Mercurial > repos > pjbriggs > ceas
comparison README.markdown @ 0:8b25779ee261 draft
Uploaded initial version to test toolshed.
| author | pjbriggs |
|---|---|
| date | Wed, 28 Jan 2015 04:50:01 -0500 |
| parents | |
| children | 82df5af2995f |
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| 1 CEASbw | |
| 2 ====== | |
| 3 | |
| 4 XML and wrapper script for the Cistrome version of the CEAS package, which can be | |
| 5 used to annotate intervals and scores with genome features. | |
| 6 | |
| 7 In addition to the `ceas` program, the Cistrome version of the package includes the | |
| 8 `ceasBW` program which can handle | |
| 9 | |
| 10 The tool assumes that the `ceas` and `ceasBW` programs are on the Galaxy user's | |
| 11 path. The official CEAS website is at | |
| 12 | |
| 13 <http://liulab.dfci.harvard.edu/CEAS/index.html> | |
| 14 | |
| 15 the Cistrome version can be found via | |
| 16 | |
| 17 <https://bitbucket.org/cistrome/cistrome-applications-harvard/overview> | |
| 18 | |
| 19 To add to Galaxy add the following to tool_conf.xml: | |
| 20 | |
| 21 <tool file="ceas/ceasbw_wrapper.xml" /> | |
| 22 | |
| 23 You also need to make a copy of the `ceas.loc` file (sample version is provided | |
| 24 here) which points to the available GDB files for different genomes. The GDB files | |
| 25 are essentially SQLite database files containing the RefSeq genes for the genome | |
| 26 in question. | |
| 27 | |
| 28 A limited number of GDB files are available for download from the CEAS website; to | |
| 29 make new ones, see the section "Build a sqlite3 file with a gene annotation table | |
| 30 and genome background annotation for CEAS" in the CEAS manual: | |
| 31 | |
| 32 <http://liulab.dfci.harvard.edu/CEAS/usermanual.html> | |
| 33 | |
| 34 The `ceas.loc` file should be placed in the `tool-data` directory of your Galaxy | |
| 35 installation. | |
| 36 | |
| 37 ### Changes ### | |
| 38 | |
| 39 1.0.2-0: first version based on our original `ceas` tool. |