Expose Command Line in Galaxy

classic Classic list List threaded Threaded
13 messages Options
| Threaded
Open this post in threaded view
|

Expose Command Line in Galaxy

M_Enders
Dear Galaxy Community,

is there any possibility to expose the command line call, generated within galaxy?

We searched the net and found this discussions:
https://github.com/galaxyproject/galaxy/issues/3252
https://github.com/galaxyproject/galaxy/issues/2954

But both are on the exposure to non-admin users. Within our instance we see the command line call nor for admin, neither for normal users!

The problem, behind the question is the error message: "An invalid option was selected for database, 'myCoolDatabaseName', please verify." In Blast (toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.01)

Local (directly from command line, without Galaxy in between) the blast works fine.

We are using the 18.05 Docker Galaxy Version.

Thanks in advance!

Mit freundlichen Grüßen

Matthias Enders
-----------------------------------------------------------------------


GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

Email: [hidden email]

Firmensitz Köln
Amtsgericht Köln, HRB 73844

-----Ursprüngliche Nachricht-----
Von: galaxy-dev <[hidden email]> Im Auftrag von [hidden email]
Gesendet: Montag, 9. Juli 2018 18:00
An: [hidden email]
Betreff: galaxy-dev Digest, Vol 145, Issue 3

Send galaxy-dev mailing list submissions to
        [hidden email]

To subscribe or unsubscribe via the World Wide Web, visit
        https://lists.galaxyproject.org/listinfo/galaxy-dev
or, via email, send a message with subject or body 'help' to
        [hidden email]

You can reach the person managing the list at
        [hidden email]

When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..."


HEY!  This is important!  If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread.
2. Strip out everything else in the digest that is not part of the thread you are responding to.

Why?
1. This will keep the subject meaningful.  People will have some idea from the subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative.

Today's Topics:

   1. From Paste to uWSGI (Jochen Bick)
   2. Re: From Paste to uWSGI (Peter Briggs)
   3. Re: From Paste to uWSGI (Martin Čech)


----------------------------------------------------------------------

Message: 1
Date: Mon, 9 Jul 2018 13:49:23 +0200
From: Jochen Bick <[hidden email]>
To: "[hidden email]"
        <[hidden email]>
Subject: [galaxy-dev] From Paste to uWSGI
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="utf-8"; format=flowed

Hi all,

we would like to update to 18.05 and thereby also update our Paste Server.

https://docs.galaxyproject.org/en/latest/admin/scaling.html

Is there any tutorial on how to update from Paste to uWSGI?


Cheers Jochen

--
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland

Phone +41 52 354 92 06
[hidden email] <mailto:[hidden email]> www.ap.ethz.ch



------------------------------

Message: 2
Date: Mon, 9 Jul 2018 15:31:16 +0000
From: Peter Briggs <[hidden email]>
To: Jochen Bick <[hidden email]>,
        "[hidden email]"
        <[hidden email]>
Subject: Re: [galaxy-dev] From Paste to uWSGI
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

Hello Jochen

I'm not aware of a tutorial but here are some observations from my (very) recent experiences upgrading a local paste-based 17.09 instance to a uwsgi-based 18.05 configuration. It's not comprehensive because the configuration will depend on decisions you need to make based on your local setup, but it might be helpful as a starting point.

Before beginning:

-- Commit to migrating from galaxy.ini to galaxy.yml (if not done previously)

Even though its possible to stick with the old galaxy.ini file, it seems best to move to the new format - my feeling is, probably the migration will have to happen at some point anyway, and also the documentation is more focussed on the newer galaxy.yml version.

-- Decide on how you're going to handle job submission (essentially, how you're going to replace the old job handler processes).

There are a number of possibilities outlined in the documentation here:

https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#deployment-options

It seems important to figure this out at the beginning because it impacts a lot of the configuration specifics that follow. For our setup case "uwsgi + mules" looked like the most appropriate:

https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uwsgi-for-web-serving-with-mules-as-job-handlers

Then once you're ready to start (nb backing up the database etc before starting are implicitly assumed!):

-- Update the Galaxy source code

The standard recipe for this seems to work okay i.e.

git fetch origin && git checkout release_18.05 && git pull --ff-only origin release_18.05

(You'll probably also need to run scripts/common_startup.sh to update the Python packages, and scripts/manage_db.py to update the database schema.)

-- Create galaxy.yml and configure the "galaxy" section:

You can make a galaxy.yml from the sample version and go through the "galaxy" section replicating the settings from galaxy.ini. (The settings in the "uwsgi" section can wait at this stage.) Don't forget to move galaxy.ini out of the way once you're done.

-- Configure the "uwsgi" section of galaxy.yml:

The options for various scenarios are given in the "Deployment/uwsgi" section:

https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uwsgi

but the required settings seem to be spread out between different sections so (for me) it felt like it took some piecing together to get it to work when I first tried this.

(Also I was thrown a little by the "socket" parameter not having a placeholder in sample galaxy.yml.)

The core uwsgi options are here:

https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#configuration-common-to-all-uwsgi-deployment-styles

then you need to set other options dependent on:

1. how job submission is handled (e.g. options for the "uwsgi + mules" setup in my case) 2. how you're proxying Galaxy (for Apache or nginx it looks like it's just setting the uwsgi "socket" option, unless you're serving Galaxy from a URL prefix in which case there are a few more options needed - these are covered in the documentation.)

-- Fix your job_conf.xml file

If you have an existing job_conf.xml file in your config directory then you might need to update that too (specifically the "handlers" section) depending on the job submission handling you've decided to use.

