# HG changeset patch # User pjbriggs # Date 1418142439 18000 # Node ID 571cb77ab9e797867495a5a2089b9e020e541c4f # Parent 496bc4eff47eaeb43b111d8e1194482a4337871e Add citation tag and README file. diff -r 496bc4eff47e -r 571cb77ab9e7 README.markdown --- a/README.markdown Wed Nov 19 07:56:27 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -weeder2 -======= - -Galaxy tool for motif discovery using weeder2. - -weeder2_wrapper ---------------- - -XML and wrapper script for weeder motif discovery package version 2.0. - -`weeder2` can be obtained from . - -To add to Galaxy add the following to tool_conf.xml: - - - -### Changes ### - -2.0.0.0: initial version - diff -r 496bc4eff47e -r 571cb77ab9e7 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Dec 09 11:27:19 2014 -0500 @@ -0,0 +1,90 @@ +weeder2: motif discovery in sequences from coregulated genes of a single species +================================================================================ + +Galaxy tool for the Weeder2 motif discovery package: + +- Zambelli, F., Pesole, G. and Pavesi, G. 2014. Using Weeder, Pscan, and PscanChIP + for the Discovery of Enriched Transcription Factor Binding Site Motifs in + Nucleotide Sequences. Current Protocols in Bioinformatics. 47:2.11:2.11.1–2.11.31. + http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0211s47/full + +See http://159.149.160.51/modtools/ + +Automated installation +====================== + +Installation via the Galaxy Tool Shed will take of installing the tool wrapper and +the Weeder2 program and data, and setting the appropriate environment variables. + +Manual Installation +=================== + +There are two files to install: + +- ``weeder2_wrapper.xml`` (the Galaxy tool definition) +- ``weeder2_wrapper.sh`` (the shell script wrapper) + +The suggested location is in a ``tools/weeder2/`` folder. You will then +need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool +by adding the line: + + + +You will also need to install ``weeder2`` from: + +- http://159.149.160.51/modtools/downloads/weeder2.html + +The tool wrapper uses the following environment variables in order to find the +appropriate files: + +- ``WEEDER_FREQFILES_DIR`` should point to the ``FreqFiles`` directory + +Also the directory holding the Weeder2 executables should be on your ``PATH``. + +If you want to run the functional tests, copy the sample test files under +sample test files under Galaxy's ``test-data/`` directory. Then: + + ./run_tests.sh -id trimmomatic + +You will need to have set the environment variables above. + +History +======= + +========== ====================================================================== +Version Changes +---------- ---------------------------------------------------------------------- +2.0.0.0 - Initial version +========== ====================================================================== + + +Developers +========== + +This tool is developed on the following GitHub repository: +https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/weeder2 + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use +the ``package_weeder2.sh`` script. + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. diff -r 496bc4eff47e -r 571cb77ab9e7 weeder2_wrapper.xml --- a/weeder2_wrapper.xml Wed Nov 19 07:56:27 2014 -0500 +++ b/weeder2_wrapper.xml Tue Dec 09 11:27:19 2014 -0500 @@ -178,4 +178,12 @@ Please kindly acknowledge both this Galaxy tool, the Weeder package and the utility scripts if you use it in your work. + + + 10.1002/0471250953.bi0211s47 +