[galaxy-dev] Large Number of jobs Failing following error

2017-05-31 Thread Evan 
My galaxy instance has suddenly begun having jobs failing. The error 
below is what is produced by the log.


galaxy.objectstore CRITICAL 2017-05-31 01:44:49,932 None delete error 
[Errno 39] Directory not empty:

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Re: [galaxy-dev] Issue with GATK2 on Galaxy Repository.

2017-05-31 Thread Nicola Soranzo 

Hi,
which version of GATK are you using? From your email it seems you may be 
using GATK3, which is not supported by the Galaxy GATK2 wrappers.


Cheers,
Nicola

On 31/05/17 04:36, OLABODE OLUWASEUN AJAYI wrote:

Hi Dev,

I am running a local instance Galaxy for developing a variant calling 
pipeline. I ran into this issue after configuring and installing GATK2 
on my local when running the GATK *Realigner Target Creator on the BAM 
file generated by Mark duplicates.*
*Can some suggest how to resolve this issue or please point to how to 
debug this issue from the GATK2 wrapper? BTW, I follow the instruction 
by ensuring that my GATK3 environment was set as stated in the 
Galaxy GATk2 readme.txt.*

*
*
Below here was the issue I encountered;

# ERROR 
--
# ERROR A USER ERROR has occurred (version 2.0-7-g7323e98):
# ERROR The invalid arguments or inputs must be corrected before the GATK 
can proceed
# ERROR Please do not post this error to the GATK forum
# ERROR
# ERROR See the documentation (rerun with -h) for this tool to view 
allowable command-line arguments.
# ERROR Visit our website and forum for extensive documentation and answers 
to
# ERROR commonly asked questionshttp://www.broadinstitute.org/gatk
# ERROR
# ERROR MESSAGE: Argument with name 'num_cpu_threads_per_data_thread' isn't 
defined.
# ERROR 
--


On Mon, May 29, 2017 at 6:44 PM, Peter Cock > wrote:


Thanks, pull request submitted:

https://github.com/galaxyproject/galaxy/pull/4121


Peter


On Mon, May 29, 2017 at 5:23 PM, Saravanaraj Ayyampalayam
mailto:ra...@uga.edu>> wrote:
> Peter,
>
> Here is the git diff output that shows the changes I made:
>
> diff --git a/lib/galaxy/jobs/runners/__init__.py
b/lib/galaxy/jobs/runners/__init__.py
> index ebf4859..6ee51c8 100644
> --- a/lib/galaxy/jobs/runners/__init__.py
> +++ b/lib/galaxy/jobs/runners/__init__.py
> @@ -419,7 +419,7 @@ class JobState( object ):
>  job_name += '_%s' % self.job_wrapper.tool.old_id
>  if self.job_wrapper.user:
>  job_name += '_%s' % self.job_wrapper.user
> -self.job_name = ''.join( map( lambda x: x if x in (
string.letters + string.digits + '_' ) else '_', job_name ) )
> +self.job_name = ''.join( map( lambda x: x if x in (
string.ascii_letters + string.digits + '_' ) else '_', job_name ) )
>
>  @staticmethod
>  def default_job_file( files_dir, id_tag ):
> diff --git a/lib/galaxy/jobs/runners/drmaa.py
b/lib/galaxy/jobs/runners/drmaa.py
> index 7c08984..5c5dc62 100644
> --- a/lib/galaxy/jobs/runners/drmaa.py
> +++ b/lib/galaxy/jobs/runners/drmaa.py
> @@ -394,7 +394,7 @@ class DRMAAJobRunner( AsynchronousJobRunner ):
>  job_name += '_%s' % job_wrapper.tool.old_id
>  if external_runjob_script is None:
>  job_name += '_%s' % job_wrapper.user
> -job_name = ''.join( x if x in ( string.letters +
string.digits + '_' ) else '_' for x in job_name )
> +job_name = ''.join( x if x in ( string.ascii_letters +
string.digits + '_' ) else '_' for x in job_name )
>  if self.restrict_job_name_length:
>  job_name = job_name[:self.restrict_job_name_length]
>  return job_name
>
> -Raj
>
>> On May 29, 2017, at 11:33 AM, Peter Cock
mailto:p.j.a.c...@googlemail.com>> wrote:
>>
>> Thanks Saravanaraj,
>>
>> You should not need to change the locale, after all many Galaxy
servers and
>> their users will be labelling their files in non-English with
>> "special" characters -
>> but perhaps en_US.UTF-8 would be safer in your case as it seems
that few
>> people use Galaxy with en_US.iso885915 otherwise this would
have been
>> reported before?
>>
>> Can you tell us both places you changed string.letters to
string.ascii_letters
>> please? I could then submit this as a pull request to get
Galaxy itself updated
>> for future release.
>>
>> Peter
>>
>> On Mon, May 29, 2017 at 4:28 PM, Saravanaraj Ayyampalayam
mailto:ra...@uga.edu>> wrote:
>>> Peter,
>>>
>>> You are correct. Changing string.letters to
string.ascii_letters fixed it. I had to change it in two places.
>>>
>>> My locale is :
>>>
>>> LANG=en_US.iso885915
>>> LC_CTYPE="en_US.iso885915"
>>> LC_NUMERIC="en_US.iso885915"
>>> LC_TIME="en_US.iso885915"
>>> LC_COLLATE="en_US.iso885915"
>>> LC_MONETARY="en_US.iso885915"
>>> LC_MESSAGES="en_US.iso885915"
>>> LC_PAPER="en_US

Re: [galaxy-dev] Issue with GATK2 on Galaxy Repository.

