Hello all Has anyone successfully integrated the phylib file type into Galaxy in their local install? It's a standard file type for multiple sequence alignment and I could not possibly be the only one who want to support it in a local install. I saw the instructions on the wiki for adding new file types. I would guess that in addition to the changes in the datatypes_conf.xml I would have to derive a new class in galaxy.datatypes.sequence from the existing Alignment class. Is there a commit where this is already included or will I actually have to code it myself? How can I find out? Thanks a lot Ulf PS.: hg tip changeset: 10201:ebe87051fadf tag: tip parent: 10199:8bf64d933704 user: Dannon Baker <dannonbaker@me.com> date: Tue Jul 02 10:48:31 2013 -0400 summary: Fix two more downgrade invocations to accept the migrate_engine parameter ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
On Wed, Sep 11, 2013 at 9:46 AM, Ulf Schaefer <Ulf.Schaefer@phe.gov.uk> wrote:
Hello all
Has anyone successfully integrated the phylib file type into Galaxy in their local install? It's a standard file type for multiple sequence alignment and I could not possibly be the only one who want to support it in a local install.
Do you mean phylip with a p at the end? If so try this: http://toolshed.g2.bx.psu.edu/view/devteam/emboss_datatypes http://emboss.sourceforge.net/docs/themes/SequenceFormats.html Note however there are both strict and relaxed interpretations of the PHYLIP standard (the original version imposed taxon name limits), and also both interlaced/interleaved and sequential forms. The EMBOSS repository has "phylipnon" for non-interleaved (i.e. sequential) PHYLIP format , and "phylip" for either. Peter
Dear Peter Thank you for your email. Yes. This is the file type I mean. Sorry for the typo. Any chance there is a pretty class with appropriate sniff functions etc. somewhere? Currently it looks a little bit like a hack on my side. Thanks a lot for your help Ulf On 11/09/13 10:16, Peter Cock wrote:
On Wed, Sep 11, 2013 at 9:46 AM, Ulf Schaefer <Ulf.Schaefer@phe.gov.uk> wrote:
Hello all
Has anyone successfully integrated the phylib file type into Galaxy in their local install? It's a standard file type for multiple sequence alignment and I could not possibly be the only one who want to support it in a local install.
Do you mean phylip with a p at the end? If so try this: http://toolshed.g2.bx.psu.edu/view/devteam/emboss_datatypes http://emboss.sourceforge.net/docs/themes/SequenceFormats.html
Note however there are both strict and relaxed interpretations of the PHYLIP standard (the original version imposed taxon name limits), and also both interlaced/interleaved and sequential forms.
The EMBOSS repository has "phylipnon" for non-interleaved (i.e. sequential) PHYLIP format , and "phylip" for either.
Peter
************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************
participants (2)
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Peter Cock -
Ulf Schaefer