Mercurial > repos > yhoogstrate > package_crossmap_0_2

comparison tool_dependencies.xml @ 23:e35fa4fad2e7 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d3d741a1024b4d689cb0b319fd6231acefdda8e8-dirty
author yhoogstrate
date Thu, 12 Nov 2015 05:03:43 -0500
parents b38e4886f937
children 6bf5799e6649
comparison
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22:b38e4886f937 23:e35fa4fad2e7
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="python" version="2.7">
4 <repository changeset_revision="9cdf46934080" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
3 <package name="nose" version="1.3.7"> 6 <package name="nose" version="1.3.7">
4 <repository changeset_revision="2e16c2edb44d" name="package_nose_1_3_7" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="2e16c2edb44d" name="package_nose_1_3_7" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package> 8 </package>
6
7 <package name="numpy" version="1.9"> 9 <package name="numpy" version="1.9">
8 <repository changeset_revision="816d3480b0b1" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="816d3480b0b1" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
9 </package> 11 </package>
10
11 <package name="cython" version="0.23.1"> 12 <package name="cython" version="0.23.1">
12 <repository changeset_revision="5212151afa22" name="package_cython_0_23_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="5212151afa22" name="package_cython_0_23_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
13 </package> 14 </package>
14 15
15 <package name="crossmap" version="0.2"> 16 <package name="crossmap" version="0.2">
16 <install version="1.0"> 17 <install version="1.0">
17 <actions> 18 <actions>
18 <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action> 19 <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action>
19 20
20 <action type="setup_python_environment"> 21 <action type="setup_python_environment">
22 <repository changeset_revision="9cdf46934080" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
23 <package name="python" version="2.7" />
24 </repository>
21 <repository changeset_revision="2e16c2edb44d" name="package_nose_1_3_7" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu"> 25 <repository changeset_revision="2e16c2edb44d" name="package_nose_1_3_7" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu">
22 <package name="nose" version="1.3.7" /> 26 <package name="nose" version="1.3.7" />
23 </repository> 27 </repository>
24 <repository changeset_revision="5212151afa22" name="package_cython_0_23_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 28 <repository changeset_revision="5212151afa22" name="package_cython_0_23_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
25 <package name="cython" version="0.23.1" /> 29 <package name="cython" version="0.23.1" />
27 <repository changeset_revision="816d3480b0b1" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> 31 <repository changeset_revision="816d3480b0b1" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
28 <package name="numpy" version="1.9" /> 32 <package name="numpy" version="1.9" />
29 </repository> 33 </repository>
30 </action> 34 </action>
31 35
32 <!-- If CrossMap is installed with - - home or - - prefix 36 <!-- If CrossMap is installed with - - home or - - prefix
33 into, it often crashes with a 'write-test' error 37 it often crashes with a 'write-test' error
34 38
35 Using - - root places the installation in: 39 Using - - root places the installation in:
36 $INSTALL_DIR / (python path dir) / 40 $INSTALL_DIR / (python path dir) /
37 --> 41 -->
38 <action type="shell_command"> 42 <action type="shell_command">
43 mv $INSTALL_DIR$SUB_DIR/../lib $INSTALL_DIR/lib &amp;&amp; 47 mv $INSTALL_DIR$SUB_DIR/../lib $INSTALL_DIR/lib &amp;&amp;
44 mv $INSTALL_DIR$SUB_DIR $INSTALL_DIR/bin 48 mv $INSTALL_DIR$SUB_DIR $INSTALL_DIR/bin
45 </action> 49 </action>
46 50
47 <action type="set_environment"> 51 <action type="set_environment">
48 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR"/lib/python2.7/site-packages"</environment_variable> 52 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable>
49 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 53 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
50 54
51 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable> 55 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable>
52 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable> 56 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
53 </action> 57 </action>