date:20160209

Re: [galaxy-dev] Galaxy broken after update to 16.01

2016-02-09 Thread Peter van Heusden

Mattias, what does your supervisord config look like? Specifically, does it
contain an environment variable to direct the Galaxy handler to the correct
virtualenv?

Peter

On 9 February 2016 at 16:03, Matthias De Smet 
wrote:

> Hi all,
>
>
> We were tracking the galaxy master branch on our local server and are
> looking to migrate to v16.01.
> The galaxy processes are managed bij supervisor as shown here (
> https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling).
> After updating all dependencies in our venv we tried to restart the server
> but got the following issue:
>
> Loading paste environment:
> config:/home/galaxy/galaxy-dist/config/galaxy.ini
> Traceback (most recent call last):
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
> line 247, in loadapp
> return loadobj(APP, uri, name=name, **kw)
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
> line 271, in loadobj
> global_conf=global_conf)
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
> line 296, in loadcontext
> global_conf=global_conf)
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
> line 320, in _loadconfig
> return loader.get_context(object_type, name, global_conf)
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
> line 458, in get_context
> section)
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
> line 517, in _context_from_explicit
> value = import_string(found_expr)
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
> line 22, in import_string
> return pkg_resources.EntryPoint.parse("x=" + s).load(False)
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pkg_resources/__init__.py",
> line 2380, in load
> return self.resolve()
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pkg_resources/__init__.py",
> line 2386, in resolve
> module = __import__(self.module_name, fromlist=['__name__'], level=0)
>   File "lib/galaxy/web/buildapp.py", line 5, in 
> from galaxy.webapps.galaxy.buildapp import app_factory
>   File "lib/galaxy/webapps/galaxy/buildapp.py", line 15, in 
> import galaxy.app
>   File "lib/galaxy/app.py", line 9, in 
> import galaxy.queues
>   File "lib/galaxy/queues.py", line 9, in 
> from kombu import Exchange, Queue, Connection
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/__init__.py",
> line 67, in __getattr__
> module = __import__(object_origins[name], None, None, [name])
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/entity.py",
> line 10, in 
> from .abstract import MaybeChannelBound, Object
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/abstract.py",
> line 12, in 
> from .connection import maybe_channel
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/connection.py",
> line 19, in 
> from kombu import exceptions
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/exceptions.py",
> line 12, in 
> from amqp import ChannelError, ConnectionError, ResourceError
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/__init__.py",
> line 34, in 
> from .connection import Connection  # noqa
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/connection.py",
> line 40, in 
> from .transport import create_transport
>   File
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/transport.py",
> line 21, in 
> import ssl
>   File "/Shared/Software/Cellar/python/2.7.11/lib/python2.7/ssl.py", line
> 97, in 
> import _ssl # if we can't import it, let the error
> propagate
> ImportError:
> /home/galaxy/galaxy-dist/.venv/lib/python2.7/lib-dynload/_ssl.so: undefined
> symbol: SSL_CTX_set_alpn_protos
>
> So far we have tried:
> - rebuilding the venv
> - reinstalling python
>
> Funny thing is, when we start the configuration with the “run.sh” script
> instead of through supervisor everything seems to work just fine.
>
> We’re at a loss, please help!
> Thanks!
> Matthias
>
>
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Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

2016-02-09 Thread Floreline TOUCHARD

Hi,

sorry for the late response ! I tested the modifications proposed in the "Allow
to select multiple database" pull request and it works !!!

Thanks a lot !
Floreline.

P.S : I'm not familiar with all github functionnalities yet, but I will
work on it ;)

2016-01-20 16:07 GMT+01:00 Peter Cock :

> On Wed, Jan 20, 2016 at 2:43 PM, Gildas Le Corguillé
>  wrote:
> > Hi,
> >
> > A long time ago, in a far far svn repo, we did this "multiple=true" on
> Peter
> > wrappers.
> >
> > I will try to propose it quickly :)
> >
> > Gildas
>
> Great - a pull request against https://github.com/peterjc/galaxy_blast
> but if your SVN repo is still online, or you can make a patch/diff file,
> we could look at that and try to port the changes. My guess is a lot
> of macro work was done in the meantime so it may not be trivial to
> repeat your changes :(
>
> Thanks,
>
> Peter
>
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[galaxy-dev] Galaxy broken after update to 16.01

