Mercurial > repos > fubar > clustalw
comparison rgclustal/README @ 0:8888e4e3f169
Migrated tool version 0.1 from old tool shed archive to new tool shed repository
| author | fubar |
|---|---|
| date | Tue, 07 Jun 2011 17:05:43 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:8888e4e3f169 |
|---|---|
| 1 This is a wrapper for ClustalW. | |
| 2 | |
| 3 This tool allows you to align multiple sequences in Galaxy, using ClustalW2_ with mostly default options which should work reasonably well for many alignments. | |
| 4 DNA or protein sequences can be aligned. The input file must be a fasta file in your current history. | |
| 5 | |
| 6 The alignments will appear as a clustal format file or optionally, as phylip or fasta format files in your history and a text log will be output to your history | |
| 7 showing the output Clustalw would normally write to standard output. | |
| 8 | |
| 9 If Clustal format is chosen, you have the option of adding basepair counts to the output | |
| 10 | |
| 11 A subsequence of the alignment can be output by setting the Output complete parameter to "Partial" and defining the offset and end of the subsequence to be output | |
| 12 | |
| 13 **Installation** | |
| 14 | |
| 15 Make sure clustalw2 is available on the path for all your nodes | |
| 16 | |
| 17 Move the test data files to your galaxy root test-data | |
| 18 Move the xml file to a subdirectory of your tools folder (eg rgenetics/) and then add a line in your tool_conf.xml to point there. | |
| 19 Run | |
| 20 sh run_functional_tests.sh -id clustalw | |
| 21 to make sure the tests work | |
| 22 | |
| 23 then restart Galaxy and you should be good to go. | |
| 24 | |
| 25 **Attribution** | |
| 26 | |
| 27 Clustal attribution and associated documentation are available at http://www.clustal.org | |
| 28 | |
| 29 An implementation of a Galaxy Clustal wrapper was written by Hans-Rudolf Hotz in an email on the developer list - | |
| 30 http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html | |
| 31 | |
| 32 This version by Ross Lazarus for the rgenetics project, builds on Hans-Rudolf's code, adding some additional controls and a log file. It also | |
| 33 deals with stderr so Cluastalw2 writing there doesn't cause the job to error out. That's encoded in the tail of the command line. | |
| 34 | |
| 35 **License** | |
| 36 | |
| 37 Assuming Hans-Rudolf is ok with a new license for this derived work, this version of his wrapper is LGPL like other rgenetics artefacts | |
| 38 | |
| 39 Written by Ross Lazarus for the Rgenetics project | |
| 40 | |
| 41 Copyright Ross Lazarus at gmail com 2011 | |
| 42 | |
| 43 All rights reserved. | |
| 44 | |
| 45 Released under the LGPL - see http://www.gnu.org/copyleft/lesser.html | |
| 46 | |
| 47 | |
| 48 | |
| 49 |