subject:"Re\: \[galaxy\-dev\] not sure what I can do about this..."

Re: [galaxy-dev] not sure what I can do about this...

2016-06-08 Thread Fernandez Edgar

Hey guys,

I successfully fixed my problem.
Here's the solution if you would like to know:

1. download zlib-1.2.8.tar.gz
2. ./configure --prefix=/usr/local/zlib-1.2.8
3. make
4. make install
5. add the following in the file config/local_env.sh
export 
LD_LIBRARY_PATH=/usr/local/zlib-1.2.8${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}



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
I  Bur. : 1-514-343-6111 poste 16568


-Original Message-
From: Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Sent: May-26-16 3:32 AM
To: Fernandez Edgar <edgar.fernan...@umontreal.ca>; Nate Coraor 
<n...@bx.psu.edu>
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] not sure what I can do about this...

Sorry Edgar,

It looks like something else is causing this error (and my guess about 
different versions of Linux on Galaxy and the cluster was
wrong):

ImportError: 
/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so:
undefined symbol: gzopen64

It may be important how the pysam wheel was compiled, perhaps Nate may be able 
to comment (CC'd).

Peter

On Wed, May 25, 2016 at 12:40 PM, Fernandez Edgar 
<edgar.fernan...@umontreal.ca> wrote:
> Hello Peter,
>
> For now, my new installation of galaxy v16.01 is on one test desktop running 
> Oracle Linux 6.
> Before changing my production installation, I'm doing my due diligent.
>
> Let me know what you think...
>
> Edgar Fernandez
___
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Re: [galaxy-dev] not sure what I can do about this...

2016-05-25 Thread Fernandez Edgar

Hello Peter,

For now, my new installation of galaxy v16.01 is on one test desktop running 
Oracle Linux 6.
Before changing my production installation, I'm doing my due diligent.

Let me know what you think...

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
I  Bur. : 1-514-343-6111 poste 16568



-Original Message-
From: Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Sent: May-24-16 5:40 PM
To: Fernandez Edgar <edgar.fernan...@umontreal.ca>
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] not sure what I can do about this...

Hi Edgar,

Are your Galaxy server AND your cluster are all running Oracle Linux 6?

If yes, my guess about the cluster using an older version of Linux compared to 
the Galaxy server is unrelated.

Peter

On Tue, May 24, 2016 at 7:47 PM, Fernandez Edgar <edgar.fernan...@umontreal.ca> 
wrote:
> Hello Peter,
>
> What would your suggestion be?
> Wait until a new version of galaxy is compatible with my Oracle Linux 6 ?
>
> Best regards,
>
> 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
> I  Bur. : 1-514-343-6111 poste 16568
>
___
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:
  https://lists.galaxyproject.org/

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Re: [galaxy-dev] not sure what I can do about this...

2016-05-24 Thread Peter Cock

Hi Edgar,

Are your Galaxy server AND your cluster are all running
Oracle Linux 6?

If yes, my guess about the cluster using an older version
of Linux compared to the Galaxy server is unrelated.

Peter

On Tue, May 24, 2016 at 7:47 PM, Fernandez Edgar
 wrote:
> Hello Peter,
>
> What would your suggestion be?
> Wait until a new version of galaxy is compatible with my Oracle Linux 6 ?
>
> Best regards,
>
> 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
> I  Bur. : 1-514-343-6111 poste 16568
>
___
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] not sure what I can do about this...

2016-05-24 Thread Fernandez Edgar

Hello Peter,

What would your suggestion be?
Wait until a new version of galaxy is compatible with my Oracle Linux 6 ?

Best regards,

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
I  Bur. : 1-514-343-6111 poste 16568

-Original Message-
From: Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Sent: May-24-16 2:29 PM
To: Fernandez Edgar <edgar.fernan...@umontreal.ca>
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] not sure what I can do about this...

Hi Fernandez,

We saw something very like that with mixed versions of Linux, specifically our 
Galaxy head node where pysam was installed had CentOS 7, but the node where 
Galaxy was trying to run the metadata detection was CentOS 6. Unfortunately I 
do not have a record of the exact traceback - but from memory it was the same 
problem in pysam with gzopen64.