2016-02-09 Thread Matthias De Smet

Hi all,


We were tracking the galaxy master branch on our local server and are looking 
to migrate to v16.01.
The galaxy processes are managed bij supervisor as shown here ( 
https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling).
After updating all dependencies in our venv we tried to restart the server but 
got the following issue:

Loading paste environment: config:/home/galaxy/galaxy-dist/config/galaxy.ini
Traceback (most recent call last):
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
 line 247, in loadapp
return loadobj(APP, uri, name=name, **kw)
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
 line 271, in loadobj
global_conf=global_conf)
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
 line 296, in loadcontext
global_conf=global_conf)
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
 line 320, in _loadconfig
return loader.get_context(object_type, name, global_conf)
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
 line 458, in get_context
section)
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
 line 517, in _context_from_explicit
value = import_string(found_expr)
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/paste/deploy/loadwsgi.py",
 line 22, in import_string
return pkg_resources.EntryPoint.parse("x=" + s).load(False)
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pkg_resources/__init__.py",
 line 2380, in load
return self.resolve()
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pkg_resources/__init__.py",
 line 2386, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "lib/galaxy/web/buildapp.py", line 5, in 
from galaxy.webapps.galaxy.buildapp import app_factory
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 15, in 
import galaxy.app
  File "lib/galaxy/app.py", line 9, in 
import galaxy.queues
  File "lib/galaxy/queues.py", line 9, in 
from kombu import Exchange, Queue, Connection
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/__init__.py", 
line 67, in __getattr__
module = __import__(object_origins[name], None, None, [name])
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/entity.py", 
line 10, in 
from .abstract import MaybeChannelBound, Object
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/abstract.py", 
line 12, in 
from .connection import maybe_channel
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/connection.py",
 line 19, in 
from kombu import exceptions
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/kombu/exceptions.py",
 line 12, in 
from amqp import ChannelError, ConnectionError, ResourceError
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/__init__.py", 
line 34, in 
from .connection import Connection  # noqa
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/connection.py",
 line 40, in 
from .transport import create_transport
  File 
"/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/amqp/transport.py", 
line 21, in 
import ssl
  File "/Shared/Software/Cellar/python/2.7.11/lib/python2.7/ssl.py", line 97, 
in 
import _ssl # if we can't import it, let the error propagate
ImportError: /home/galaxy/galaxy-dist/.venv/lib/python2.7/lib-dynload/_ssl.so: 
undefined symbol: SSL_CTX_set_alpn_protos

So far we have tried:
- rebuilding the venv
- reinstalling python

Funny thing is, when we start the configuration with the “run.sh” script 
instead of through supervisor everything seems to work just fine.

We’re at a loss, please help!
Thanks!
Matthias

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[galaxy-dev] NGS.plot script freeze

2016-02-09 Thread Philipp Rathert

Dear All,

we are trying to use NGS-plot on our local docker-galaxy-stable instance.

The script freezes whenever we click on the tool.

Does anybody have an idea what is wrong and how to fix this?
There is no error message or anything.
Thank you very much.

Kind regards,

Philipp

 

 

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Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

2016-02-09 Thread Peter Cock

Good to know :)

https://github.com/peterjc/galaxy_blast/pull/77

The pull request looks good - sadly distracted by TravisCI
failures from Galaxy/planemo/dependency changes.

Thanks,

Peter

On Tue, Feb 9, 2016 at 3:28 PM, Floreline TOUCHARD
 wrote:
> Hi,
>
> sorry for the late response ! I tested the modifications proposed in the
> "Allow to select multiple database" pull request and it works !!!
>
> Thanks a lot !
> Floreline.
>
> P.S : I'm not familiar with all github functionnalities yet, but I will work
> on it ;)
>
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Re: [galaxy-dev] A Report Calc tool which provides a scripting language and interpreter for text mining and quality control

2016-02-09 Thread Dooley, Damion

Hi folks,
I'm back with one more feeler to gauge interest in the approach we are
trying out for a Galaxy quality control tool to interject into existing
bioinformatics pipelines.  With some nudging (thanks Bob) I've implemented
basic infix math expressions.  As well we're trying out the inclusion of
ontology metadata within report data to encourage data
import/export/comparison.  The goal is to make it easy to see and change
quality control metrics (without having to recompile code or modify Galaxy
workflow mechanics.)

