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annotate README.markdown @ 3:82df5af2995f draft

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Renamed from "ceasbw..." to "ceas...".
author pjbriggs
date Wed, 22 Apr 2015 05:34:06 -0400
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1 CEAS
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2 ====
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4 XML and wrapper script for the CEAS package, which can be used to annotate intervals
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5 and scores with genome features.
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7 This tool uses the Cistrome version of the package, which provides two versions of
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8 the `ceas` program: in addition to the `ceas` program (the same as that available
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9 from the main CEAS website), it also includes the `ceasBW` program (which can handle
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10 bigwig input).
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12 The tool assumes that the `ceas` and `ceasBW` programs are on the Galaxy user's
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13 path.
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15 The official CEAS website is at:
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17 <http://liulab.dfci.harvard.edu/CEAS/index.html>
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19 The Cistrome version can be found via
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21 <https://bitbucket.org/cistrome/cistrome-applications-harvard/overview>
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23 To add to Galaxy add the following to tool_conf.xml:
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25 <tool file="ceas/ceasbw_wrapper.xml" />
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27 You also need to make a copy of the `ceas.loc` file (sample version is provided
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28 here) which points to the available GDB files for different genomes. The GDB files
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29 are essentially SQLite database files containing the RefSeq genes for the genome
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30 in question.
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32 A limited number of GDB files are available for download from the CEAS website; to
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33 make new ones, see the section "Build a sqlite3 file with a gene annotation table
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34 and genome background annotation for CEAS" in the CEAS manual:
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36 <http://liulab.dfci.harvard.edu/CEAS/usermanual.html>
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38 The `ceas.loc` file should be placed in the `tool-data` directory of your Galaxy
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39 installation.
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41 ### Changes ###
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43 1.0.2-0: first version based on our original `ceas` tool.