Mercurial > repos > fubar > clustalw
view rgclustal/README @ 0:8888e4e3f169
Migrated tool version 0.1 from old tool shed archive to new tool shed repository
author | fubar |
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date | Tue, 07 Jun 2011 17:05:43 -0400 |
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This is a wrapper for ClustalW. This tool allows you to align multiple sequences in Galaxy, using ClustalW2_ with mostly default options which should work reasonably well for many alignments. DNA or protein sequences can be aligned. The input file must be a fasta file in your current history. 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 showing the output Clustalw would normally write to standard output. If Clustal format is chosen, you have the option of adding basepair counts to the output 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 **Installation** Make sure clustalw2 is available on the path for all your nodes Move the test data files to your galaxy root test-data 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. Run sh run_functional_tests.sh -id clustalw to make sure the tests work then restart Galaxy and you should be good to go. **Attribution** Clustal attribution and associated documentation are available at http://www.clustal.org An implementation of a Galaxy Clustal wrapper was written by Hans-Rudolf Hotz in an email on the developer list - http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html 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 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. **License** Assuming Hans-Rudolf is ok with a new license for this derived work, this version of his wrapper is LGPL like other rgenetics artefacts Written by Ross Lazarus for the Rgenetics project Copyright Ross Lazarus at gmail com 2011 All rights reserved. Released under the LGPL - see http://www.gnu.org/copyleft/lesser.html