The QC scripting language/interpreter as a Galaxy tool lets us read in
text file(s) - some assembly contig data say - and then run a program (a
set of rules) like:

   store( 200 report/contigs/contig_count_QC_threshold )
   store( 20 report/contigs/contig_N50_QC_threshold )
   store( 2000 report/contigs/contig_N99_QC_threshold )

   if( ( genome_size_ratio > genome_size_ratio_QC_threshold ) fail(qc
"Failed genome size ratio threshold") )
   store( statisticN( contig_lengths 50 ) report/contigs/contig_N50 )
   store( statisticN( contig_lengths 99 ) report/contigs/contig_N99 )
   if( contig_N50 < contig_N50_QC_threshold fail(qc "Failed minimum N50
contig length threshold")  )
   if( contig_N99 < contig_N99_QC_threshold fail(qc "Failed minimum N99
contig length threshold")  )
   if( report/contigs/contigs_count > contig_count_QC_threshold fail(job
"Failed minimum contig count threshold" ) )
 

Which is like a generic, basic function(parameter1 parameter2...) type of
language.

On a good run this yields a JSON report like:

{
   "title": "RCQC Quality Control Report",
   "tool_version": "0.0.7",
   "job": {
  "status": "ok"
   },
   "quality_control": {
  "status": "ok"
   },
   "date": "2016-02-09 09:21",
   "contigs": {
  "contig_lengths": [ 128, 172, 221, 224, 238, 230, 240, 246, 407, ...
, 242, 2284, 1506],
  "genome_size_ratio_QC_threshold": 0.10001,
  "contig_N99_QC_threshold": 2000,
  "assembly_genome_size": 4615592,
  "genome_size_ratio": 0.04970310891496809,
  "contig_N50": 427122,
  "contig_N99": 8542,
  "contig_count_QC_threshold": 200,
  "contig_count": 44,
  "reference_genome_identifier": "serovar Typhimurium LT2",
  "reference_genome_size": 4857000,
  "contig_N50_QC_threshold": 20
   },
   "@context": {
  "contigs": "http://purl.obolibrary.org/obo/SO_0001462;,
  "genome_size_ratio_QC_threshold":
"http://purl.obolibrary.org/obo/GenEpiO_0001564;,
  "contig_N99_QC_threshold":
"http://purl.obolibrary.org/obo/GenEpiO_0001566;,
  "assembly_genome_size":
"http://purl.obolibrary.org/obo/GenEpiO_0001561;,
  "genome_size_ratio":
"http://purl.obolibrary.org/obo/GenEpiO_0001563;,
  "contig_N50": "http://purl.obolibrary.org/obo/OBI_0001941;,
  "contig_N99": "http://purl.obolibrary.org/obo/GenEpiO_0001570;,
  "contig_count_QC_threshold":
"http://purl.obolibrary.org/obo/GenEpiO_0001571;,
  "contig_count": "http://purl.obolibrary.org/obo/GenEpiO_093;,
  "reference_genome_identifier":
"http://purl.obolibrary.org/obo/GenEpiO_0001562;,
  "date": "http://purl.obolibrary.org/obo/IAO_416;,
  "reference_genome_size":
"http://purl.obolibrary.org/obo/GenEpiO_0001560;,
  "contig_N50_QC_threshold":
"http://purl.obolibrary.org/obo/GenEpiO_0001565;
   }
}


So we'd appreciate any advice on roadblocks or desired features you
perceive on this...

- Damion
>

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Re: [galaxy-dev] Galaxy broken after update to 16.01

Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[galaxy-dev] Galaxy broken after update to 16.01

[galaxy-dev] NGS.plot script freeze

Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

Re: [galaxy-dev] A Report Calc tool which provides a scripting language and interpreter for text mining and quality control

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