(We'd already fought problems with Python mis-matches, GLIBC versions, etc and 
had carefully built Python on CentOS 6 in order to run on both CentOS 6 and 7.)

At this point we gave up, and will run the Galaxy node on the same version of 
Linux as the Cluster - and plan to upgrade the cluster before the Galaxy node. 
That way all the stuff Galaxy installs (e.g. via the ToolShed) ought to work on 
the cluster.

Peter

On Tue, May 24, 2016 at 7:08 PM, Fernandez Edgar <edgar.fernan...@umontreal.ca> 
wrote:
>
> Hello guys,
>
>
>
> I’m still stuck on this error.
>
> I’ve installed a brand new galaxy v16.01
>
> And when I start it, I get the big error mentioned below.
>
> Here’s the last message in the error:
>
> ImportError: 
> /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/lib
> chtslib.so: undefined symbol: gzopen64
>
>
>
> Thanks for your assistance!
>
>
>
> Cheers,
>
>
>
> Edgar Fernandez
___
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] not sure what I can do about this...

2016-05-24 Thread Fernandez Edgar

Hello guys,

I’m still stuck on this error.
I’ve installed a brand new galaxy v16.01
And when I start it, I get the big error mentioned below.
Here’s the last message in the error:
ImportError: 
/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so:
 undefined symbol: gzopen64

Thanks for your assistance!

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-19-16 8:48 AM
To: 'galaxy-...@bx.psu.edu' <galaxy-...@bx.psu.edu>
Subject: RE: [galaxy-dev] not sure what I can do about this...

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<mailto: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)<https://ulns.dit.umontreal.ca/rhn/channels/ChannelDetail.do?cid=149>
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.a

Re: [galaxy-dev] not sure what I can do about this...

2016-05-24 Thread Peter Cock

Hi Fernandez,

We saw something very like that with mixed versions of Linux,
specifically our Galaxy head node where pysam was installed
had CentOS 7, but the node where Galaxy was trying to run
the metadata detection was CentOS 6. Unfortunately I do
not have a record of the exact traceback - but from memory
it was the same problem in pysam with gzopen64.

(We'd already fought problems with Python mis-matches,
GLIBC versions, etc and had carefully built Python on
CentOS 6 in order to run on both CentOS 6 and 7.)

At this point we gave up, and will run the Galaxy node on the
same version of Linux as the Cluster - and plan to upgrade
the cluster before the Galaxy node. That way all the stuff
Galaxy installs (e.g. via the ToolShed) ought to work on the
cluster.

Peter

On Tue, May 24, 2016 at 7:08 PM, Fernandez Edgar
 wrote:
>
> Hello guys,
>
>
>
> I’m still stuck on this error.
>
> I’ve installed a brand new galaxy v16.01
>
> And when I start it, I get the big error mentioned below.
>
> Here’s the last message in the error:
>
> ImportError: 
> /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so:
>  undefined symbol: gzopen64
>
>
>
> Thanks for your assistance!
>
>
>
> Cheers,
>
>
>
> Edgar Fernandez
___
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] not sure what I can do about this...

2016-05-20 Thread Marius van den Beek

Hi Edgar,

it’s a good idea to use python2.7 for galaxy, since 16.01 is the last
release supporting python 2.6.
In general you can create a new virrtualenv with a a specific python
interpreter like this:

virtualenv -p  

If you create a new new virtualenv .venv in your galaxy source folder,
run.sh will pick this up.
If you are using a different way to start galaxy, you can use something
along the lines of

/scripts/paster.py
serve config/galaxy.ini>

Hope that will get you past the problems starting up galaxy.

Cheers,
Marius


On 19 May 2016 at 14:48, Fernandez Edgar <edgar.fernan...@umontreal.ca>
wrote:

> 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)
> <https://ulns.dit.umontreal.ca/rhn/channels/ChannelDetail.do?cid=149>
>
> 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/gala

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)<https://ulns.dit.umontreal.ca/rhn/channels/ChannelDetail.do?cid=149>
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 &

Re: [galaxy-dev] not sure what I can do about this...

2016-05-18 Thread Fernandez Edgar

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 *
ImportError: 
/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so:
 undefined symbol: gzopen64
Removing PID file paster.pid

PLEASE HELP ME !

Best regards,

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
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Re: [galaxy-dev] not sure what I can do about this...

2015-09-29 Thread Björn Grüning

Hi Edgar,

please download the latest version of tbl2asn from here:

ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/

and replace it with your version, this will probably fix your error.

Cheers,
Bjoern

Am 29.09.2015 um 14:05 schrieb Fernandez Edgar:
> Hello Gents,
> 
> So someone asked me to install the package Prokka on Galaxy.
> I did and everything went well!
> 
> However, the following error comes up, when they try to work with Prokka:
> 
> Fatal error: Exit code 2 ()
> 
> [tbl2asn] This copy of tbl2asn is more than a year old.  Please download the 
> current version.
> 
> [20:20:53] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 
> 1 -y 'Annotated using prokka 1.10 from http://www.vicbioinformatics.com' -Z 
> outdir\/prokka\.err -i outdir\/prokka\.fsa 2> /dev/null
> 
> 
> According to a google search, there is very little on this error.
> And it has been around for a while but I didn't find a posted solution.
> 
> Any suggestions?
> 
> Cordialement / Regards,
> 
> Edgar Fernandez
> System Administrator (Linux)
> Direction Générale des Technologies de l'Information et de la Communication
> *  Bur. : 1-514-343-6111 poste 16568
> 
> Université de Montréal
> PAVILLON ROGER-GAUDRY, bureau X-218
> 
> 
> 
> 
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> 
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>   http://galaxyproject.org/search/mailinglists/
> 
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Re: [galaxy-dev] not sure what I can do about this...

2015-09-29 Thread Fernandez Edgar

Hello Björn,

Thank you for answering!
When I installed Prokka from the Galaxy ToolShed, all the dependencies were 
installed too.
tbl2asn is one of those dependencies...
How would I replace it?

Cordialement / Regards, 
Edgar Fernandez


-Message d'origine-
De : Björn Grüning [mailto:bjoern.gruen...@gmail.com] 
Envoyé : September-29-15 8:10 AM
À : Fernandez Edgar; galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] not sure what I can do about this...

Hi Edgar,

please download the latest version of tbl2asn from here:

ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/

and replace it with your version, this will probably fix your error.

Cheers,
Bjoern

Am 29.09.2015 um 14:05 schrieb Fernandez Edgar:
> Hello Gents,
> 
> So someone asked me to install the package Prokka on Galaxy.
> I did and everything went well!
> 
> However, the following error comes up, when they try to work with Prokka:
> 
> Fatal error: Exit code 2 ()
> 
> [tbl2asn] This copy of tbl2asn is more than a year old.  Please download the 
> current version.
> 
> [20:20:53] Could not run command: tbl2asn -V b -a r10k -l paired-ends 
> -M n -N 1 -y 'Annotated using prokka 1.10 from 
> http://www.vicbioinformatics.com' -Z outdir\/prokka\.err -i 
> outdir\/prokka\.fsa 2> /dev/null
> 
> 
> According to a google search, there is very little on this error.
> And it has been around for a while but I didn't find a posted solution.
> 
> Any suggestions?
> 
> Cordialement / Regards,
> 
> Edgar Fernandez
> System Administrator (Linux)
> Direction Générale des Technologies de l'Information et de la 
> Communication
> *  Bur. : 1-514-343-6111 poste 16568
> 
> Université de Montréal
> PAVILLON ROGER-GAUDRY, bureau X-218
> 
> 
> 
> 
> ___
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> in your mail client.  To manage your subscriptions to this and other 
> Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
> 
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>   http://galaxyproject.org/search/mailinglists/
> 
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Re: [galaxy-dev] not sure what I can do about this...

2015-09-29 Thread Peter Cock

On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar
 wrote:
> Hello Björn,
>
> Thank you for answering!
> When I installed Prokka from the Galaxy ToolShed, all the dependencies were 
> installed too.
> tbl2asn is one of those dependencies...
> How would I replace it?
>
> Cordialement / Regards,
> Edgar Fernandez

The way the NCBI deliberately make tbl2asn expire is very
annoying for packaging and breaks strict reproducibility :(

I think Bjoern was suggesting manually updating the copy of tbl2asn
which the Tool Shed had downloaded (as a quick short term solution).
You'd need to find this file within the Tool Shed dependencies folder...

