Mercurial > repos > pjbriggs > ceas
comparison tool_dependencies.xml @ 2:d2283cca00cd draft
CEAS tool version 1.0.2-3: updates to get R 3.1.2 and bx-python 0.7.1 dependencies from the toolshed.
author | pjbriggs |
---|---|
date | Tue, 18 Oct 2016 09:31:10 -0400 |
parents | f411ce97a351 |
children |
comparison
equal
deleted
inserted
replaced
1:df9033b88b53 | 2:d2283cca00cd |
---|---|
1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool_dependency> | 2 <tool_dependency> |
3 <!-- Local version of R 3.1.2 dependency --> | 3 <!-- R 3.1.2 from main/test toolshed --> |
4 <package name="R" version="3.1.2"> | 4 <package name="R" version="3.1.2"> |
5 <install version="1.0"> | 5 <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
6 <actions> | 6 </package> |
7 <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.2.tar.gz</action> | 7 <!-- bx_python from main/test toolshed --> |
8 <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> | 8 <package name="bx-python" version="0.7.1"> |
9 <action type="make_install" /> | 9 <repository changeset_revision="7ce9cf37130f" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
10 <action type="set_environment"> | |
11 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
12 </action> | |
13 </actions> | |
14 </install> | |
15 </package> | 10 </package> |
16 <!-- Python mysqldb package --> | 11 <!-- Python mysqldb package --> |
17 <package name="python_mysqldb" version="1.2.5"> | 12 <package name="python_mysqldb" version="1.2.5"> |
18 <install version="1.0"> | 13 <install version="1.0"> |
19 <actions> | 14 <actions> |
28 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | 23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> |
29 </action> | 24 </action> |
30 </actions> | 25 </actions> |
31 </install> | 26 </install> |
32 <readme>Installs Python module MySQLdb 1.2.5</readme> | 27 <readme>Installs Python module MySQLdb 1.2.5</readme> |
33 </package> | |
34 <!-- bx_python | |
35 This is cribbed from devteam's 'package_bx_python_0_7' in the main | |
36 toolshed: | |
37 https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7 | |
38 --> | |
39 <package name="bx_python" version="0.7.1"> | |
40 <install version="1.0"> | |
41 <actions> | |
42 <action type="setup_virtualenv"> | |
43 numpy==1.7.1 | |
44 bx-python==0.7.1 | |
45 </action> | |
46 <action type="set_environment"> | |
47 <environment_variable action="set_to" name="BX_PYTHON_PATH">$INSTALL_DIR</environment_variable> | |
48 </action> | |
49 </actions> | |
50 </install> | |
51 <readme> | |
52 Installation of bx-python 0.7.1 along with numpy 1.7.1. The installation can be | |
53 accessed via BX_PYTHON_PATH. | |
54 </readme> | |
55 </package> | 28 </package> |
56 <!-- cistrome_ceas | 29 <!-- cistrome_ceas |
57 Installs the version of CEAS package found in the Cistrome | 30 Installs the version of CEAS package found in the Cistrome |
58 distribution: | 31 distribution: |
59 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview | 32 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview |