Mercurial > repos > bgruening > bismark
comparison documentation/readme.rst @ 7:fcadce4d9a06 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
| author | bgruening |
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| date | Sat, 06 May 2017 13:18:09 -0400 |
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| 6:0f8646f22b8d | 7:fcadce4d9a06 |
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| 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 |