Mercurial > repos > jankanis > blast2html

annotate tool_dependencies.xml @ 56:d2fb88c1e866

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
fix interpreter setting
author Jan Kanis <jan.code@jankanis.nl>
date Mon, 26 May 2014 14:20:17 +0200
parents c0c4f52ca313
children 159989f6bfa6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
41
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1 <?xml version="1.0"?>
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
2 <tool_dependency>
46
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
3 <package name="cython" version="0.20.1">
48
49de6a204554 fix prior_installation_required flag
Jan Kanis <jan.code@jankanis.nl>
parents: 47
diff changeset
4 <repository name="package_cython_0_20_1" owner="iuc" prior_installation_required="True"
46
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
5 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="c3a8c46fcb97" />
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
6 </package>
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
7
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
8 <package name="libxml2" version="2.9.1">
48
49de6a204554 fix prior_installation_required flag
Jan Kanis <jan.code@jankanis.nl>
parents: 47
diff changeset
9 <repository name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True"
46
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
10 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="3af7ad13a6fb" />
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
11 </package>
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
12
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
13 <package name="libxslt" version="1.1.28">
48
49de6a204554 fix prior_installation_required flag
Jan Kanis <jan.code@jankanis.nl>
parents: 47
diff changeset
14 <repository name="package_libxslt_1_1_28" owner="devteam" prior_installation_required="True"
46
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
15 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee" />
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
16 </package>
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
17
53
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
18 <package name="python3" version="3.4.1">
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
19 <repository name="package_python3_4" owner="jankanis" prior_installation_required="True"
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
20 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="9dbfc4fcef0a" />
41
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
21 </package>
53
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
22
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
23 <package name="blast2html_venv" version="0.1">
41
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
24 <install version="1.0">
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
25 <actions>
46
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
26 <action type="set_environment_for_install">
48
49de6a204554 fix prior_installation_required flag
Jan Kanis <jan.code@jankanis.nl>
parents: 47
diff changeset
27 <repository name="package_cython_0_20_1" owner="iuc"
46
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
28 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="c3a8c46fcb97">
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
29 <package name="cython" version="0.20.1" />
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
30 </repository>
48
49de6a204554 fix prior_installation_required flag
Jan Kanis <jan.code@jankanis.nl>
parents: 47
diff changeset
31 <repository name="package_libxml2_2_9_1" owner="devteam"
46
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
32 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="3af7ad13a6fb">
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
33 <package name="libxml2" version="2.9.1" />
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
34 </repository>
48
49de6a204554 fix prior_installation_required flag
Jan Kanis <jan.code@jankanis.nl>
parents: 47
diff changeset
35 <repository name="package_libxslt_1_1_28" owner="devteam"
46
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
36 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee">
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
37 <package name="libxslt" version="1.1.28" />
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
38 </repository>
55
c0c4f52ca313 fix depended repository name
Jan Kanis <jan.code@jankanis.nl>
parents: 54
diff changeset
39 <repository name="package_python3_4" owner="jankanis"
54
6d96d48a10f8 add changeset revision in xml
Jan Kanis <jan.code@jankanis.nl>
parents: 53
diff changeset
40 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="9dbfc4fcef0a">
53
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
41 <package name="python3" version="3.4.1" />
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
42 </repository>
46
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
43 </action>
53
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
44
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
45 <action type="shell_command">
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
46 # Unset any saved environment settings from parent virtual
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
47 # environments, e.g. for python 2 or if Galaxy itself is running
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
48 # from within a virtual environment.
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
49 unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
50 pyvenv blast2html_venv
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
51 . blast2html_venv/bin/activate
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
52 pip3 install lxml jinja2
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
53 </action>
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
54
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
55 <action type="set_environment">
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
56 <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python3.4/site-packages</environment_variable>
46
518580263e96 change tool_dependencies.xml
Jan Kanis <jan.code@jankanis.nl>
parents: 45
diff changeset
57 </action>
41
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
58 </actions>
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
59 </install>
53
4217bb9cf1d3 depend on python 3; fix internal links with multiple iterations
Jan Kanis <jan.code@jankanis.nl>
parents: 51
diff changeset
60 <readme>A Python 3 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme>
41
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
61 </package>
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
62
637f96ffb9a4 more dependency updates, now including the python package dependencies
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
63 </tool_dependency>