2017-05-31 Thread Björn Grüning 
Hi,

can you please check the exact version of the GATK jar file?
Currently, only 2.8 is supported. We stopped maintaining it, due to
licensing issues - which might be resolved in a 4.0 version.

If you have GATK2.8, it should work hopefully.
Cheers,
Bjoern

Am 31.05.2017 um 05:36 schrieb OLABODE OLUWASEUN AJAYI:
> Hi Dev,
> 
> I am running a local instance Galaxy for developing a variant calling
> pipeline. I ran into this issue after configuring and installing GATK2
> on my local when running the GATK *Realigner Target Creator on the BAM
> file generated by Mark duplicates.*
> *Can some suggest how to resolve this issue or please point to how to
> debug this issue from the GATK2 wrapper? BTW, I follow the instruction
> by ensuring that my GATK3 environment was set as stated in the
> Galaxy GATk2 readme.txt.*
> *
> *
> Below here was the issue I encountered;
> 
> # ERROR 
> --
> # ERROR A USER ERROR has occurred (version 2.0-7-g7323e98): 
> # ERROR The invalid arguments or inputs must be corrected before the GATK 
> can proceed
> # ERROR Please do not post this error to the GATK forum
> # ERROR
> # ERROR See the documentation (rerun with -h) for this tool to view 
> allowable command-line arguments.
> # ERROR Visit our website and forum for extensive documentation and 
> answers to 
> # ERROR commonly asked questions http://www.broadinstitute.org/gatk
> # ERROR
> # ERROR MESSAGE: Argument with name 'num_cpu_threads_per_data_thread' 
> isn't defined.
> # ERROR 
> --
> 
> 
> 
> On Mon, May 29, 2017 at 6:44 PM, Peter Cock  > wrote:
> 
> Thanks, pull request submitted:
> 
> https://github.com/galaxyproject/galaxy/pull/4121
> 
> 
> Peter
> 
> 
> On Mon, May 29, 2017 at 5:23 PM, Saravanaraj Ayyampalayam
> mailto:ra...@uga.edu>> wrote:
> > Peter,
> >
> > Here is the git diff output that shows the changes I made:
> >
> > diff --git a/lib/galaxy/jobs/runners/__init__.py
> b/lib/galaxy/jobs/runners/__init__.py
> > index ebf4859..6ee51c8 100644
> > --- a/lib/galaxy/jobs/runners/__init__.py
> > +++ b/lib/galaxy/jobs/runners/__init__.py
> > @@ -419,7 +419,7 @@ class JobState( object ):
> >  job_name += '_%s' % self.job_wrapper.tool.old_id
> >  if self.job_wrapper.user:
> >  job_name += '_%s' % self.job_wrapper.user
> > -self.job_name = ''.join( map( lambda x: x if x in (
> string.letters + string.digits + '_' ) else '_', job_name ) )
> > +self.job_name = ''.join( map( lambda x: x if x in (
> string.ascii_letters + string.digits + '_' ) else '_', job_name ) )
> >
> >  @staticmethod
> >  def default_job_file( files_dir, id_tag ):
> > diff --git a/lib/galaxy/jobs/runners/drmaa.py
> b/lib/galaxy/jobs/runners/drmaa.py
> > index 7c08984..5c5dc62 100644
> > --- a/lib/galaxy/jobs/runners/drmaa.py
> > +++ b/lib/galaxy/jobs/runners/drmaa.py
> > @@ -394,7 +394,7 @@ class DRMAAJobRunner( AsynchronousJobRunner ):
> >  job_name += '_%s' % job_wrapper.tool.old_id
> >  if external_runjob_script is None:
> >  job_name += '_%s' % job_wrapper.user
> > -job_name = ''.join( x if x in ( string.letters +
> string.digits + '_' ) else '_' for x in job_name )
> > +job_name = ''.join( x if x in ( string.ascii_letters +
> string.digits + '_' ) else '_' for x in job_name )
> >  if self.restrict_job_name_length:
> >  job_name = job_name[:self.restrict_job_name_length]
> >  return job_name
> >
> > -Raj
> >
> >> On May 29, 2017, at 11:33 AM, Peter Cock
> mailto:p.j.a.c...@googlemail.com>> wrote:
> >>
> >> Thanks Saravanaraj,
> >>
> >> You should not need to change the locale, after all many Galaxy
> servers and
> >> their users will be labelling their files in non-English with
> >> "special" characters -
> >> but perhaps en_US.UTF-8 would be safer in your case as it seems
> that few
> >> people use Galaxy with en_US.iso885915 otherwise this would have been
> >> reported before?
> >>
> >> Can you tell us both places you changed string.letters to
> string.ascii_letters
> >> please? I could then submit this as a pull request to get Galaxy
> itself updated
> >> for future release.
> >>
> >> Peter
> >>
> >> On Mon, May 29, 2017 at 4:28 PM, Saravanaraj Ayyampalayam
> mailto:ra...@uga.edu>> wrote:
> >>> Peter,
> >>>
> >>> You are correct. Changing string.letters to string.ascii_letters
> fixed it. I had to change it in tw