[galaxy-dev] tool error on TopHat test during metadata manipulations

2016-05-19 Thread Nick 

 Hi,

All our workflows with TopHat finished with status: "tool error" &  "Unable to 
finish job".

We tested them on Galaxy 15.11 and 16.01 (latest works with python 2.6).
Our batch system is SGE. TopHat is v2.0.14 revision 4eb3c3beb9c7

TopHat calculations on the cluster are fine and finished without any errors but
during the running set_metadata_XYZ.py script (which is also called from 
submited script) job fails and reports above mentioned error status.

Logs are:

galaxy.jobs.runners.drmaa DEBUG 2016-05-19 13:53:18,054 (481/1533559) state 
change: job finished normally
galaxy.jobs.output_checker INFO 2016-05-19 13:53:19,389 Job 481: Log: tool 
progress
galaxy.jobs.output_checker INFO 2016-05-19 13:53:19,389 Job 481: Log: tool 
progress
galaxy.datatypes.metadata DEBUG 2016-05-19 13:53:21,759 setting metadata 
externally failed for HistoryDatasetAssociation 1965: [Errno2] No such file or 
directory
galaxy.jobs.runners ERROR 2016-05-19 13:53:24,367 (481/1533559) Job wrapper 
finish method failed
Traceback (most recent call last):
  File "/ptmp/galaxy1/galaxy/lib/galaxy/jobs/runners/__init__.py", line 590, 
in finish_job
job_state.job_wrapper.finish( stdout, stderr, exit_code )
  File "/ptmp/galaxy1/galaxy/lib/galaxy/jobs/__init__.py", line 1221, in finish
dataset.datatype.set_meta( dataset, overwrite=False )
  File "/ptmp/galaxy1/galaxy/lib/galaxy/datatypes/binary.py", line 314, in 
set_meta
exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' 
) )
  File "/usr/lib64/python2.6/subprocess.py", line 470, in call
return Popen(*popenargs, **kwargs).wait()
  File "/usr/lib64/python2.6/subprocess.py", line 623, in __init__
errread, errwrite)
  File "/usr/lib64/python2.6/subprocess.py", line 1141, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory


As I understand Galaxy operates with pickle data ( which were saved before 
submiting job in file with id 1965: 
metadata_in_HistoryDatasetAssociation_1965_sPyPfZ )
during running function set_metadata() and does not find some files and exit
with error message [false, "[Errno 2] No such file or directory"] writen to the
file metadata_results_HistoryDatasetAssociation_1965_k5I9PM and kill job.

What causes this error and how to fix this behavior? 

Thanx in advance,

Nick

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Re: [galaxy-dev] Update on Qiime in Galaxy?

2016-05-19 Thread Oksana Korol 
Hey Bjoern,

I've just started learning qiime, so probably not the best person to write
tests / do clean up at the moment. Galaxy tool would have made my life much
easier, by way of figuring out this beast :).

Oksana

Hi Oksana,

>
> afaik a few more tests would be nice:
>
> https://github.com/galaxyproject/tools-iuc/pull/431
>
> But it looks more a less good.
> If you want to do the final cleanup, this PR is probably ready to merge.
>
>


> Thanks!
> Bjoern
>
> P.S. CC Bérénice as she was working on it as well
>
>
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Re: [galaxy-dev] Update on Qiime in Galaxy?

2016-05-19 Thread Björn Grüning 
Hi Oksana,

afaik a few more tests would be nice:

https://github.com/galaxyproject/tools-iuc/pull/431

But it looks more a less good.
If you want to do the final cleanup, this PR is probably ready to merge.

Thanks!
Bjoern

P.S. CC Bérénice as she was working on it as well

Am 19.05.2016 um 17:02 schrieb Oksana Korol:
> Hi galaxy tool development team and community,
> 
> In the recent metagenomics hackathon it looks like there has been lots
> of good work done on qiime. What is the status on the tools in qiime
> branch of iuc repo:
> https://github.com/galaxyproject/tools-iuc/tree/qiime/tools/qiime? I can
> see that the package the tools depend on (
> package_python_2_7_qiime_1_9_1) is already available on main toolshed.
> What is the plan for making the wrappers, that depend on this package,
> available on main toolshed as well?
> 
> Thanks a bunch!
> -- 
> ::
> Oksana Korol
> 
> 
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[galaxy-dev] Update on Qiime in Galaxy?

