Mercurial > repos > yating-l > jbrowsearchivecreator

comparison tool_dependencies.xml @ 19:62dee5369e80 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit afd782e8741a859506794bea92475f620265c50e
author sargentl
date Thu, 13 Sep 2018 17:43:23 -0400
parents 7cb67cbbd8e5
children
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18:79b23a8afb15 19:62dee5369e80
16 <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 16 <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
17 </package> 17 </package>
18 18
19 <package name="biopython" version="1.68"> 19 <package name="biopython" version="1.68">
20 <readme> 20 <readme>
21 This package is based on package_biopython_1_67 owned by biopython. 21 This package is based on package_biopython_1_67 owned by biopython.
22 https://toolshed.g2.bx.psu.edu/repository?user_id=fd5c6d0f82f315d8 22 https://toolshed.g2.bx.psu.edu/repository?user_id=fd5c6d0f82f315d8
23 23
24 This Galaxy Tool Shed package installs Biopython from source, having 24 This Galaxy Tool Shed package installs Biopython from source, having
25 first installed NumPy which is a build time depencency. This requires 25 first installed NumPy which is a build time depencency. This requires
26 and assumes a standard C compiler is already installed, along with 26 and assumes a standard C compiler is already installed, along with
39 <package name="numpy" version="1.9" /> 39 <package name="numpy" version="1.9" />
40 </repository> 40 </repository>
41 </action> 41 </action>
42 <action type="make_directory">$INSTALL_DIR/lib/python</action> 42 <action type="make_directory">$INSTALL_DIR/lib/python</action>
43 <action type="shell_command"> 43 <action type="shell_command">
44 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 44 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
45 export PATH=$PATH:$PATH_NUMPY &amp;&amp; 45 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
46 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp; 46 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
47 python setup.py install --install-lib $INSTALL_DIR/lib/python 47 python2 setup.py install --install-lib $INSTALL_DIR/lib/python
48 </action> 48 </action>
49 <action type="set_environment"> 49 <action type="set_environment">
50 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> 50 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
51 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> 51 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
52 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> 52 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
64 <action type="make_directory">$INSTALL_DIR/jbrowse</action> 64 <action type="make_directory">$INSTALL_DIR/jbrowse</action>
65 <action type="shell_command"> 65 <action type="shell_command">
66 export HOME=$INSTALL_DIR/jbrowse &amp;&amp; ./setup.sh 66 export HOME=$INSTALL_DIR/jbrowse &amp;&amp; ./setup.sh
67 </action> 67 </action>
68 <action type="move_directory_files"> 68 <action type="move_directory_files">
69 <source_directory>.</source_directory> 69 <source_directory>.</source_directory>
70 <destination_directory>$INSTALL_DIR/jbrowse</destination_directory> 70 <destination_directory>$INSTALL_DIR/jbrowse</destination_directory>
71 </action> 71 </action>
72 <action type="set_environment"> 72 <action type="set_environment">
73 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse</environment_variable> 73 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse</environment_variable>
74 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/bin</environment_variable> 74 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/bin</environment_variable>
75 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/src</environment_variable> 75 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/src</environment_variable>
76 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/extlib</environment_variable> 76 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/extlib</environment_variable>