-- Use supervisor to manage your uwsgi processes

The docs for this are here:

https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#starting-and-stopping

Essentially supervisor replaces "run.sh", so this becomes how you start and stop Galaxy (e.g. "supervisorctl start galaxy:" replaces "GALAXY_RUN_ALL=1 sh run.sh --daemon".)

I think this is quite straightforward from the docs but again you need to tailor it for how you're handling job submission (e.g the "uwsgi + mules" doesn't need any handlers defining, but it looks like other strategies needs extra stuff defining here).

-- Set up the proxying

Assuming you're proxing via either Apache or nginx (we're using nginx), these are covered in the relevant sections:

https://docs.galaxyproject.org/en/release_18.05/admin/apache.html
https://docs.galaxyproject.org/en/release_18.05/admin/nginx.html

The main difference I noticed for nginx is that you no longer need to use the "upstream"/"proxy_pass" directives, as nginx can talk directly to uwsgi using a "uwsgi_pass" directive that connects to the socket defined in the "uwsgi" section of galaxy.yml previously.

(There's also a "gotcha" if you're nginx configuration also tries to serve "static/scripts/packed", which needs to be removed - this is noted in the "breaking changes" for the 18.05 docs but is easy to miss.)

Hopefully this is some help. There's lots of documentation, which is a good thing but which can sometimes make it harder to see where to start.

Good luck with the update,

Best wishes

Peter

--
Peter Briggs [hidden email] Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482


________________________________________
From: galaxy-dev [[hidden email]] on behalf of Jochen Bick [[hidden email]]
Sent: Monday, July 09, 2018 12:49 PM
To: [hidden email]
Subject: [galaxy-dev] From Paste to uWSGI

Hi all,

we would like to update to 18.05 and thereby also update our Paste Server.

https://docs.galaxyproject.org/en/latest/admin/scaling.html

Is there any tutorial on how to update from Paste to uWSGI?


Cheers Jochen

--
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland

Phone +41 52 354 92 06
[hidden email] <mailto:[hidden email]> www.ap.ethz.ch

___________________________________________________________
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/


------------------------------

Message: 3
Date: Mon, 9 Jul 2018 11:36:27 -0400
From: Martin Čech <[hidden email]>
To: Peter Briggs <[hidden email]>
Cc: "[hidden email]"
        <[hidden email]>
Subject: Re: [galaxy-dev] From Paste to uWSGI
Message-ID:
        <CAHKBquGXMTog-MUgLbPWD2wgmXvpOxiQGRa4+QCWk5EAHGK3=[hidden email]>
Content-Type: text/plain; charset="utf-8"

Another recently updated resource for uwsgi is the training slides:
https://galaxyproject.github.io/dagobah-training/2018-gccbosc/10-uwsgi/uwsgi.html#1

M.

On Mon, Jul 9, 2018 at 11:31 AM Peter Briggs <[hidden email]>
wrote:

> Hello Jochen
>
> I'm not aware of a tutorial but here are some observations from my
> (very) recent experiences upgrading a local paste-based 17.09 instance
> to a uwsgi-based 18.05 configuration. It's not comprehensive because
> the configuration will depend on decisions you need to make based on
> your local setup, but it might be helpful as a starting point.
>
> Before beginning:
>
> -- Commit to migrating from galaxy.ini to galaxy.yml (if not done
> previously)
>
> Even though its possible to stick with the old galaxy.ini file, it
> seems best to move to the new format - my feeling is, probably the
> migration will have to happen at some point anyway, and also the
> documentation is more focussed on the newer galaxy.yml version.
>
> -- Decide on how you're going to handle job submission (essentially,
> how you're going to replace the old job handler processes).
>
> There are a number of possibilities outlined in the documentation here:
>
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#dep
> loyment-options
>
> It seems important to figure this out at the beginning because it
> impacts a lot of the configuration specifics that follow. For our
> setup case "uwsgi
> + mules" looked like the most appropriate:
>
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uws
> gi-for-web-serving-with-mules-as-job-handlers
>
> Then once you're ready to start (nb backing up the database etc before
> starting are implicitly assumed!):
>
> -- Update the Galaxy source code
>
> The standard recipe for this seems to work okay i.e.
>
> git fetch origin && git checkout release_18.05 && git pull --ff-only
> origin release_18.05
>
> (You'll probably also need to run scripts/common_startup.sh to update
> the Python packages, and scripts/manage_db.py to update the database
> schema.)
>
> -- Create galaxy.yml and configure the "galaxy" section:
>
> You can make a galaxy.yml from the sample version and go through the
> "galaxy" section replicating the settings from galaxy.ini. (The
> settings in the "uwsgi" section can wait at this stage.) Don't forget
> to move galaxy.ini out of the way once you're done.
>
> -- Configure the "uwsgi" section of galaxy.yml:
>
> The options for various scenarios are given in the "Deployment/uwsgi"
> section:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uws
> gi
>
> but the required settings seem to be spread out between different
> sections so (for me) it felt like it took some piecing together to get
> it to work when I first tried this.
>
> (Also I was thrown a little by the "socket" parameter not having a
> placeholder in sample galaxy.yml.)
>
> The core uwsgi options are here:
>
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#con
> figuration-common-to-all-uwsgi-deployment-styles
>
> then you need to set other options dependent on:
>
> 1. how job submission is handled (e.g. options for the "uwsgi + mules"
> setup in my case)
> 2. how you're proxying Galaxy (for Apache or nginx it looks like it's
> just setting the uwsgi "socket" option, unless you're serving Galaxy
> from a URL prefix in which case there are a few more options needed -
> these are covered in the documentation.)
>
> -- Fix your job_conf.xml file
>
> If you have an existing job_conf.xml file in your config directory
> then you might need to update that too (specifically the "handlers"
> section) depending on the job submission handling you've decided to use.
>
> -- Use supervisor to manage your uwsgi processes
>
> The docs for this are here:
>
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#sta
> rting-and-stopping
>
> Essentially supervisor replaces "run.sh", so this becomes how you
> start and stop Galaxy (e.g. "supervisorctl start galaxy:" replaces
> "GALAXY_RUN_ALL=1 sh run.sh --daemon".)
>
> I think this is quite straightforward from the docs but again you need
> to tailor it for how you're handling job submission (e.g the "uwsgi + mules"
> doesn't need any handlers defining, but it looks like other strategies
> needs extra stuff defining here).
>
> -- Set up the proxying
>
> Assuming you're proxing via either Apache or nginx (we're using
> nginx), these are covered in the relevant sections:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/apache.html
> https://docs.galaxyproject.org/en/release_18.05/admin/nginx.html
>
> The main difference I noticed for nginx is that you no longer need to
> use the "upstream"/"proxy_pass" directives, as nginx can talk directly
> to uwsgi using a "uwsgi_pass" directive that connects to the socket
> defined in the "uwsgi" section of galaxy.yml previously.
>
> (There's also a "gotcha" if you're nginx configuration also tries to
> serve "static/scripts/packed", which needs to be removed - this is
> noted in the "breaking changes" for the 18.05 docs but is easy to
> miss.)
>
> Hopefully this is some help. There's lots of documentation, which is a
> good thing but which can sometimes make it harder to see where to start.
>
> Good luck with the update,
>
> Best wishes
>
> Peter
>
> --
> Peter Briggs [hidden email] Bioinformatics Core
> Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
>
> ________________________________________
> From: galaxy-dev [[hidden email]] on
> behalf of Jochen Bick [[hidden email]]
> Sent: Monday, July 09, 2018 12:49 PM
> To: [hidden email]
> Subject: [galaxy-dev] From Paste to uWSGI
>
> Hi all,
>
> we would like to update to 18.05 and thereby also update our Paste Server.
>
> https://docs.galaxyproject.org/en/latest/admin/scaling.html
>
> Is there any tutorial on how to update from Paste to uWSGI?
>
>
> Cheers Jochen
>
> --
> ETH Zurich
> *Jochen Bick*
> Animal Physiology
> Institute of Agricultural Sciences
> Postal address: Universitätstrasse 2
> <https://maps.google.com/?q=Universit%C3%A4tstrasse+2&entry=gmail&sour
> ce=g>
> / LFW B 58.1
> 8092 Zurich, Switzerland
> Office: Eschikon 27
> 8315 Lindau, Switzerland
>
> Phone +41 52 354 92 06 <+41%2052%20354%2092%2006>
> [hidden email] <mailto:[hidden email]>
> www.ap.ethz.ch
>
> ___________________________________________________________
> 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/
> ___________________________________________________________
> 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/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20180709/a7d44c29/attachment-0001.html>

------------------------------

Subject: Digest Footer

_______________________________________________
galaxy-dev mailing list
[hidden email]
https://lists.galaxyproject.org/listinfo/galaxy-dev

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

------------------------------

End of galaxy-dev Digest, Vol 145, Issue 3
******************************************
___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Expose Command Line in Galaxy

Hans-Rudolf Hotz
Hi Matthias

If for whatever reasons the  "i" (view details) icon doesn't work for
you, you can use the Galaxy Report Webapp (for docker installations see:
https://github.com/bgruening/docker-galaxy-stable#Galaxy-Report-Webapp )
as an alternative.

You can find your (failed) job via "Jobs in error per day this month".
Once you clicked on the 'job id' you will get the executed command line/


Hope this helps.
Regards, Hans-Rudolf





On 07/10/2018 08:58 AM, Matthias Enders wrote:

