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1 CEAS: Cis-regulatory Element Annotation System
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2 ==============================================
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3
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4 Galaxy tool wrapper for the CEAS (Cis-regulatory Element Annotation System), which
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5 can be used to annotate intervals and scores with genome features.
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6
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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 core 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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11
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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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14
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15 The official CEAS website is at:
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16
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17 - http://liulab.dfci.harvard.edu/CEAS/index.html
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18
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19 The Cistrome version can be found via
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20
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21 - https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
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22
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23 Automated installation
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24 ======================
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25
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26 Installation via the Galaxy Tool Shed will take care of installing the tool wrapper
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27 and the CEAS programs, and setting the appropriate environment variables.
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28
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29 In addition this will also install a data manager which can be used to install
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30 reference GDB data files necessary for the tool.
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31
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32 Manual Installation
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33 ===================
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34
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35 There are two files to install:
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36
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37 - ``ceas_wrapper.xml`` (the Galaxy tool definition)
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38 - ``ceas_wrapper.sh`` (the shell script wrapper)
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39
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40 The suggested location is in a ``tools/ceas/`` folder. You will then
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41 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
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42 by adding the line:
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43
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44 <tool file="ceas/ceasbw_wrapper.xml" />
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45
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46 You also need to make a copy of the ``ceas.loc`` file (a sample version is
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47 provided here) which points to the available GDB files for different genomes.
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48
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49 This file should be placed in the ``tool-data`` directory of your Galaxy
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50 installation.
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51
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52 Reference Data
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53 ==============
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54
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55 CEAS requires reference data in the form of GDB files (essentially, SQLite database
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56 files) containing the RefSeq genes for the genome in question.
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57
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58 A limited number of GDB files are available for download from the CEAS website; to
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59 make new ones, see the section "Build a sqlite3 file with a gene annotation table
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60 and genome background annotation for CEAS" in the CEAS manual:
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61
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62 - http://liulab.dfci.harvard.edu/CEAS/usermanual.html
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63
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64 History
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65 =======
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66
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67 ========== ======================================================================
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68 Version Changes
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69 ---------- ----------------------------------------------------------------------
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70 1.0.2-2 - Major updates to fix various bugs, add tests and enable ceasBW to
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71 be used without an existing chromosome sizes file.
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72 1.0.2-1 - Modified to work with Cistrome-version of CEAS (includes additional
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73 'ceasBW' program which can take bigWig input)
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74 1.0.2-0 - Initial version.
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75 ========== ======================================================================
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76
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77 Developers
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78 ==========
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79
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80 This tool is developed on the following GitHub repository:
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81 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/ceas
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82
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83 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
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84 the ``package_ceas.sh`` script.
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