Assuming this comment:
Finally, we will talk to the devteam to rewrite EMBOSS to depend on our separate data type repositories.
refers to the emboss_5 repository owned by devteam, then what is being proposed should work (although I may not be fully understanding what is being proposed). If the emboss datatypes are split up and the emboss_5 repository's repository_dependencies.xml file is altered, then a new installable revision of the emboss_5 repository will be created. This implies that any previous installation cannot be updated to include the split up emboss datatypes. Instead, a new installation of the emboss_5 repository will be required. This new installation may depend on emboss datatypes that conflict with those in the older emboss_5 installation, and the 2nd version of the conflicting datatypes will not be loaded into the Galaxy datatypes registry. However, if the datatypes are the same, this shouldn't be a problem since the 1st version will have been loaded. On Jul 16, 2014, at 4:52 PM, John Chilton <jmchilton@gmail.com> wrote:
Is this going to work? I get that this would be a better design if done from the beginning, but what happens if you install an emboss repository upgrade (on an existing install) that brings in conflicting types from other repositories that already exist and have been previously installed? Does the tool shed have a mechanism to handle that?
-John
On Wed, Jul 16, 2014 at 9:20 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Eric,
Forgive me, I'm not 100% clear on the custom plugin system used by galaxy, but if I "subclass" from the text data type, will sniffers I implement override text's and function? The lack of being able to add an entry to the sniffer section (unlike with the tabular example) led me to believe my genbank datatype wouldn't be sniffed.
Thats true, if you want to override functions, you need to subclass it on a python level not on the XML level.
Additionally, I'd still like to be able to add completely new datatypes, do you know of any working examples of this? As mentioned in my original post, duplicating an existing datatype and changing names on it surprisingly doesn't work.
https://github.com/bgruening/galaxytools/tree/master/datatypes/msa_datatypes https://github.com/bgruening/galaxytools/blob/master/chemicaltoolbox/datatyp...
Is that enough, to get started?
I'd be lovely to have the emboss datatypes split out.
Ok, than lets start :) I will try to fork emboss into my galaxytools/datatypes repository and try to split them. You will get commit access and can improve your genbank datatype (and a few more ;)). Finally, we will talk to the devteam to rewrite EMBOSS to depend on our separate data type repositories. OK?
Ciao, Bjoenr
Cheers, Eric
On July 16, 2014 8:34:55 AM CDT, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Indeed - ideally (once working) we can upload under the IUC ToolShed as a community maintained resource rather than under a personal account which becomes a single point of failure (the bus factor).
We (the ICU) have previously discussed doing this so that the EMBOSS datatypes could become more of a meta-entry depending on other smaller specific datatype defining ToolShed repositories. But it hasn't reached the top of my personal TODO list yet ;)
Peter
On Wed, Jul 16, 2014 at 1:47 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Eric,
please have a look at:
https://github.com/bgruening/galaxytools/blob/master/datatypes/msa_datatypes...
You need somthing like: <datatype extension="genbank" type="galaxy.datatypes.data:Text" subclass="True" />
Lets try to split the EMBOSS datatypes a little bit into small
chunks. E.g.
sequences_datatypes, msa_datatypes ... and so on ...
Cheers, Bjoern
Am 14.07.2014 20:31, schrieb Eric Rasche:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
I'm trying to add a new datatype to my galaxy instance for genbank files, however I'm running into various issues. I've followed the tutorial (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes)
however that example subclasses tabular, and I'd like to subclass
Text
as they're plain text files, and I'd like to be able to define a
sniffer
for them (not possible if your type=galaxy.datatypes.data:Text)
I figured the call ought to be something like
<datatype extension="gb" type="galaxy.datatypes.data:Genbank" subclass="True" />
however, everything I try fails with
> Error importing datatype module galaxy.datatypes.data: 'module'
object
> > has no attribute 'Genbank'
To avoid this particular issue, I tried writing a separate datatype
just
for genbank files (type="galaxy.datatypes.genbank:Genbank"), however that fails with the same error:
> galaxy.datatypes.registry ERROR 2014-07-14 13:23:23,100 Error
importing
> > datatype module galaxy.datatypes.genbank: 'module' object has no
attribute
> > 'genbank' > Traceback (most recent call last): > File
"/home/hxr/work/galaxy-central/lib/galaxy/datatypes/registry.py",
> > line 206, in load_datatypes > module = getattr( module, mod ) > AttributeError: 'module' object has no attribute 'genbank'
Here's my lib/galaxy/datatypes/genbank.py looks like:
> import pkg_resources > pkg_resources.require( "bx-python" ) > import logging > from galaxy.datatypes import data > log = logging.getLogger(__name__) > > class Genbank( data.Text ): > file_ext = "gb" > > def sniff( self, filename ): > header = open(filename).read(5) > return header == 'LOCUS'
To debug this, I've tried copying the tabular data type completely, removed all the classes other than Tabular, and renamed it
"Genbank",
however this fails too with the same error.
Can anyone offer some insight?
Cheers, Eric -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (GNU/Linux)
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___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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