb" version="1.2.5">
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9 <install version="1.0">
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10 <actions>
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11 <action type="download_by_url">https://pypi.python.org/packages/source/M/MySQL-python/MySQL-python-1.2.5.zip</action>
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12 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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13 <action type="shell_command">
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14 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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15 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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16 </action>
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17 <action type="set_environment">
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18 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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19 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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20 </action>
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21 </actions>
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22 </install>
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23 <readme>Installs Python module MySQLdb 1.2.5</readme>
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24 </package>
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25 <!-- bx_python
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26 This is cribbed from devteam's 'package_bx_python_0_7' in the main
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27 toolshed:
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28 https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7
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29 -->
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30 <package name="bx_python" version="0.7.1">
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31 <install version="1.0">
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32 <actions>
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33 <action type="setup_virtualenv">
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34 numpy==1.7.1
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35 bx-python==0.7.1
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36 </action>
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37 <action type="set_environment">
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38 <environment_variable action="set_to" name="BX_PYTHON_PATH">$INSTALL_DIR</environment_variable>
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39 </action>
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40 </actions>
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41 </install>
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42 <readme>
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43 Installation of bx-python 0.7.1 along with numpy 1.7.1. The installation can be
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44 accessed via BX_PYTHON_PATH.
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45 </readme>
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46 </package>
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47 <!-- cistrome_ceas
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48 Installs the version of CEAS package found in the Cistrome
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49 distribution:
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50 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
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51 -->
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52 <package name="cistrome_ceas" version="1.0.2.d8c0751">
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53 <install version="1.0">
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54 <actions>
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55 <action type="shell_command">
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56 hg clone https://bitbucket.org/cistrome/cistrome-applications-harvard cistrome_ceas
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57 </action>
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58 <action type="shell_command">
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59 hg update d8c0751
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60 </action>
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61 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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62 <action type="shell_command">
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63 cd published-packages/CEAS/
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64 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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65 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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66 </action>
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67 <action type="set_environment">
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68 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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69 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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70 </action>
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71 </actions>
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72 </install>
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73 <readme>Installs version 1.0.2 of CEAS from cistrome (commit id d8c0751,
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74 datestamp 20140929), which includes ceasBW (a version of ceas which can
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75 handle bigWig file input from MACS2.
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76
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77 Cistrome code is at
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78 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
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79
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80 The CEAS code is under the published-packages/CEAS/ subdirectory
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81
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82 Cistrome data files and documentation can be found at
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83 http://liulab.dfci.harvard.edu/CEAS/index.html
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84 </readme>
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85 </package>
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86 <!-- fetchChromSize from UCSC tools -->
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87 <package name="ucsc_fetchChromSizes" version="1.0">
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88 <install version="1.0">
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89 <actions>
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90 <action type="download_binary">
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91 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
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92 </action>
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93 <action type="chmod">
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94 <file mode="755">$INSTALL_DIR/fetchChromSizes</file>
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95 </action>
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96 <action type="set_environment">
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97 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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98 </action>
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99 </actions>
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100 </install>
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101 <readme>Installs the binary executable for the fetchChromSizes utility
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102 from UCSC tools
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103 </readme>
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104 </package>
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105 </tool_dependency>