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comparison documentation/readme.rst @ 7:fcadce4d9a06 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
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6:0f8646f22b8d 7:fcadce4d9a06
1 ===============
2 Bismark Wrapper
3 ===============
4
5 Bismark_ uses Bowtie or Bowtie2 to map bisulfite converted sequence reads to a reference genome and determine cytosine methylation states.
6
7 Publication: http://www.ncbi.nlm.nih.gov/pubmed/21493656
8
9 User Guide: http://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide_v0.7.12.pdf
10
11 .. _bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
12
13 Preparation
14 ===========
15
16 Create your reference index with *bismark_genome_preparation* in your normal Galaxy Bowtie2/Botwie index directory. It will create a Bisulfite_Genome folder directly in your Bowtie2/Bowtie index directory.
17 If you follow that approach you do not need to specify or modify an extra .loc file.
18 That wrapper will extract the path to the Bisulfite_Genome folder from ./tool-data/bowtie2_indices.loc or ./tool-data/bowtie_indices.loc.
19
20 =======
21 History
22 =======
23
24 - v0.7: Initial public release
25 - v0.7.8: update and add Tool Shed Integration
26 - v0.7.11.1 change default output to BAM, from now on samtools are required
27 - v0.7.11.2 added multi-threading to samtools (samtools > 0.1.19 is required)
28 - v0.7.12 upgrade to bismark 0.7.12 and fix a major slowdown
29 - v0.7.12.1 define a dependency to samtools 0.1.19
30
31
32 ===============================
33 Wrapper Licence (MIT/BSD style)
34 ===============================
35
36 Permission to use, copy, modify, and distribute this software and its
37 documentation with or without modifications and for any purpose and
38 without fee is hereby granted, provided that any copyright notices
39 appear in all copies and that both those copyright notices and this
40 permission notice appear in supporting documentation, and that the
41 names of the contributors or copyright holders not be used in
42 advertising or publicity pertaining to distribution of the software
43 without specific prior permission.
44
45 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
46 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
47 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
48 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
49 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
50 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
51 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
52 OR PERFORMANCE OF THIS SOFTWARE.
53