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comparison tool_dependencies.xml @ 53:4217bb9cf1d3

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depend on python 3; fix internal links with multiple iterations
author Jan Kanis <jan.code@jankanis.nl>
date Mon, 26 May 2014 13:07:13 +0200
parents b15a20c2372a
children 6d96d48a10f8
comparison
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52:d6c7b5de2833 53:4217bb9cf1d3
13 <package name="libxslt" version="1.1.28"> 13 <package name="libxslt" version="1.1.28">
14 <repository name="package_libxslt_1_1_28" owner="devteam" prior_installation_required="True" 14 <repository name="package_libxslt_1_1_28" owner="devteam" prior_installation_required="True"
15 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee" /> 15 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee" />
16 </package> 16 </package>
17 17
18 <package name="argparse" version="1.2.1"> 18 <package name="python3" version="3.4.1">
19 <install version="1.0"> 19 <repository name="package_python3_4" owner="jankanis" prior_installation_required="True"
20 <actions> 20 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="9dbfc4fcef0a" />
21 <action type="setup_virtualenv">
22 argparse == 1.2.1
23 </action>
24 </actions>
25 </install>
26 <readme>The Python argparse library. This is included in the stdlib for python 2.7 and up, but not for 2.6</readme>
27 </package> 21 </package>
28 22
29 <package name="python_six" version="1.3.0"> 23 <package name="blast2html_venv" version="0.1">
30 <install version="1.0">
31 <actions>
32 <action type="setup_virtualenv">
33 six >= 1.3.0
34 </action>
35 </actions>
36 </install>
37 <readme>The Python six library for python 2/3 compatibility</readme>
38 </package>
39
40 <package name="lxml" version="2.2.3">
41 <install version="1.0"> 24 <install version="1.0">
42 <actions> 25 <actions>
43 <action type="set_environment_for_install"> 26 <action type="set_environment_for_install">
44 <repository name="package_cython_0_20_1" owner="iuc" 27 <repository name="package_cython_0_20_1" owner="iuc"
45 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="c3a8c46fcb97"> 28 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="c3a8c46fcb97">
51 </repository> 34 </repository>
52 <repository name="package_libxslt_1_1_28" owner="devteam" 35 <repository name="package_libxslt_1_1_28" owner="devteam"
53 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee"> 36 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee">
54 <package name="libxslt" version="1.1.28" /> 37 <package name="libxslt" version="1.1.28" />
55 </repository> 38 </repository>
39 <repository name="python3" owner="jankanis">
40 <package name="python3" version="3.4.1" />
41 </repository>
56 </action> 42 </action>
57 <action type="shell_command"> 43
58 echo '*******************************************************************************' 44 <action type="shell_command">
59 echo $PATH 45 # Unset any saved environment settings from parent virtual
60 echo xslt-config at: `which -a xslt-config` 46 # environments, e.g. for python 2 or if Galaxy itself is running
61 </action> 47 # from within a virtual environment.
62 <action type="setup_virtualenv"> 48 unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME
63 lxml == 2.2.3 49 pyvenv blast2html_venv
50 . blast2html_venv/bin/activate
51 pip3 install lxml jinja2
52 </action>
53
54 <action type="set_environment">
55 <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python3.4/site-packages</environment_variable>
64 </action> 56 </action>
65 </actions> 57 </actions>
66 </install> 58 </install>
67 <readme>The Python lxml library</readme> 59 <readme>A Python 3 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme>
68 </package>
69
70 <package name="jinja2" version="2.7.2">
71 <install version="1.0">
72 <actions>
73 <action type="setup_virtualenv">
74 jinja2 == 2.7.2
75 </action>
76 </actions>
77 </install>
78 <readme>The Jinja 2 template engine for Python</readme>
79 </package> 60 </package>
80 61
81 </tool_dependency> 62 </tool_dependency>