Mercurial > repos > bebatut > prinseq
diff README.md @ 4:acaf871de2ea draft default tip
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty
author | bebatut |
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date | Wed, 27 Jan 2016 03:55:09 -0500 |
parents | 10ac5c567b73 |
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--- a/README.md Tue Nov 17 06:02:09 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -Galaxy wrapper for PRINSEQ -=========================== - -PRINSEQ is a tool for easy and rapid quality control and data processing of -metagenomic and metatranscriptomic datasets. This tool allow to process the -sequences with filtering and trimming. For more information, check the -[user manual](http://prinseq.sourceforge.net/manual.html) - -# Installation - -## Automated installation - -On a Galaxy instance, the wrapper can be automatically installed using the -ToolShed. This will automatically install the dependencies, configure the Galaxy -instance for the tool and data, ... - -## Manual installation - -For manual installation, the files `prinseq.xml` must be put in the `tools/prinseq/` - folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as -normal: - -``` -<section name="Control quality" id="prinseq"> - <tool file="prinseq/prinseq.xml" /> -</section> -``` - -PRINSEQ must be installed somewhere on the system path. It can be done using: - -``` -planemo dependency_script ~/repositories/galaxytools/tools/prinseq/ -bash dep_install.sh -source env.sh -``` - -To test the Galaxy integration, the functional tests can be runned: - -``` -./run_tests.sh -sid prinseq -``` - -# Bug Reports - -Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues). - -# Developers - -A release can be pushed to the test or main "Galaxy Tool Shed", using the following -Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`): - -``` -planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/prinseq/ -``` - -or: - -``` -planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/prinseq/ -``` - -# License (Apache 2) - -This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details \ No newline at end of file