Mercurial > repos > pjbriggs > ceas
annotate 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 |
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date | Tue, 18 Oct 2016 09:31:10 -0400 |
parents | f411ce97a351 |
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rev | line source |
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0 | 1 <?xml version="1.0"?> |
2 <tool_dependency> | |
2
d2283cca00cd
CEAS tool version 1.0.2-3: updates to get R 3.1.2 and bx-python 0.7.1 dependencies from the toolshed.
pjbriggs
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3 <!-- R 3.1.2 from main/test toolshed --> |
0 | 4 <package name="R" version="3.1.2"> |
2
d2283cca00cd
CEAS tool version 1.0.2-3: updates to get R 3.1.2 and bx-python 0.7.1 dependencies from the toolshed.
pjbriggs
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5 <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
d2283cca00cd
CEAS tool version 1.0.2-3: updates to get R 3.1.2 and bx-python 0.7.1 dependencies from the toolshed.
pjbriggs
parents:
0
diff
changeset
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6 </package> |
d2283cca00cd
CEAS tool version 1.0.2-3: updates to get R 3.1.2 and bx-python 0.7.1 dependencies from the toolshed.
pjbriggs
parents:
0
diff
changeset
|
7 <!-- bx_python from main/test toolshed --> |
d2283cca00cd
CEAS tool version 1.0.2-3: updates to get R 3.1.2 and bx-python 0.7.1 dependencies from the toolshed.
pjbriggs
parents:
0
diff
changeset
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8 <package name="bx-python" version="0.7.1"> |
d2283cca00cd
CEAS tool version 1.0.2-3: updates to get R 3.1.2 and bx-python 0.7.1 dependencies from the toolshed.
pjbriggs
parents:
0
diff
changeset
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9 <repository changeset_revision="7ce9cf37130f" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
0 | 10 </package> |
11 <!-- Python mysqldb package --> | |
12 <package name="python_mysqldb" version="1.2.5"> | |
13 <install version="1.0"> | |
14 <actions> | |
15 <action type="download_by_url">https://pypi.python.org/packages/source/M/MySQL-python/MySQL-python-1.2.5.zip</action> | |
16 <action type="make_directory">$INSTALL_DIR/lib/python</action> | |
17 <action type="shell_command"> | |
18 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && | |
19 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin | |
20 </action> | |
21 <action type="set_environment"> | |
22 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> | |
23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
24 </action> | |
25 </actions> | |
26 </install> | |
27 <readme>Installs Python module MySQLdb 1.2.5</readme> | |
28 </package> | |
29 <!-- cistrome_ceas | |
30 Installs the version of CEAS package found in the Cistrome | |
31 distribution: | |
32 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview | |
33 --> | |
34 <package name="cistrome_ceas" version="1.0.2.d8c0751"> | |
35 <install version="1.0"> | |
36 <actions> | |
37 <action type="shell_command"> | |
38 hg clone https://bitbucket.org/cistrome/cistrome-applications-harvard cistrome_ceas | |
39 </action> | |
40 <action type="shell_command"> | |
41 hg update d8c0751 | |
42 </action> | |
43 <action type="make_directory">$INSTALL_DIR/lib/python</action> | |
44 <action type="shell_command"> | |
45 cd published-packages/CEAS/ | |
46 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && | |
47 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin | |
48 </action> | |
49 <action type="set_environment"> | |
50 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> | |
51 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
52 </action> | |
53 </actions> | |
54 </install> | |
55 <readme>Installs version 1.0.2 of CEAS from cistrome (commit id d8c0751, | |
56 datestamp 20140929), which includes ceasBW (a version of ceas which can | |
57 handle bigWig file input from MACS2. | |
58 | |
59 Cistrome code is at | |
60 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview | |
61 | |
62 The CEAS code is under the published-packages/CEAS/ subdirectory | |
63 | |
64 Cistrome data files and documentation can be found at | |
65 http://liulab.dfci.harvard.edu/CEAS/index.html | |
66 </readme> | |
67 </package> | |
68 <!-- fetchChromSize from UCSC tools --> | |
69 <package name="ucsc_fetchChromSizes" version="1.0"> | |
70 <install version="1.0"> | |
71 <actions> | |
72 <action type="download_binary"> | |
73 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template> | |
74 </action> | |
75 <action type="chmod"> | |
76 <file mode="755">$INSTALL_DIR/fetchChromSizes</file> | |
77 </action> | |
78 <action type="set_environment"> | |
79 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> | |
80 </action> | |
81 </actions> | |
82 </install> | |
83 <readme>Installs the binary executable for the fetchChromSizes utility | |
84 from UCSC tools | |
85 </readme> | |
86 </package> | |
87 </tool_dependency> |