Hello all,
I've looked at the provided Galaxy wrappers, and the Galaxy Tool Shed, http://community.g2.bx.psu.edu/ but haven't seen any "classic" multiple alignment tools wrapped for Galaxy. To be clear I'm talking about things like ClustalW, MUSCLE, T-Coffee, and so on (not tools for mapping sequencing reads onto a reference genome).
Is anyone working on this sort of thing in Galaxy?
Thanks,
Peter
Peter
A while ago, I started to write a simple tool definition file for 'clustalw2' (see attachment). There are still a lot of options missing, but feel free to use it as a starting point.
Hans
On 11/11/2010 05:58 PM, Peter wrote:
Hello all,
I've looked at the provided Galaxy wrappers, and the Galaxy Tool Shed, http://community.g2.bx.psu.edu/ but haven't seen any "classic" multiple alignment tools wrapped for Galaxy. To be clear I'm talking about things like ClustalW, MUSCLE, T-Coffee, and so on (not tools for mapping sequencing reads onto a reference genome).
Is anyone working on this sort of thing in Galaxy?
Thanks,
Peter _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
On Thu, Nov 11, 2010 at 5:08 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Peter
A while ago, I started to write a simple tool definition file for 'clustalw2' (see attachment). There are still a lot of options missing, but feel free to use it as a starting point.
Hans
Thanks Hans.
Are there any others who've looked at this sort of thing?
Peter
Peter,
Not sure what is all in the EMBOSS and EMBASSY suite that are already part of galaxy: http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/ But I spotted some Smith Waterman stuff. http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/alignment_local_g...
I am working myself on the suite of complete (pairwise) genome alignments and plotters using the MUMmer algorithms. They are near finished....
Cheers,
Alex
Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Peter [biopython@maubp.freeserve.co.uk] Verzonden: donderdag 11 november 2010 18:19 Aan: Hans-Rudolf Hotz CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Classic alignment tools (ClustalW, MUSCLE, T-Coffee, etc)
On Thu, Nov 11, 2010 at 5:08 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Peter
A while ago, I started to write a simple tool definition file for 'clustalw2' (see attachment). There are still a lot of options missing, but feel free to use it as a starting point.
Hans
Thanks Hans.
Are there any others who've looked at this sort of thing?
Peter _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Peter, actually just found it. In the EMBOSS suite its called emma (for ClustalW) http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/emma.html
EMBOSS suite is default in galaxy present but locally you need to enable the wrappers/tools first.
Alex
________________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Peter [biopython@maubp.freeserve.co.uk] Verzonden: donderdag 11 november 2010 18:19 Aan: Hans-Rudolf Hotz CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Classic alignment tools (ClustalW, MUSCLE, T-Coffee, etc)
On Thu, Nov 11, 2010 at 5:08 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Peter
A while ago, I started to write a simple tool definition file for 'clustalw2' (see attachment). There are still a lot of options missing, but feel free to use it as a starting point.
Hans
Thanks Hans.
Are there any others who've looked at this sort of thing?
Peter _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
never mind. See that emma is lacking the wrapper for galaxy in EMBOSS.
________________________________________ Van: Bossers, Alex Verzonden: donderdag 11 november 2010 20:27 Aan: Peter CC: galaxy-dev@lists.bx.psu.edu Onderwerp: RE: [galaxy-dev] Classic alignment tools (ClustalW, MUSCLE, T-Coffee, etc)
Peter, actually just found it. In the EMBOSS suite its called emma (for ClustalW) http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/emma.html
EMBOSS suite is default in galaxy present but locally you need to enable the wrappers/tools first.
Alex
________________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Peter [biopython@maubp.freeserve.co.uk] Verzonden: donderdag 11 november 2010 18:19 Aan: Hans-Rudolf Hotz CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Classic alignment tools (ClustalW, MUSCLE, T-Coffee, etc)
On Thu, Nov 11, 2010 at 5:08 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Peter
A while ago, I started to write a simple tool definition file for 'clustalw2' (see attachment). There are still a lot of options missing, but feel free to use it as a starting point.
Hans
Thanks Hans.
Are there any others who've looked at this sort of thing?
Peter _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
On Thu, Nov 11, 2010 at 7:27 PM, Bossers, Alex Alex.Bossers@wur.nl wrote:
Peter, actually just found it. In the EMBOSS suite its called emma (for ClustalW) http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/emma.html
EMBOSS suite is default in galaxy present but locally you need to enable the wrappers/tools first.
Alex
Hi Alex,
I'm aware then Galaxy has wrappers for some of EMBOSS v5, which is pretty old but would include emma: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/emma.html
However, unless I'm missing something Galaxy doesn't have a wrapper for emma (or clustalw): http://bitbucket.org/galaxy/galaxy-central/src/tip/tools/emboss_5/
Peter
galaxy-dev@lists.galaxyproject.org
-
Bossers, Alex -
Hans-Rudolf Hotz -
Peter