> Dear Galaxy Community,
>
> is there any possibility to expose the command line call, generated within galaxy?
>
> We searched the net and found this discussions:
> https://github.com/galaxyproject/galaxy/issues/3252
> https://github.com/galaxyproject/galaxy/issues/2954
>
> But both are on the exposure to non-admin users. Within our instance we see the command line call nor for admin, neither for normal users!
>
> The problem, behind the question is the error message: "An invalid option was selected for database, 'myCoolDatabaseName', please verify." In Blast (toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.01)
>
> Local (directly from command line, without Galaxy in between) the blast works fine.
>
> We are using the 18.05 Docker Galaxy Version.
>
> Thanks in advance!
>
> Mit freundlichen Grüßen
>
> Matthias Enders
> -----------------------------------------------------------------------
>
>
> GERMAN SEED ALLIANCE GmbH
> c/o Norddeutsche Pflanzenzucht
> Hans-Georg Lembke KG
> Hohenlieth, 24363 Holtsee
> Tel.: +49 (0)4351/ 736-189
> Fax: + 49 (0)4351/ 736-271
> Mobil: +49 (0)151/ 14247360
>
> Email: [hidden email]
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
>
> -----Ursprüngliche Nachricht-----
> Von: galaxy-dev <[hidden email]> Im Auftrag von [hidden email]
> Gesendet: Montag, 9. Juli 2018 18:00
> An: [hidden email]
> Betreff: galaxy-dev Digest, Vol 145, Issue 3
>
> Send galaxy-dev mailing list submissions to
> [hidden email]
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.galaxyproject.org/listinfo/galaxy-dev
> or, via email, send a message with subject or body 'help' to
> [hidden email]
>
> You can reach the person managing the list at
> [hidden email]
>
> When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..."
>
>
> HEY!  This is important!  If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread.
> 2. Strip out everything else in the digest that is not part of the thread you are responding to.
>
> Why?
> 1. This will keep the subject meaningful.  People will have some idea from the subject line if they should read it or not.
> 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative.
>
> Today's Topics:
>
>     1. From Paste to uWSGI (Jochen Bick)
>     2. Re: From Paste to uWSGI (Peter Briggs)
>     3. Re: From Paste to uWSGI (Martin Čech)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 9 Jul 2018 13:49:23 +0200
> From: Jochen Bick <[hidden email]>
> To: "[hidden email]"
> <[hidden email]>
> Subject: [galaxy-dev] From Paste to uWSGI
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset="utf-8"; format=flowed
>
> Hi all,
>
> we would like to update to 18.05 and thereby also update our Paste Server.
>
> https://docs.galaxyproject.org/en/latest/admin/scaling.html
>
> Is there any tutorial on how to update from Paste to uWSGI?
>
>
> Cheers Jochen
>
> --
> ETH Zurich
> *Jochen Bick*
> Animal Physiology
> Institute of Agricultural Sciences
> Postal address: Universitätstrasse 2 / LFW B 58.1
> 8092 Zurich, Switzerland
> Office: Eschikon 27
> 8315 Lindau, Switzerland
>
> Phone +41 52 354 92 06
> [hidden email] <mailto:[hidden email]> www.ap.ethz.ch
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 9 Jul 2018 15:31:16 +0000
> From: Peter Briggs <[hidden email]>
> To: Jochen Bick <[hidden email]>,
> "[hidden email]"
> <[hidden email]>
> Subject: Re: [galaxy-dev] From Paste to uWSGI
> Message-ID:
> <[hidden email]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello Jochen
>
> I'm not aware of a tutorial but here are some observations from my (very) recent experiences upgrading a local paste-based 17.09 instance to a uwsgi-based 18.05 configuration. It's not comprehensive because the configuration will depend on decisions you need to make based on your local setup, but it might be helpful as a starting point.
>
> Before beginning:
>
> -- Commit to migrating from galaxy.ini to galaxy.yml (if not done previously)
>
> Even though its possible to stick with the old galaxy.ini file, it seems best to move to the new format - my feeling is, probably the migration will have to happen at some point anyway, and also the documentation is more focussed on the newer galaxy.yml version.
>
> -- Decide on how you're going to handle job submission (essentially, how you're going to replace the old job handler processes).
>
> There are a number of possibilities outlined in the documentation here:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#deployment-options
>
> It seems important to figure this out at the beginning because it impacts a lot of the configuration specifics that follow. For our setup case "uwsgi + mules" looked like the most appropriate:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uwsgi-for-web-serving-with-mules-as-job-handlers
>
> Then once you're ready to start (nb backing up the database etc before starting are implicitly assumed!):
>
> -- Update the Galaxy source code
>
> The standard recipe for this seems to work okay i.e.
>
> git fetch origin && git checkout release_18.05 && git pull --ff-only origin release_18.05
>
> (You'll probably also need to run scripts/common_startup.sh to update the Python packages, and scripts/manage_db.py to update the database schema.)
>
> -- Create galaxy.yml and configure the "galaxy" section:
>
> You can make a galaxy.yml from the sample version and go through the "galaxy" section replicating the settings from galaxy.ini. (The settings in the "uwsgi" section can wait at this stage.) Don't forget to move galaxy.ini out of the way once you're done.
>
> -- Configure the "uwsgi" section of galaxy.yml:
>
> The options for various scenarios are given in the "Deployment/uwsgi" section:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uwsgi
>
> but the required settings seem to be spread out between different sections so (for me) it felt like it took some piecing together to get it to work when I first tried this.
>
> (Also I was thrown a little by the "socket" parameter not having a placeholder in sample galaxy.yml.)
>
> The core uwsgi options are here:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#configuration-common-to-all-uwsgi-deployment-styles
>
> then you need to set other options dependent on:
>
> 1. how job submission is handled (e.g. options for the "uwsgi + mules" setup in my case) 2. how you're proxying Galaxy (for Apache or nginx it looks like it's just setting the uwsgi "socket" option, unless you're serving Galaxy from a URL prefix in which case there are a few more options needed - these are covered in the documentation.)
>
> -- Fix your job_conf.xml file
>
> If you have an existing job_conf.xml file in your config directory then you might need to update that too (specifically the "handlers" section) depending on the job submission handling you've decided to use.
>
> -- Use supervisor to manage your uwsgi processes
>
> The docs for this are here:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#starting-and-stopping
>
> Essentially supervisor replaces "run.sh", so this becomes how you start and stop Galaxy (e.g. "supervisorctl start galaxy:" replaces "GALAXY_RUN_ALL=1 sh run.sh --daemon".)
>
> I think this is quite straightforward from the docs but again you need to tailor it for how you're handling job submission (e.g the "uwsgi + mules" doesn't need any handlers defining, but it looks like other strategies needs extra stuff defining here).
>
> -- Set up the proxying
>
> Assuming you're proxing via either Apache or nginx (we're using nginx), these are covered in the relevant sections:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/apache.html
> https://docs.galaxyproject.org/en/release_18.05/admin/nginx.html
>
> The main difference I noticed for nginx is that you no longer need to use the "upstream"/"proxy_pass" directives, as nginx can talk directly to uwsgi using a "uwsgi_pass" directive that connects to the socket defined in the "uwsgi" section of galaxy.yml previously.
>
> (There's also a "gotcha" if you're nginx configuration also tries to serve "static/scripts/packed", which needs to be removed - this is noted in the "breaking changes" for the 18.05 docs but is easy to miss.)
>
> Hopefully this is some help. There's lots of documentation, which is a good thing but which can sometimes make it harder to see where to start.
>
> Good luck with the update,
>
> Best wishes
>
> Peter
>
> --
> Peter Briggs [hidden email] Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
>
> ________________________________________
> From: galaxy-dev [[hidden email]] on behalf of Jochen Bick [[hidden email]]
> Sent: Monday, July 09, 2018 12:49 PM
> To: [hidden email]
> Subject: [galaxy-dev] From Paste to uWSGI
>
> Hi all,
>
> we would like to update to 18.05 and thereby also update our Paste Server.
>
> https://docs.galaxyproject.org/en/latest/admin/scaling.html
>
> Is there any tutorial on how to update from Paste to uWSGI?
>
>
> Cheers Jochen
>
> --
> ETH Zurich
> *Jochen Bick*
> Animal Physiology
> Institute of Agricultural Sciences
> Postal address: Universitätstrasse 2 / LFW B 58.1
> 8092 Zurich, Switzerland
> Office: Eschikon 27
> 8315 Lindau, Switzerland
>
> Phone +41 52 354 92 06
> [hidden email] <mailto:[hidden email]> www.ap.ethz.ch
>
> ___________________________________________________________
> 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/
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 9 Jul 2018 11:36:27 -0400
> From: Martin Čech <[hidden email]>
> To: Peter Briggs <[hidden email]>
> Cc: "[hidden email]"
> <[hidden email]>
> Subject: Re: [galaxy-dev] From Paste to uWSGI
> Message-ID:
> <CAHKBquGXMTog-MUgLbPWD2wgmXvpOxiQGRa4+QCWk5EAHGK3=[hidden email]>
> Content-Type: text/plain; charset="utf-8"
>
> Another recently updated resource for uwsgi is the training slides:
> https://galaxyproject.github.io/dagobah-training/2018-gccbosc/10-uwsgi/uwsgi.html#1
>
> M.
>
> On Mon, Jul 9, 2018 at 11:31 AM Peter Briggs <[hidden email]>
> wrote:
>
>> Hello Jochen
>>
>> I'm not aware of a tutorial but here are some observations from my
>> (very) recent experiences upgrading a local paste-based 17.09 instance
>> to a uwsgi-based 18.05 configuration. It's not comprehensive because
>> the configuration will depend on decisions you need to make based on
>> your local setup, but it might be helpful as a starting point.
>>
>> Before beginning:
>>
>> -- Commit to migrating from galaxy.ini to galaxy.yml (if not done
>> previously)
>>
>> Even though its possible to stick with the old galaxy.ini file, it
>> seems best to move to the new format - my feeling is, probably the
>> migration will have to happen at some point anyway, and also the
>> documentation is more focussed on the newer galaxy.yml version.
>>
>> -- Decide on how you're going to handle job submission (essentially,
>> how you're going to replace the old job handler processes).
>>
>> There are a number of possibilities outlined in the documentation here:
>>
>>
>> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#dep
>> loyment-options
>>
>> It seems important to figure this out at the beginning because it
>> impacts a lot of the configuration specifics that follow. For our
>> setup case "uwsgi
>> + mules" looked like the most appropriate:
>>
>>
>> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uws
>> gi-for-web-serving-with-mules-as-job-handlers
>>
>> Then once you're ready to start (nb backing up the database etc before
>> starting are implicitly assumed!):
>>
>> -- Update the Galaxy source code
>>
>> The standard recipe for this seems to work okay i.e.
>>
>> git fetch origin && git checkout release_18.05 && git pull --ff-only
>> origin release_18.05
>>
>> (You'll probably also need to run scripts/common_startup.sh to update
>> the Python packages, and scripts/manage_db.py to update the database
>> schema.)
>>
>> -- Create galaxy.yml and configure the "galaxy" section:
>>
>> You can make a galaxy.yml from the sample version and go through the
>> "galaxy" section replicating the settings from galaxy.ini. (The
>> settings in the "uwsgi" section can wait at this stage.) Don't forget
>> to move galaxy.ini out of the way once you're done.
>>
>> -- Configure the "uwsgi" section of galaxy.yml:
>>
>> The options for various scenarios are given in the "Deployment/uwsgi"
>> section:
>>
>> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uws
>> gi
>>
>> but the required settings seem to be spread out between different
>> sections so (for me) it felt like it took some piecing together to get
>> it to work when I first tried this.
>>
>> (Also I was thrown a little by the "socket" parameter not having a
>> placeholder in sample galaxy.yml.)
>>
>> The core uwsgi options are here:
>>
>>
>> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#con
>> figuration-common-to-all-uwsgi-deployment-styles
>>
>> then you need to set other options dependent on:
>>
>> 1. how job submission is handled (e.g. options for the "uwsgi + mules"
>> setup in my case)
>> 2. how you're proxying Galaxy (for Apache or nginx it looks like it's
>> just setting the uwsgi "socket" option, unless you're serving Galaxy
>> from a URL prefix in which case there are a few more options needed -
>> these are covered in the documentation.)
>>
>> -- Fix your job_conf.xml file
>>
>> If you have an existing job_conf.xml file in your config directory
>> then you might need to update that too (specifically the "handlers"
>> section) depending on the job submission handling you've decided to use.
>>
>> -- Use supervisor to manage your uwsgi processes
>>
>> The docs for this are here:
>>
>>
>> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#sta
>> rting-and-stopping
>>
>> Essentially supervisor replaces "run.sh", so this becomes how you
>> start and stop Galaxy (e.g. "supervisorctl start galaxy:" replaces
>> "GALAXY_RUN_ALL=1 sh run.sh --daemon".)
>>
>> I think this is quite straightforward from the docs but again you need
>> to tailor it for how you're handling job submission (e.g the "uwsgi + mules"
>> doesn't need any handlers defining, but it looks like other strategies
>> needs extra stuff defining here).
>>
>> -- Set up the proxying
>>
>> Assuming you're proxing via either Apache or nginx (we're using
>> nginx), these are covered in the relevant sections:
>>
>> https://docs.galaxyproject.org/en/release_18.05/admin/apache.html
>> https://docs.galaxyproject.org/en/release_18.05/admin/nginx.html
>>
>> The main difference I noticed for nginx is that you no longer need to
>> use the "upstream"/"proxy_pass" directives, as nginx can talk directly
>> to uwsgi using a "uwsgi_pass" directive that connects to the socket
>> defined in the "uwsgi" section of galaxy.yml previously.
>>
>> (There's also a "gotcha" if you're nginx configuration also tries to
>> serve "static/scripts/packed", which needs to be removed - this is
>> noted in the "breaking changes" for the 18.05 docs but is easy to
>> miss.)
>>
>> Hopefully this is some help. There's lots of documentation, which is a
>> good thing but which can sometimes make it harder to see where to start.
>>
>> Good luck with the update,
>>
>> Best wishes
>>
>> Peter
>>
>> --
>> Peter Briggs [hidden email] Bioinformatics Core
>> Facility University of Manchester
>> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>>
>>
>> ________________________________________
>> From: galaxy-dev [[hidden email]] on
>> behalf of Jochen Bick [[hidden email]]
>> Sent: Monday, July 09, 2018 12:49 PM
>> To: [hidden email]
>> Subject: [galaxy-dev] From Paste to uWSGI
>>
>> Hi all,
>>
>> we would like to update to 18.05 and thereby also update our Paste Server.
>>
>> https://docs.galaxyproject.org/en/latest/admin/scaling.html
>>
>> Is there any tutorial on how to update from Paste to uWSGI?
>>
>>
>> Cheers Jochen
>>
>> --
>> ETH Zurich
>> *Jochen Bick*
>> Animal Physiology
>> Institute of Agricultural Sciences
>> Postal address: Universitätstrasse 2
>> <https://maps.google.com/?q=Universit%C3%A4tstrasse+2&entry=gmail&sour
>> ce=g>
>> / LFW B 58.1
>> 8092 Zurich, Switzerland
>> Office: Eschikon 27
>> 8315 Lindau, Switzerland
>>
>> Phone +41 52 354 92 06 <+41%2052%20354%2092%2006>
>> [hidden email] <mailto:[hidden email]>
>> www.ap.ethz.ch
>>
>> ___________________________________________________________
>> 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/
>> ___________________________________________________________
>> 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/
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20180709/a7d44c29/attachment-0001.html>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> https://lists.galaxyproject.org/listinfo/galaxy-dev
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
> ------------------------------
>
> End of galaxy-dev Digest, Vol 145, Issue 3
> ******************************************
> ___________________________________________________________
> 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/
>
___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Expose Command Line in Galaxy

