Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
Committed On Tue, Feb 1, 2011 at 10:27 AM, Peter wrote: > Hi Kanewi, > > Sorry - make that three changesets on this branch to consider > mering/transplanting: > https://bitbucket.org/peterjc/galaxy-central/changeset/blastplus_jan31 > > Parameter handling, > https://bitbucket.org/peterjc/galaxy-central/changeset/aa82d8273063 > > Cope with errors on stderr, > https://bitbucket.org/peterjc/galaxy-central/changeset/1bd227e7eb4c > > Ensure blast jobs get killed, > https://bitbucket.org/peterjc/galaxy-central/changeset/607b7268693a > > Peter > ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
Hi Kanewi, Sorry - make that three changesets on this branch to consider mering/transplanting: https://bitbucket.org/peterjc/galaxy-central/changeset/blastplus_jan31 Parameter handling, https://bitbucket.org/peterjc/galaxy-central/changeset/aa82d8273063 Cope with errors on stderr, https://bitbucket.org/peterjc/galaxy-central/changeset/1bd227e7eb4c Ensure blast jobs get killed, https://bitbucket.org/peterjc/galaxy-central/changeset/607b7268693a Peter ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
Hi Kanwei, On Mon, Jan 31, 2011 at 5:16 PM, Peter wrote: > On Wed, Jan 5, 2011 at 9:07 PM, Daniel Blankenberg wrote: >> Hi Peter, >> >> We had some discussion today about Kanwei's email and opted for the >> nicer looking access method. I've added a note to the ToolConfigSyntax >> wiki page about special characters. >> >> Thanks, >> >> Dan > > Thanks Dan, > > Kanwei - could you merge/transplant this changeset to use the new > parameter settings in the NCBI BLAST+ wrappers please: > > https://bitbucket.org/peterjc/galaxy-central/changeset/aa82d8273063 > > This is currently the only commit on this new branch, > > https://bitbucket.org/peterjc/galaxy-central/changeset/blastplus_jan31 > > This took a while because I wanted to get the other BLAST+ changes > merged first - and that's done now. > > Thanks, > > Peter Actually there are two commits on that branch now, I've added a workaround for Galaxy issue 325 which is causing us real problems with BLAST warnings being treated as errors: https://bitbucket.org/peterjc/galaxy-central/changeset/1bd227e7eb4c Once issue 325 is fixed, this wrapper script can be removed. Even my proposed first step of getting Galaxy to check the return code would allow a simpler workaround of redirecting stderr to stdout in the XML for the BLAST+ tools. Thanks, Peter ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
On Wed, Jan 5, 2011 at 9:07 PM, Daniel Blankenberg wrote: > Hi Peter, > > We had some discussion today about Kanwei's email and opted for the > nicer looking access method. I've added a note to the ToolConfigSyntax > wiki page about special characters. > > Thanks, > > Dan Thanks Dan, Kanwei - could you merge/transplant this changeset to use the new parameter settings in the NCBI BLAST+ wrappers please: https://bitbucket.org/peterjc/galaxy-central/changeset/aa82d8273063 This is currently the only commit on this new branch, https://bitbucket.org/peterjc/galaxy-central/changeset/blastplus_jan31 This took a while because I wanted to get the other BLAST+ changes merged first - and that's done now. Thanks, Peter ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
Hi Peter,
We had some discussion today about Kanwei's email and opted for the nicer
looking access method. I've added a note to the ToolConfigSyntax wiki page
about special characters.
Thanks,
Dan
On Jan 5, 2011, at 3:07 PM, Peter wrote:
> On Wed, Jan 5, 2011 at 8:02 PM, Daniel Blankenberg wrote:
>> Hi Peter,
>>
>> The method to access additional fields from .loc files has been changed in
>> 4804:376cce23623d to be of the form:
>> ${param.fields.path}.
>>
>
> :)
>
> Did you see Kanwei's email pointing out that while this is nice, it won't
> work with special characters (e.g. hyphens), or another problem would
> be reserved Python names (e.g. in)? I don't think this will be a problem
> in practice, but should be touched on in the documentation for this
> (and setting up loc files).
>
> Peter
___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
On Wed, Jan 5, 2011 at 8:02 PM, Daniel Blankenberg wrote:
> Hi Peter,
>
> The method to access additional fields from .loc files has been changed in
> 4804:376cce23623d to be of the form:
> ${param.fields.path}.
