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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty
author bebatut
date Wed, 27 Jan 2016 03:55:09 -0500
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1 Galaxy wrapper for PRINSEQ
2 ===========================
3
4 PRINSEQ is a tool for easy and rapid quality control and data processing of
5 metagenomic and metatranscriptomic datasets. This tool allow to process the
6 sequences with filtering and trimming. For more information, check the
7 [user manual](http://prinseq.sourceforge.net/manual.html)
8
9 # Installation
10
11 ## Automated installation
12
13 On a Galaxy instance, the wrapper can be automatically installed using the
14 ToolShed. This will automatically install the dependencies, configure the Galaxy
15 instance for the tool and data, ...
16
17 ## Manual installation
18
19 For manual installation, the files `prinseq.xml` must be put in the `tools/prinseq/`
20 folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as
21 normal:
22
23 ```
24 <section name="Control quality" id="prinseq">
25 <tool file="prinseq/prinseq.xml" />
26 </section>
27 ```
28
29 PRINSEQ must be installed somewhere on the system path. It can be done using:
30
31 ```
32 planemo dependency_script ~/repositories/galaxytools/tools/prinseq/
33 bash dep_install.sh
34 source env.sh
35 ```
36
37 To test the Galaxy integration, the functional tests can be runned:
38
39 ```
40 ./run_tests.sh -sid prinseq
41 ```
42
43 # Bug Reports
44
45 Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues).
46
47 # Developers
48
49 A release can be pushed to the test or main "Galaxy Tool Shed", using the following
50 Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`):
51
52 ```
53 planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/prinseq/
54 ```
55
56 or:
57
58 ```
59 planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/prinseq/
60 ```
61
62 # License (Apache 2)
63
64 This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details