M_Enders
In reply to this post by M_Enders
Dear Björn,

thanks for the very fast reply. Unfortunately, this part is not visible in our instance. (see screenshot). As you can see in the topmost bar, this is done, while being loged in as admin.

Mit freundlichen Grüßen

Matthias Enders
-----------------------------------------------------------------------


GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

Email: [hidden email]

Firmensitz Köln
Amtsgericht Köln, HRB 73844

-----Ursprüngliche Nachricht-----
Von: Björn Grüning <[hidden email]>
Gesendet: Dienstag, 10. Juli 2018 09:15
An: Matthias Enders <[hidden email]>; [hidden email]
Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy
Priorität: Hoch

Hi Matthias,

please have a look at the attached screenshot. Given that you are an admin and click on the info-symbol of the dataset you should see the commandline.

This is with a 18.05 Docker.
Cheers,
Bjoern

Am 10.07.2018 um 08:58 schrieb Matthias Enders:

> Dear Galaxy Community,
>
> is there any possibility to expose the command line call, generated
> within galaxy?
>
> We searched the net and found this discussions:
> https://github.com/galaxyproject/galaxy/issues/3252
> https://github.com/galaxyproject/galaxy/issues/2954
>
> But both are on the exposure to non-admin users. Within our instance
> we see the command line call nor for admin, neither for normal users!
>
> The problem, behind the question is the error message: "An invalid
> option was selected for database, 'myCoolDatabaseName', please
> verify." In Blast
> (toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrap
> per/0.2.01)
>
>  Local (directly from command line, without Galaxy in between) the
> blast works fine.
>
> We are using the 18.05 Docker Galaxy Version.
>
> Thanks in advance!
>
> Mit freundlichen Grüßen
>
> Matthias Enders
> ----------------------------------------------------------------------
> -
>
>
>
> GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg
> Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: +
> 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360
>
> Email: [hidden email]
>
> Firmensitz Köln Amtsgericht Köln, HRB 73844
>
> -----Ursprüngliche Nachricht----- Von: galaxy-dev
> <[hidden email]> Im Auftrag von
> [hidden email] Gesendet: Montag, 9. Juli
> 2018 18:00 An: [hidden email] Betreff: galaxy-dev
> Digest, Vol 145, Issue 3
>
> Send galaxy-dev mailing list submissions to
> [hidden email]
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email,
> send a message with subject or body 'help' to
> [hidden email]
>
> You can reach the person managing the list at
> [hidden email]
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of galaxy-dev digest..."
>
>
> HEY!  This is important!  If you reply to a thread in a digest, please
> 1. Change the subject of your response from "Galaxy-dev Digest Vol
> ..." to the original subject for the thread. 2. Strip out everything
> else in the digest that is not part of the thread you are responding
> to.
>
> Why? 1. This will keep the subject meaningful.  People will have some
> idea from the subject line if they should read it or not. 2. Not doing
> this greatly increases the number of emails that match search queries,
> but that aren't actually informative.
>
> Today's Topics:
>
> 1. From Paste to uWSGI (Jochen Bick) 2. Re: From Paste to uWSGI (Peter
> Briggs) 3. Re: From Paste to uWSGI (Martin Čech)
>
>
> ----------------------------------------------------------------------
>
>  Message: 1 Date: Mon, 9 Jul 2018 13:49:23 +0200 From: Jochen Bick
> <[hidden email]> To: "[hidden email]"
> <[hidden email]> Subject: [galaxy-dev] From Paste
> to uWSGI Message-ID:
> <[hidden email]> Content-Type:
> text/plain; charset="utf-8"; format=flowed
>
> Hi all,
>
> we would like to update to 18.05 and thereby also update our Paste
> Server.
>
> https://docs.galaxyproject.org/en/latest/admin/scaling.html
>
> Is there any tutorial on how to update from Paste to uWSGI?
>
>
> Cheers Jochen
>
> -- ETH Zurich *Jochen Bick* Animal Physiology Institute of
> Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B
> 58.1 8092 Zurich, Switzerland Office: Eschikon 27 8315 Lindau,
> Switzerland
>
> Phone +41 52 354 92 06 [hidden email]
> <mailto:[hidden email]> www.ap.ethz.ch
>
>
>
> ------------------------------
>
> Message: 2 Date: Mon, 9 Jul 2018 15:31:16 +0000 From: Peter Briggs
> <[hidden email]> To: Jochen Bick
> <[hidden email]>, "[hidden email]"
> <[hidden email]> Subject: Re: [galaxy-dev] From
> Paste to uWSGI Message-ID:
> <[hidden email]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello Jochen
>
> I'm not aware of a tutorial but here are some observations from my
> (very) recent experiences upgrading a local paste-based 17.09 instance
> to a uwsgi-based 18.05 configuration. It's not comprehensive because
> the configuration will depend on decisions you need to make based on
> your local setup, but it might be helpful as a starting point.
>
> Before beginning:
>
> -- Commit to migrating from galaxy.ini to galaxy.yml (if not done
> previously)
>
> Even though its possible to stick with the old galaxy.ini file, it
> seems best to move to the new format - my feeling is, probably the
> migration will have to happen at some point anyway, and also the
> documentation is more focussed on the newer galaxy.yml version.
>
> -- Decide on how you're going to handle job submission (essentially,
> how you're going to replace the old job handler processes).
>
> There are a number of possibilities outlined in the documentation
> here:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#dep
> loyment-options
>
>  It seems important to figure this out at the beginning because it
> impacts a lot of the configuration specifics that follow. For our
> setup case "uwsgi + mules" looked like the most appropriate:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uws
> gi-for-web-serving-with-mules-as-job-handlers
>
>  Then once you're ready to start (nb backing up the database etc
> before starting are implicitly assumed!):
>
> -- Update the Galaxy source code
>
> The standard recipe for this seems to work okay i.e.
>
> git fetch origin && git checkout release_18.05 && git pull --ff-only
> origin release_18.05
>
> (You'll probably also need to run scripts/common_startup.sh to update
> the Python packages, and scripts/manage_db.py to update the database
> schema.)
>
> -- Create galaxy.yml and configure the "galaxy" section:
>
> You can make a galaxy.yml from the sample version and go through the
> "galaxy" section replicating the settings from galaxy.ini. (The
> settings in the "uwsgi" section can wait at this stage.) Don't forget
> to move galaxy.ini out of the way once you're done.
