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Repository 'clustalw'
http://toolshed.g2.bx.psu.edu/view/fubar/clustalw
clustalw
unrestricted
multiple sequence alignment program for DNA or proteins
Galaxy wrapper for the Clustalw multiple alignment program - aligns multiple DNA or protein sequences input as fasta using default parameters. Heavily modified from a script posted by Hans-Rudolf Hotz at http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html

Sure there are plenty of good web implementations, but having it built in to Galaxy makes it even handier. If Fasta is chosen as the output format, the weblogo3 tool will create a very nice sequence logo of the multiple alignment.
3:9c4d943fbef7
fubar
True
227

Repository README files - may contain important installation or license information

Updated july 11 2013 for automated toolshed installation

** 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**

As of July 2013, automated installation from the tool shed should have worked.

Otherwise, the old skool way was:

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




Dependencies of this repository

Name Version Type
clustalw 2.1 package

Contents of this repository

Name Description Version
ClustalW multiple sequence alignment program for DNA or proteins 0.2

Automated tool test results

Time tested: 2014-01-29 02:50:56
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 12311:0ab0eb81d982
Galaxy database version: 118
Tool shed revision: 12297:25d75b83632b
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: clustalw
Tool version: clustalw
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/fubar/clustalw/clustalw/0.2)
Stderr:
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 29, in do_it
    stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 27, in stage_data_in_history
    upload_waits.append( galaxy_interactor.stage_data_async( test_data, history, shed_tool_id ) )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 326, in stage_data_async
    wait=(not async) )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 218, in upload_file
    tc.formfile( "tool_form", "file_data", filename )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/eggs/twill-0.9-py2.7.egg/twill/commands.py", line 481, in formfile
    fp = open(filename, 'rb')
IOError: [Errno 2] No such file or directory: u'/tmp/shed_tools/toolshed.g2.bx.psu.edu/repos/fubar/clustalw/9c4d943fbef7/clustalw/.hg/store/data/test-data/rgClustal_testin.fasta'
TypeNameVersion
clustalw package 2.1
Installation directory
/ToolDepsMain/clustalw/2.1/fubar/clustalw/9c4d943fbef7
Time tested: 2014-01-28 07:05:37
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 12298:a6fed0f56ec8
Galaxy database version: 118
Tool shed revision: 12297:25d75b83632b
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: clustalw
Tool version: clustalw
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/fubar/clustalw/clustalw/0.2)
Stderr:
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 106, in test_tool
    self.do_it( td )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/functional/test_toolbox.py", line 29, in do_it
    stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 27, in stage_data_in_history
    upload_waits.append( galaxy_interactor.stage_data_async( test_data, history, shed_tool_id ) )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/interactor.py", line 326, in stage_data_async
    wait=(not async) )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/test/base/twilltestcase.py", line 218, in upload_file
    tc.formfile( "tool_form", "file_data", filename )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-main-tool-shed-py27/build/eggs/twill-0.9-py2.7.egg/twill/commands.py", line 481, in formfile
    fp = open(filename, 'rb')
IOError: [Errno 2] No such file or directory: u'/tmp/shed_tools/toolshed.g2.bx.psu.edu/repos/fubar/clustalw/9c4d943fbef7/clustalw/.hg/store/data/test-data/rgClustal_testin.fasta'
TypeNameVersion
clustalw package 2.1
Installation directory
/ToolDepsMain/clustalw/2.1/fubar/clustalw/9c4d943fbef7

Categories
Assembly
Fasta Manipulation