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