Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster
On Wed, Mar 20, 2013 at 3:47 PM, Peter Cock wrote: > On Wed, Mar 20, 2013 at 3:43 PM, Raj Ayyampalayam wrote: >> Hi Guys, >> >> Thanks for the quick response. I installed the latest blast datatypes from >> the toolshed and that fixed the issue. > > Great - thanks for letting us know so promptly. > >> Peter, can you also fix the $outfile.extra_files_path to >> $outfile.files_path on line 5 in the makedb wrapper xml file. > > What do you mean 'fix' it? It should be using extra_files_path > shouldn't it? This is a composite datatype in Galaxy. Are you perhaps running jobs as real user? That might explain when this difference is important: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-April/009579.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-March/013889.html Thanks, Peter ___ 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/
Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster
On Wed, Mar 20, 2013 at 3:43 PM, Raj Ayyampalayam wrote: > Hi Guys, > > Thanks for the quick response. I installed the latest blast datatypes from > the toolshed and that fixed the issue. Great - thanks for letting us know so promptly. > Peter, can you also fix the $outfile.extra_files_path to > $outfile.files_path on line 5 in the makedb wrapper xml file. What do you mean 'fix' it? It should be using extra_files_path shouldn't it? This is a composite datatype in Galaxy. Peter ___ 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/
Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster
Hi Guys,
Thanks for the quick response. I installed the latest blast datatypes
from the toolshed and that fixed the issue.
Peter, can you also fix the $outfile.extra_files_path to
$outfile.files_path on line 5 in the makedb wrapper xml file.
Thanks,
-Raj
On Wednesday, March 20, 2013 10:42:43 AM, Peter Cock wrote:
On Wed, Mar 20, 2013 at 1:55 PM, Peter Cock wrote:
On Wed, Mar 20, 2013 at 1:52 PM, Nicola Soranzo wrote:
Il giorno mer, 20/03/2013 alle 12.41 +, Peter Cock ha scritto:
The patch just removes the MetadataElement call - is that wise?
Hi Peter,
my question instead is, what are they for? With 'name' they have no
meaning.
Looking at the code, I don't see a recent API change regarding
the name:
https://bitbucket.org/galaxy/galaxy-central/history-node/default/lib/galaxy/datatypes/metadata.py?at=default
Is there perhaps a universe_wsgi.ini setting which might be involved,
since I've not seen this error locally?
$ cd lib/galaxy/datatypes/
$ grep 'MetadataElement(' *.py|grep -v name
returns nothing, so the 'name' parameter is really mandatory.
Best,
Nicola
Good question - I'd have to ask Edward what he thought this did,
but you seem to be right that as the code stands this metadata
element is rather pointless.
(I'm still puzzled why we don't see the error here though).
I'll apply your patch and test it locally...
Peter
Nicola - It looks good here, uploaded to the ToolShed as v0.0.15
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
Raj - Could you apply the update from the ToolShed and
confirm if that fixes the problem for you?
Edward - have you received my direct email off list?
Thanks,
Peter
--
Bio-informatics consultant
QBCG (http://qbcg.uga.edu)
706-542-6092
706-583-0442
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Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster
On Wed, Mar 20, 2013 at 1:55 PM, Peter Cock wrote:
> On Wed, Mar 20, 2013 at 1:52 PM, Nicola Soranzo wrote:
>> Il giorno mer, 20/03/2013 alle 12.41 +, Peter Cock ha scritto:
>>>
>>> The patch just removes the MetadataElement call - is that wise?
>>
>> Hi Peter,
>> my question instead is, what are they for? With 'name' they have no
>> meaning.
>>
>>> Looking at the code, I don't see a recent API change regarding
>>> the name:
>>>
>>> https://bitbucket.org/galaxy/galaxy-central/history-node/default/lib/galaxy/datatypes/metadata.py?at=default
>>>
>>> Is there perhaps a universe_wsgi.ini setting which might be involved,
>>> since I've not seen this error locally?
>>
>> $ cd lib/galaxy/datatypes/
>> $ grep 'MetadataElement(' *.py|grep -v name
>>
>> returns nothing, so the 'name' parameter is really mandatory.
>>
>> Best,
>> Nicola
>>
>
> Good question - I'd have to ask Edward what he thought this did,
> but you seem to be right that as the code stands this metadata
> element is rather pointless.
>
> (I'm still puzzled why we don't see the error here though).
>
> I'll apply your patch and test it locally...
>
> Peter
Nicola - It looks good here, uploaded to the ToolShed as v0.0.15
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
Raj - Could you apply the update from the ToolShed and
confirm if that fixes the problem for you?
Edward - have you received my direct email off list?
