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Repository ceas
Name: ceas
Owner: pjbriggs
Synopsis: CEAS Cis-regulatory Element Annotation System
CEAS can be characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad binding factors.

This tool uses the version of CEAS included in the Cistrome package which can handle bigWig input, and includes a data manager to download or create the gene annotation table files.
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/pjbriggs/ceas
Type: unrestricted
Revision: 2:d2283cca00cd
This revision can be installed: True
Times cloned / installed: 588

Repository README files - may contain important installation or license information

CEAS: Cis-regulatory Element Annotation System ============================================== Galaxy tool wrapper for the CEAS (Cis-regulatory Element Annotation System), which can be used to annotate intervals and scores with genome features. This tool uses the Cistrome version of the package, which provides two versions of the core program: in addition to the ``ceas`` program (the same as that available from the main CEAS website), it also includes the ``ceasBW`` program (which can handle bigwig input). The tool assumes that the ``ceas`` and ``ceasBW`` programs are on the Galaxy user's path. The official CEAS website is at: - http://liulab.dfci.harvard.edu/CEAS/index.html The Cistrome version can be found via - https://bitbucket.org/cistrome/cistrome-applications-harvard/overview Automated installation ====================== Installation via the Galaxy Tool Shed will take care of installing the tool wrapper and the CEAS programs, and setting the appropriate environment variables. In addition this will also install a data manager which can be used to install reference GDB data files necessary for the tool. Manual Installation =================== There are two files to install: - ``ceas_wrapper.xml`` (the Galaxy tool definition) - ``ceas_wrapper.sh`` (the shell script wrapper) The suggested location is in a ``tools/ceas/`` folder. You will then need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool by adding the line: You also need to make a copy of the ``ceas.loc`` file (a sample version is provided here) which points to the available GDB files for different genomes. This file should be placed in the ``tool-data`` directory of your Galaxy installation. Reference Data ============== CEAS requires reference data in the form of GDB files (essentially, SQLite database files) containing the RefSeq genes for the genome in question. A limited number of GDB files are available for download from the CEAS website; to make new ones, see the section "Build a sqlite3 file with a gene annotation table and genome background annotation for CEAS" in the CEAS manual: - http://liulab.dfci.harvard.edu/CEAS/usermanual.html History ======= ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- 1.0.2-3 - Switch to getting R 3.1.2 and bx-python 0.7.1 dependencies from the toolshed (rather than installing as part of the tool) 1.0.2-2 - Major updates to fix various bugs, add tests and enable ceasBW to be used without an existing chromosome sizes file. 1.0.2-1 - Modified to work with Cistrome-version of CEAS (includes additional 'ceasBW' program which can take bigWig input) 1.0.2-0 - Initial version. ========== ====================================================================== Developers ========== This tool is developed on the following GitHub repository: https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/ceas For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use the ``package_ceas.sh`` script.
Dependencies of this repository

Repository package_readline_6_2 revision 5313ca2fbce6 owned by iuc (prior install required)
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Repository package_pixman_0_32_4 revision 93cd8e03820c owned by devteam (prior install required)
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Repository package_fontconfig_2_11_1 revision d88d844df0cb owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_freetype_2_5_2 revision 1e86d1cf79a4 owned by iuc (prior install required)
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Name Version Type
R 3.1.2 package
bx-python 0.7.1 package
cistrome_ceas 1.0.2.d8c0751 package
python_mysqldb 1.2.5 package
ucsc_fetchChromSizes 1.0 package

Contents of this repository

Name Description Version Minimum Galaxy Version
Annotate intervals and scores with genome features 1.0.2-3 any
Fetch and install annotation databases for CEAS 0.0.1 any

Name Version Data Tables
ceas_fetch_annotations 0.0.1 ceas_annotations

Categories
ChIP-seq - Tools for analyzing and manipulating ChIP-seq data.
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis