not sure what I can do about this...

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not sure what I can do about this...

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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Re: not sure what I can do about this...

Björn Grüning-3
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
>
>
>
>
> ___________________________________________________________
> 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/
>
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Re: not sure what I can do about this...

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:[hidden email]]
Envoyé : September-29-15 8:10 AM
À : Fernandez Edgar; [hidden email]
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
>
>
>
>
> ___________________________________________________________
> 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/
>
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Re: not sure what I can do about this...

Peter Cock
On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar
<[hidden email]> 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: not sure what I can do about this...

takadonet
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 <[hidden email]> wrote:
On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar
<[hidden email]> 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: not sure what I can do about this...

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
   if (MoreThanYearOld ()) {

8870     too_old = TRUE;

8871     Message (MSG_POST, "This copy of tbl2asn is more than a year old.  Please download the current version.");

8872   }

 

 

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:[hidden email]]
Envoyé : September-29-15 10:27 AM
À : Peter Cock; Fernandez Edgar; Nicola Soranzo (TGAC)
Cc : Björn Grüning; [hidden email]
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 <[hidden email]> wrote:

On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar
<[hidden email]> 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: not sure what I can do about this...

Eric Rasche-2
Hi Fernandez,

2015-09-29 10:02 GMT-05:00 Fernandez Edgar <[hidden email]>:

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

 

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


8869
   if (MoreThanYearOld ()) {

8870     too_old = TRUE;

8871     Message (MSG_POST, "This copy of tbl2asn is more than a year old.  Please download the current version.");

8872   }

 

 

In the meantime, would you suggest I change the files located inside my galaxy installation?

Or should I wait for Philip’s release?



I would replace the files. We (The IUC, specifically Björn and myself) have talked about solutions to this problem but haven't finished building them yet.

 

 

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?


You can fetch a precompiled version of tbl2asn here: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/

I recommend replacing all of those (or just the first and last, assuming you're on linux) as (eventually) none of them will work.

Hopefully in the future we'll be able to fix this.


 

Cordialement / Regards,

Edgar Fernandez

 

De : Philip Mabon [mailto:[hidden email]]
Envoyé : September-29-15 10:27 AM
À : Peter Cock; Fernandez Edgar; Nicola Soranzo (TGAC)
Cc : Björn Grüning; [hidden email]
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 <[hidden email]> wrote:

On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar
<[hidden email]> 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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Cheers,
Eric

--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048

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Re: not sure what I can do about this...

Nicola Soranzo-2
In reply to this post by Peter Cock
On 29/09/15 15:24, Peter Cock wrote:
> 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

I can update prokka, no problem. Just let me know when the new
package_tbl2asn is available.

Cheers,
Nicola
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Re: not sure what I can do about this...

takadonet
Just waiting on this merge request and I will have a new version on the toolshed.




On Tue, Sep 29, 2015 at 1:25 PM Nicola Soranzo <[hidden email]> wrote:
On 29/09/15 15:24, Peter Cock wrote:
> 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

I can update prokka, no problem. Just let me know when the new
package_tbl2asn is available.

Cheers,
Nicola

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Re: not sure what I can do about this...

takadonet

On Tue, Sep 29, 2015 at 1:47 PM Philip Mabon <[hidden email]> wrote:
Just waiting on this merge request and I will have a new version on the toolshed.




On Tue, Sep 29, 2015 at 1:25 PM Nicola Soranzo <[hidden email]> wrote:
On 29/09/15 15:24, Peter Cock wrote:
> 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

I can update prokka, no problem. Just let me know when the new
package_tbl2asn is available.

Cheers,
Nicola

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Re: not sure what I can do about this...

Nicola Soranzo-2
Thanks Philip,
I've updated the prokka package accordingly and I have also updated other dependencies (Prokka 1.11, Barrnap 0.7, BLAST 2.2.31, HMMER 3.1b2).

Edgar, I'd like to know if the new version installs and works for you, since I'm not using it at the moment.

Cheers,
Nicola

On 30/09/15 14:30, Philip Mabon wrote:

On Tue, Sep 29, 2015 at 1:47 PM Philip Mabon <[hidden email]> wrote:
Just waiting on this merge request and I will have a new version on the toolshed.




On Tue, Sep 29, 2015 at 1:25 PM Nicola Soranzo <[hidden email]> wrote:
On 29/09/15 15:24, Peter Cock wrote:
> 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

I can update prokka, no problem. Just let me know when the new
package_tbl2asn is available.

Cheers,
Nicola


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Re: not sure what I can do about this...

takadonet
I will give it a try today or tomorrow.

Thanks

On Thu, Oct 1, 2015 at 1:21 PM Nicola Soranzo <[hidden email]> wrote:
Thanks Philip,
I've updated the prokka package accordingly and I have also updated other dependencies (Prokka 1.11, Barrnap 0.7, BLAST 2.2.31, HMMER 3.1b2).

Edgar, I'd like to know if the new version installs and works for you, since I'm not using it at the moment.