2016-05-19 Thread Oksana Korol 
Hi galaxy tool development team and community,

In the recent metagenomics hackathon it looks like there has been lots of
good work done on qiime. What is the status on the tools in qiime branch of
iuc repo: https://github.com/galaxyproject/tools-iuc/tree/qiime/tools/qiime?
I can see that the package the tools depend on (
package_python_2_7_qiime_1_9_1) is already available on main toolshed. What
is the plan for making the wrappers, that depend on this package, available
on main toolshed as well?

Thanks a bunch!
-- 
::
Oksana Korol
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Re: [galaxy-dev] not sure what I can do about this...

2016-05-19 Thread Fernandez Edgar 
Hey Guys,

I’ve fixed my first problem with the environment.
But I’m still getting the second one.

Also, did any of you guys try to deploy galaxy with Microsoft Azure?
I’m actually looking into it and I was wondering if you had any input…

Let me know if you have any info on my libchtslib.so: input error or Microsoft 
Azure.

Cheers!

Edgar Fernandez
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
Université de Montréal

PAVILLON ROGER-GAUDRY, bureau X-210
•  Bur. : 1-514-343-6111 poste 16568


From: Fernandez Edgar
Sent: May-18-16 2:00 PM
To: galaxy-...@bx.psu.edu
Subject: RE: [galaxy-dev] not sure what I can do about this...

Hey Guys,

Hope everyone is doing well.

So I’m back at galaxy v16.01

I’m having a small problem.
My python system version is 2.6.6

So I installed python version 2.7.8 from  Software Collection Library release 
1.2 packages for Oracle Linux 6 
(x86_64)
This means I need to source an environment before being about to use it.
So what I’ve created a file config/local_env.sh with:
# Source python27
export PATH=/opt/rh/python27/root/usr/bin${PATH:+:${PATH}}
export 
LD_LIBRARY_PATH=/opt/rh/python27/root/usr/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
export MANPATH=/opt/rh/python27/root/usr/share/man:${MANPATH}
# For systemtap
export 
XDG_DATA_DIRS=/opt/rh/python27/root/usr/share${XDG_DATA_DIRS:+:${XDG_DATA_DIRS}}
# For pkg-config
export 
PKG_CONFIG_PATH=/opt/rh/python27/root/usr/lib64/pkgconfig${PKG_CONFIG_PATH:+:${PKG_CONFIG_PATH}}

These export comes directly with the installation of python 2.7.8 in the file 
/opt/rh/python27/enable.
But when I started my galaxy it didn’t stick.

I had to insert those exports into the file run.sh right before the following 
line:
./scripts/common_startup.sh $common_startup_args || exit 1

Any suggestions to make it work?

Also, I get this error :
Traceback (most recent call last):
  File "./scripts/paster.py", line 27, in 
serve.run()
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 
1061, in run
invoke(command, command_name, options, args[1:])
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 
1067, in invoke
exit_code = runner.run(args)
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 
223, in run
result = self.command()
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/serve.py", line 
639, in command
app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", 
line 295, in loadapp
return loadobj(APP, uri, name=name, **kw)
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", 
line 319, in loadobj
global_conf=global_conf)
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", 
line 344, in loadcontext
global_conf=global_conf)
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", 
line 368, in _loadconfig
return loader.get_context(object_type, name, global_conf)
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", 
line 506, in get_context
section)
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", 
line 565, in _context_from_explicit
value = import_string(found_expr)
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/util/pastescript/loadwsgi.py", 
line 125, in import_string
return pkg_resources.EntryPoint.parse("x=" + s).load(False)
  File 
"/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pkg_resources.py",
 line 2260, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/web/buildapp.py", line 5, in 

from galaxy.webapps.galaxy.buildapp import app_factory
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/webapps/galaxy/buildapp.py", line 
15, in 
import galaxy.app
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/app.py", line 6, in 
from galaxy import config, jobs
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/jobs/__init__.py", line 19, in 

from galaxy import model, util
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/model/__init__.py", line 26, in 

import galaxy.datatypes.registry
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/registry.py", line 9, 
in 
import tabular
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/tabular.py", line 18, 
in 
from galaxy.datatypes.sniff import get_headers
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/sniff.py", line 19, in 

from galaxy.datatypes.binary import Binary
  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/binary.py", line 13, in 

import pysam
  File 
"/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/__init__.py",
 line 1, in 
from pysam.libchtslib import