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annotate tool_dependencies.xml @ 4:4e2883bb058d draft

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Synchronise version with one on main toolshed (version of 30/06/2015)
author pjbriggs
date Wed, 10 Aug 2016 11:04:42 -0400
parents 695d61decd06
children 55ed5e1b7a07
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <!-- Local version of R 3.1.2 dependency -->
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4 <package name="R" version="3.1.2">
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5 <install version="1.0">
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6 <actions>
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7 <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.2.tar.gz</action>
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8 <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
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9 <action type="make_install" />
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10 <action type="set_environment">
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11 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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12 </action>
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13 </actions>
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14 </install>
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15 </package>
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16 <!-- Python mysqldb package -->
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17 <package name="python_mysqldb" version="1.2.5">
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18 <install version="1.0">
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19 <actions>
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20 <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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21 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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22 <action type="shell_command">
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23 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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24 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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25 </action>
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26 <action type="set_environment">
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27 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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28 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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29 </action>
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30 </actions>
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31 </install>
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32 <readme>Installs Python module MySQLdb 1.2.5</readme>
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33 </package>
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34 <!-- bx_python
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35 This is cribbed from devteam's 'package_bx_python_0_7' in the main
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36 toolshed:
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37 https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7
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38 -->
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39 <package name="bx_python" version="0.7.1">
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40 <install version="1.0">
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41 <actions>
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42 <action type="setup_virtualenv">
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43 numpy==1.7.1
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44 bx-python==0.7.1
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45 </action>
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46 <action type="set_environment">
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47 <environment_variable action="set_to" name="BX_PYTHON_PATH">$INSTALL_DIR</environment_variable>
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48 </action>
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49 </actions>
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50 </install>
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51 <readme>
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52 Installation of bx-python 0.7.1 along with numpy 1.7.1. The installation can be
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53 accessed via BX_PYTHON_PATH.
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54 </readme>
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55 </package>
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56 <!-- cistrome_ceas
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57 Installs the version of CEAS package found in the Cistrome
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58 distribution:
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59 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
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60 -->
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61 <package name="cistrome_ceas" version="1.0.2.d8c0751">
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62 <install version="1.0">
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63 <actions>
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64 <action type="shell_command">
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65 hg clone https://bitbucket.org/cistrome/cistrome-applications-harvard cistrome_ceas
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66 </action>
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67 <action type="shell_command">
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68 hg update d8c0751
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69 </action>
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70 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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71 <action type="shell_command">
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72 cd published-packages/CEAS/
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73 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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74 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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75 </action>
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76 <action type="set_environment">
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77 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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78 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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79 </action>
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80 </actions>
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81 </install>
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82 <readme>Installs version 1.0.2 of CEAS from cistrome (commit id d8c0751,
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83 datestamp 20140929), which includes ceasBW (a version of ceas which can
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84 handle bigWig file input from MACS2.
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85
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86 Cistrome code is at
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87 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
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88
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89 The CEAS code is under the published-packages/CEAS/ subdirectory
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90
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91 Cistrome data files and documentation can be found at
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92 http://liulab.dfci.harvard.edu/CEAS/index.html
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93 </readme>
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94 </package>
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95 <!-- fetchChromSize from UCSC tools -->
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96 <package name="ucsc_fetchChromSizes" version="1.0">
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97 <install version="1.0">
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98 <actions>
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99 <action type="download_binary">
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100 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
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101 </action>
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102 <action type="chmod">
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103 <file mode="755">$INSTALL_DIR/fetchChromSizes</file>
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104 </action>
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105 <action type="set_environment">
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106 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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107 </action>
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108 </actions>
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109 </install>
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110 <readme>Installs the binary executable for the fetchChromSizes utility
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111 from UCSC tools
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112 </readme>
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113 </package>
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114 </tool_dependency>