Cheers,
Nicola


On 30/09/15 14:30, Philip Mabon wrote:

On Tue, Sep 29, 2015 at 1:47 PM Philip Mabon <[hidden email]> wrote:
Just waiting on this merge request and I will have a new version on the toolshed.




On Tue, Sep 29, 2015 at 1:25 PM Nicola Soranzo <[hidden email]> wrote:
On 29/09/15 15:24, Peter Cock wrote:
> 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

I can update prokka, no problem. Just let me know when the new
package_tbl2asn is available.

Cheers,
Nicola


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Re: not sure what I can do about this...

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 <module>

    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 <module>

    from galaxy.webapps.galaxy.buildapp import app_factory

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/webapps/galaxy/buildapp.py", line 15, in <module>

    import galaxy.app

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/app.py", line 6, in <module>

    from galaxy import config, jobs

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/jobs/__init__.py", line 19, in <module>

    from galaxy import model, util

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/model/__init__.py", line 26, in <module>

    import galaxy.datatypes.registry

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/registry.py", line 9, in <module>

    import tabular

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/tabular.py", line 18, in <module>

    from galaxy.datatypes.sniff import get_headers

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/sniff.py", line 19, in <module>

    from galaxy.datatypes.binary import Binary

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/binary.py", line 13, in <module>

    import pysam

  File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/__init__.py", line 1, in <module>

    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


___________________________________________________________
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:
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Re: not sure what I can do about this...

fernandez Edgar
In reply to this post by takadonet

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: [hidden email]
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 <module>

    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 <module>

    from galaxy.webapps.galaxy.buildapp import app_factory

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/webapps/galaxy/buildapp.py", line 15, in <module>

    import galaxy.app

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/app.py", line 6, in <module>

    from galaxy import config, jobs

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/jobs/__init__.py", line 19, in <module>

    from galaxy import model, util

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/model/__init__.py", line 26, in <module>

    import galaxy.datatypes.registry

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/registry.py", line 9, in <module>

    import tabular

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/tabular.py", line 18, in <module>

    from galaxy.datatypes.sniff import get_headers

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/sniff.py", line 19, in <module>

    from galaxy.datatypes.binary import Binary

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/binary.py", line 13, in <module>

    import pysam

  File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/__init__.py", line 1, in <module>

    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


___________________________________________________________
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/
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Re: not sure what I can do about this...

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 <path/to/python/interpreter> <path/to/new/virtualenv/>

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

<path/to/virtualenv/bin/python <path/to/galaxy>/scripts/paster.py serve <path/to/galaxy/>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 <[hidden email]> 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: [hidden email]
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 <module>

    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 <module>

    from galaxy.webapps.galaxy.buildapp import app_factory

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/webapps/galaxy/buildapp.py", line 15, in <module>

    import galaxy.app

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/app.py", line 6, in <module>

    from galaxy import config, jobs

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/jobs/__init__.py", line 19, in <module>

    from galaxy import model, util

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/model/__init__.py", line 26, in <module>

    import galaxy.datatypes.registry

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/registry.py", line 9, in <module>

    import tabular

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/tabular.py", line 18, in <module>

    from galaxy.datatypes.sniff import get_headers

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/sniff.py", line 19, in <module>

    from galaxy.datatypes.binary import Binary

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/binary.py", line 13, in <module>

    import pysam

  File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/__init__.py", line 1, in <module>

    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


___________________________________________________________
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/


___________________________________________________________
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/
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Re: not sure what I can do about this...

fernandez Edgar
In reply to this post by takadonet

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: '[hidden email]' <[hidden email]>
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: [hidden email]
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 <module>

    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 <module>

    from galaxy.webapps.galaxy.buildapp import app_factory

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/webapps/galaxy/buildapp.py", line 15, in <module>

    import galaxy.app

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/app.py", line 6, in <module>

    from galaxy import config, jobs

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/jobs/__init__.py", line 19, in <module>

    from galaxy import model, util

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/model/__init__.py", line 26, in <module>

    import galaxy.datatypes.registry

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/registry.py", line 9, in <module>

    import tabular

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/tabular.py", line 18, in <module>

    from galaxy.datatypes.sniff import get_headers

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/sniff.py", line 19, in <module>

    from galaxy.datatypes.binary import Binary

  File "/home/galaxy/galaxy-v16.01/lib/galaxy/datatypes/binary.py", line 13, in <module>

    import pysam

  File "/home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/__init__.py", line 1, in <module>

    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: not sure what I can do about this...

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
<[hidden email]> 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
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: not sure what I can do about this...

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:[hidden email]]
Sent: May-24-16 2:29 PM
To: Fernandez Edgar <[hidden email]>
Cc: [hidden email]
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 <[hidden email]> 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/

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  http://galaxyproject.org/search/mailinglists/
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Re: not sure what I can do about this...

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
<[hidden email]> 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/
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Re: not sure what I can do about this...

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:[hidden email]]
Sent: May-24-16 5:40 PM
To: Fernandez Edgar <[hidden email]>
Cc: [hidden email]
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 <[hidden email]> 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/
12