Philip - can you update package_tbl2asn_23_7 or add a new
package if the version number has changed? Or would you like
the IUC group to look after this in future?

https://toolshed.g2.bx.psu.edu/view/takadonet/package_tbl2asn_23_7/

Nicola - once that's done, can you update the prokka dependency
list - or would that fall to your old colleagues at CRS4?

https://toolshed.g2.bx.psu.edu/view/crs4/prokka/

Peter
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Re: [galaxy-dev] not sure what I can do about this...

2015-09-29 Thread Fernandez Edgar

Guys, I can express how thankful I am for your help!!!

Personally, I would comment out the following line in the tbl2asn code:

8869<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8869>
   if 
(MoreThanYearOld<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=MoreThanYearOld>
 ()) {
8870<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8870>
 too_old = 
TRUE<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=TRUE>;
8871<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8871>
 Message<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=Message> 
(MSG_POST<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=MSG_POST>, 
"This copy of tbl2asn is more than a year old.  Please download the current 
version.");
8872<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8872>
   }

In the meantime, would you suggest I change the files located inside my galaxy 
installation?
Or should I wait for Philip’s release?

I ask because I found the following binary files:
-rwxr-x--- 1 galaxy users 7349340 Sep 15 08:52
./tool-data/toolshed.dependency.dir/tbl2asn/23.7/takadonet/package_tbl2asn_23_7/2271d52a8531/bin/tbl2asn

-rwxrwxr-x 1 galaxy users 12675348 Jul 28  2014
./tool-data/toolshed.dependency.dir/prokka/1.10/crs4/prokka/3ad7ef0ba385/binaries/darwin/tbl2asn

-rwxrwxr-x 1 galaxy users 6872896 Jul 28  2014
./tool-data/toolshed.dependency.dir/prokka/1.10/crs4/prokka/3ad7ef0ba385/binaries/linux/tbl2asn

Oddly, they’re all different.
What exactly can I do with this and how can I compile the tblasn.c file?

Cordialement / Regards,
Edgar Fernandez

De : Philip Mabon [mailto:philipma...@gmail.com]
Envoyé : September-29-15 10:27 AM
À : Peter Cock; Fernandez Edgar; Nicola Soranzo (TGAC)
Cc : Björn Grüning; galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] not sure what I can do about this...

I will make a new package for tbl2asn. Our lab is not too happy that tbl2asn 
expires and causes lots of issues for us.

On Tue, Sep 29, 2015 at 9:24 AM Peter Cock 
<p.j.a.c...@googlemail.com<mailto:p.j.a.c...@googlemail.com>> wrote:
On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar
<edgar.fernan...@umontreal.ca<mailto:edgar.fernan...@umontreal.ca>> wrote:
> Hello Björn,
>
> Thank you for answering!
> When I installed Prokka from the Galaxy ToolShed, all the dependencies were 
> installed too.
> tbl2asn is one of those dependencies...
> How would I replace it?
>
> Cordialement / Regards,
> Edgar Fernandez

The way the NCBI deliberately make tbl2asn expire is very
annoying for packaging and breaks strict reproducibility :(

I think Bjoern was suggesting manually updating the copy of tbl2asn
which the Tool Shed had downloaded (as a quick short term solution).
You'd need to find this file within the Tool Shed dependencies folder...

Philip - can you update package_tbl2asn_23_7 or add a new
package if the version number has changed? Or would you like
the IUC group to look after this in future?

https://toolshed.g2.bx.psu.edu/view/takadonet/package_tbl2asn_23_7/

Nicola - once that's done, can you update the prokka dependency
list - or would that fall to your old colleagues at CRS4?

https://toolshed.g2.bx.psu.edu/view/crs4/prokka/

Peter
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Re: [galaxy-dev] not sure what I can do about this...

Re: [galaxy-dev] not sure what I can do about this...

Re: [galaxy-dev] not sure what I can do about this...

Re: [galaxy-dev] not sure what I can do about this...

Re: [galaxy-dev] not sure what I can do about this...

Re: [galaxy-dev] not sure what I can do about this...

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