Thanks,
Peter
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Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster
On Wed, Mar 20, 2013 at 1:52 PM, Nicola Soranzo wrote:
> Il giorno mer, 20/03/2013 alle 12.41 +, Peter Cock ha scritto:
>>
>> The patch just removes the MetadataElement call - is that wise?
>
> Hi Peter,
> my question instead is, what are they for? With 'name' they have no
> meaning.
>
>> Looking at the code, I don't see a recent API change regarding
>> the name:
>>
>> https://bitbucket.org/galaxy/galaxy-central/history-node/default/lib/galaxy/datatypes/metadata.py?at=default
>>
>> Is there perhaps a universe_wsgi.ini setting which might be involved,
>> since I've not seen this error locally?
>
> $ cd lib/galaxy/datatypes/
> $ grep 'MetadataElement(' *.py|grep -v name
>
> returns nothing, so the 'name' parameter is really mandatory.
>
> Best,
> Nicola
>
Good question - I'd have to ask Edward what he thought this did,
but you seem to be right that as the code stands this metadata
element is rather pointless.
(I'm still puzzled why we don't see the error here though).
I'll apply your patch and test it locally...
Peter
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Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster
Il giorno mer, 20/03/2013 alle 12.41 +, Peter Cock ha scritto:
> On Wed, Mar 20, 2013 at 10:08 AM, Nicola Soranzo wrote:
> > Il giorno mar, 19/03/2013 alle 15.20 -0400, Raj Ayyampalayam ha
> > scritto:
> >> One of the first few tools I tested was the ncbi makebkastdb tool. When
> >> I try to run it the history for that particular job is immediately shown
> >> as follows:
> >>
> >> 0: (unnamed dataset)
> >> Failed to retrieve dataset information.
> >> An error occurred with this dataset:/hasattr(): attribute name must be
> >> string/
> >
> > Hi Raj,
> > this error in the history should be fixed by this patch:
> >
> > https://bitbucket.org/nsoranzo/peterjc-galaxy-central-tools2/commits/35163cbc6c694f598ed1a1875353c58b275e2423
> >
> > I have sent a pull request to Peter (the maintainer), hopefully he will
> > release soon a new version of blast_datatypes with this fix.
> >
> > Best,
> > Nicola
>
> The patch just removes the MetadataElement call - is that wise?
Hi Peter,
my question instead is, what are they for? With 'name' they have no
meaning.
> Looking at the code, I don't see a recent API change regarding
> the name:
>
> https://bitbucket.org/galaxy/galaxy-central/history-node/default/lib/galaxy/datatypes/metadata.py?at=default
>
> Is there perhaps a universe_wsgi.ini setting which might be involved,
> since I've not seen this error locally?
$ cd lib/galaxy/datatypes/
$ grep 'MetadataElement(' *.py|grep -v name
returns nothing, so the 'name' parameter is really mandatory.
Best,
Nicola
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Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster
On Wed, Mar 20, 2013 at 10:08 AM, Nicola Soranzo wrote: > Il giorno mar, 19/03/2013 alle 15.20 -0400, Raj Ayyampalayam ha > scritto: >> One of the first few tools I tested was the ncbi makebkastdb tool. When >> I try to run it the history for that particular job is immediately shown >> as follows: >> >> 0: (unnamed dataset) >> Failed to retrieve dataset information. >> An error occurred with this dataset:/hasattr(): attribute name must be >> string/ > > Hi Raj, > this error in the history should be fixed by this patch: > > https://bitbucket.org/nsoranzo/peterjc-galaxy-central-tools2/commits/35163cbc6c694f598ed1a1875353c58b275e2423 > > I have sent a pull request to Peter (the maintainer), hopefully he will > release soon a new version of blast_datatypes with this fix. > > Best, > Nicola The patch just removes the MetadataElement call - is that wise? Looking at the code, I don't see a recent API change regarding the name: https://bitbucket.org/galaxy/galaxy-central/history-node/default/lib/galaxy/datatypes/metadata.py?at=default Is there perhaps a universe_wsgi.ini setting which might be involved, since I've not seen this error locally? Peter ___ 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/
Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster
Il giorno mar, 19/03/2013 alle 15.20 -0400, Raj Ayyampalayam ha scritto: > One of the first few tools I tested was the ncbi makebkastdb tool. When > I try to run it the history for that particular job is immediately shown > as follows: > > 0: (unnamed dataset) > Failed to retrieve dataset information. > An error occurred with this dataset:/hasattr(): attribute name must be > string/ Hi Raj, this error in the history should be fixed by this patch: https://bitbucket.org/nsoranzo/peterjc-galaxy-central-tools2/commits/35163cbc6c694f598ed1a1875353c58b275e2423 I have sent a pull request to Peter (the maintainer), hopefully he will release soon a new version of blast_datatypes with this fix. Best, Nicola ___ 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/
