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

[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 
> 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 
> 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 <
> 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.iso885915"
> >>> LC_NAME="en_US.iso885915"
> >>> LC_ADDRESS="en_US.iso885915"
> >>> LC_TELEPHONE="en_US.iso885915"
> >>> LC_MEASUREMENT="en_US.iso885915"
> >>> LC_IDENTIFICATION="en_US.iso885915"
> >>> LC_ALL=
> >>>
> >>> I will talk to our sysadmin and see if I can change the locale to
> en_US.UTF-8.
> >>>
> >>> Thank you very much.
> >>> -Raj
> >>>
> >>>
>  On May 29, 2017, at 10:58 AM, Peter Cock 
> wrote:
> 
>  Curious, my new 

[galaxy-dev] jupyter notebook / nginx / ssl

[cristel thomas]

Hi Galaxy developers,
we are trying to get notebooks to run on our production server, with half
success: we can get jupyter to load, and it does access the history, but
notebooks uploaded to history do not load, and any modification to the
notebook provided can be saved but do not show up when the notebook is
re-opened.

we're running NGINX and have SSL certs in place.

Any idea how to fix this?
Thanks
Cris
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