>
:)
Did you see Kanwei's email pointing out that while this is nice, it won't
work with special characters (e.g. hyphens), or another problem would
be reserved Python names (e.g. in)? I don't think this will be a problem
in practice, but should be touched on in the documentation for this
(and setting up loc files).
Peter
___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
Hi Peter,
The method to access additional fields from .loc files has been changed in
4804:376cce23623d to be of the form:
${param.fields.path}.
Thanks again for your input,
Dan
On Jan 4, 2011, at 12:35 PM, Peter wrote:
> On Tue, Jan 4, 2011 at 2:26 AM, Daniel Blankenberg wrote:
>> Hi Peter (and -dev),
>>
>> Would something like ${param.fields.path} be preferred over
>> ${param.get_fields( 'path' )}?
>>
>> Thanks,
>>
>> Dan
>
> That looks nicer to type in the XML wrapper, but I am not
> overly bothered. Could we use either syntax for things like
> filters and conditional checks (in other parameters)?
>
> Peter
___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
I would think the get_fields way is more robust since you wouldn't run
into issues with special characters
On Tue, Jan 4, 2011 at 12:35 PM, Peter wrote:
> On Tue, Jan 4, 2011 at 2:26 AM, Daniel Blankenberg wrote:
>> Hi Peter (and -dev),
>>
>> Would something like ${param.fields.path} be preferred over
>> ${param.get_fields( 'path' )}?
>>
>> Thanks,
>>
>> Dan
>
> That looks nicer to type in the XML wrapper, but I am not
> overly bothered. Could we use either syntax for things like
> filters and conditional checks (in other parameters)?
>
> Peter
> ___
> galaxy-dev mailing list
> galaxy-dev@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
On Tue, Jan 4, 2011 at 2:26 AM, Daniel Blankenberg wrote:
> Hi Peter (and -dev),
>
> Would something like ${param.fields.path} be preferred over
> ${param.get_fields( 'path' )}?
>
> Thanks,
>
> Dan
That looks nicer to type in the XML wrapper, but I am not
overly bothered. Could we use either syntax for things like
filters and conditional checks (in other parameters)?
Peter
___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
Hi Peter (and -dev),
Would something like ${param.fields.path} be preferred over ${param.get_fields(
'path' )}?
Thanks,
Dan
On Jan 3, 2011, at 4:28 PM, Peter wrote:
> Hi Dan,
>
> On Wed, Nov 24, 2010 at 2:49 PM, Daniel Blankenberg wrote:
>> Hi Peter,
>>
>>> I have to say the proposed way to get at the path from within the
>>> wrapper XML file looks very nasty. Is this a short term solution?
>>
>> Yes, that is very nasty and a bad stop-gap solution that needs to not
>> propogate.
>>
>> Data tables are pretty new and need lots of enhancement, something along
>> the lines of what you expected (e.g. $param.path) is the intention. Any
>> other data table suggestions?
>
> I see that has now landed on the trunk,
> https://bitbucket.org/galaxy/galaxy-central/changeset/7be369e7cc6f
>
> Is that stable and ready for public use now? I'll need to look at making
> updates to the BLAST+ wrappers to take advantage of this (probably
> after clearing though my back log of other BLAST+ stuff like the
> extended tabular output).
>
> Peter
___
galaxy-dev mailing list
galaxy-dev@lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
Hi Dan, On Wed, Nov 24, 2010 at 2:49 PM, Daniel Blankenberg wrote: > Hi Peter, > >> I have to say the proposed way to get at the path from within the >> wrapper XML file looks very nasty. Is this a short term solution? > > Yes, that is very nasty and a bad stop-gap solution that needs to not > propogate. > > Data tables are pretty new and need lots of enhancement, something along > the lines of what you expected (e.g. $param.path) is the intention. Any > other data table suggestions? I see that has now landed on the trunk, https://bitbucket.org/galaxy/galaxy-central/changeset/7be369e7cc6f Is that stable and ready for public use now? I'll need to look at making updates to the BLAST+ wrappers to take advantage of this (probably after clearing though my back log of other BLAST+ stuff like the extended tabular output). Peter ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