>
> -- Configure the "uwsgi" section of galaxy.yml:
>
> The options for various scenarios are given in the "Deployment/uwsgi"
> section:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uws
> gi
>
>  but the required settings seem to be spread out between different
> sections so (for me) it felt like it took some piecing together to get
> it to work when I first tried this.
>
> (Also I was thrown a little by the "socket" parameter not having a
> placeholder in sample galaxy.yml.)
>
> The core uwsgi options are here:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#con
> figuration-common-to-all-uwsgi-deployment-styles
>
>  then you need to set other options dependent on:
>
> 1. how job submission is handled (e.g. options for the "uwsgi + mules"
> setup in my case) 2. how you're proxying Galaxy (for Apache or nginx
> it looks like it's just setting the uwsgi "socket" option, unless
> you're serving Galaxy from a URL prefix in which case there are a few
> more options needed - these are covered in the
> documentation.)
>
> -- Fix your job_conf.xml file
>
> If you have an existing job_conf.xml file in your config directory
> then you might need to update that too (specifically the "handlers"
> section) depending on the job submission handling you've decided to
> use.
>
> -- Use supervisor to manage your uwsgi processes
>
> The docs for this are here:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#sta
> rting-and-stopping
>
>  Essentially supervisor replaces "run.sh", so this becomes how you
> start and stop Galaxy (e.g. "supervisorctl start galaxy:" replaces
> "GALAXY_RUN_ALL=1 sh run.sh --daemon".)
>
> I think this is quite straightforward from the docs but again you need
> to tailor it for how you're handling job submission (e.g the "uwsgi +
> mules" doesn't need any handlers defining, but it looks like other
> strategies needs extra stuff defining here).
>
> -- Set up the proxying
>
> Assuming you're proxing via either Apache or nginx (we're using
> nginx), these are covered in the relevant sections:
>
> https://docs.galaxyproject.org/en/release_18.05/admin/apache.html
> https://docs.galaxyproject.org/en/release_18.05/admin/nginx.html
>
> The main difference I noticed for nginx is that you no longer need to
> use the "upstream"/"proxy_pass" directives, as nginx can talk directly
> to uwsgi using a "uwsgi_pass" directive that connects to the socket
> defined in the "uwsgi" section of galaxy.yml previously.
>
> (There's also a "gotcha" if you're nginx configuration also tries to
> serve "static/scripts/packed", which needs to be removed - this is
> noted in the "breaking changes" for the 18.05 docs but is easy to
> miss.)
>
> Hopefully this is some help. There's lots of documentation, which is a
> good thing but which can sometimes make it harder to see where to
> start.
>
> Good luck with the update,
>
> Best wishes
>
> Peter
>
> -- Peter Briggs [hidden email] Bioinformatics Core
> Facility University of Manchester B.1083 Michael Smith Bldg Tel:
> (0161) 2751482
>
>
> ________________________________________ From: galaxy-dev
> [[hidden email]] on behalf of Jochen Bick
> [[hidden email]] Sent: Monday, July 09, 2018 12:49 PM To:
> [hidden email] Subject: [galaxy-dev] From Paste to
> uWSGI
>
> Hi all,
>
> we would like to update to 18.05 and thereby also update our Paste
> Server.
>
> https://docs.galaxyproject.org/en/latest/admin/scaling.html
>
> Is there any tutorial on how to update from Paste to uWSGI?
>
>
> Cheers Jochen
>
> -- ETH Zurich *Jochen Bick* Animal Physiology Institute of
> Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B
> 58.1 8092 Zurich, Switzerland Office: Eschikon 27 8315 Lindau,
> Switzerland
>
> Phone +41 52 354 92 06 [hidden email]
> <mailto:[hidden email]> www.ap.ethz.ch
>
> ___________________________________________________________ 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/
>
>
> ------------------------------
>
> Message: 3 Date: Mon, 9 Jul 2018 11:36:27 -0400 From: Martin Čech
> <[hidden email]> To: Peter Briggs <[hidden email]>
> Cc: "[hidden email]"
> <[hidden email]> Subject: Re: [galaxy-dev] From
> Paste to uWSGI Message-ID:
> <CAHKBquGXMTog-MUgLbPWD2wgmXvpOxiQGRa4+QCWk5EAHGK3=[hidden email]>
> Content-Type: text/plain; charset="utf-8"
>
> Another recently updated resource for uwsgi is the training slides:
> https://galaxyproject.github.io/dagobah-training/2018-gccbosc/10-uwsgi
> /uwsgi.html#1
>
>  M.
>
> On Mon, Jul 9, 2018 at 11:31 AM Peter Briggs
> <[hidden email]> wrote:
>
>> Hello Jochen
>>
>> I'm not aware of a tutorial but here are some observations from my
>> (very) recent experiences upgrading a local paste-based 17.09
>> instance to a uwsgi-based 18.05 configuration. It's not comprehensive
>> because the configuration will depend on decisions you need to make
>> based on your local setup, but it might be helpful as a starting
>> point.
>>
>> Before beginning:
>>
>> -- Commit to migrating from galaxy.ini to galaxy.yml (if not done
>> previously)
>>
>> Even though its possible to stick with the old galaxy.ini file, it
>> seems best to move to the new format - my feeling is, probably the
>> migration will have to happen at some point anyway, and also the
>> documentation is more focussed on the newer galaxy.yml version.
>>
>> -- Decide on how you're going to handle job submission (essentially,
>> how you're going to replace the old job handler processes).
>>
>> There are a number of possibilities outlined in the documentation
>> here:
>>
>>
>> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#de
>> p
>>
>>
loyment-options

>>
>> It seems important to figure this out at the beginning because it
>> impacts a lot of the configuration specifics that follow. For our
>> setup case "uwsgi + mules" looked like the most appropriate:
>>
>>
>> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uw
>> s
>>
>>
gi-for-web-serving-with-mules-as-job-handlers

>>
>> Then once you're ready to start (nb backing up the database etc
>> before starting are implicitly assumed!):
>>
>> -- Update the Galaxy source code
>>
>> The standard recipe for this seems to work okay i.e.
>>
>> git fetch origin && git checkout release_18.05 && git pull --ff-only
>> origin release_18.05
>>
>> (You'll probably also need to run scripts/common_startup.sh to update
>> the Python packages, and scripts/manage_db.py to update the database
>> schema.)
>>
>> -- Create galaxy.yml and configure the "galaxy" section:
>>
>> You can make a galaxy.yml from the sample version and go through the
>> "galaxy" section replicating the settings from galaxy.ini.
>> (The settings in the "uwsgi" section can wait at this stage.) Don't
>> forget to move galaxy.ini out of the way once you're done.
>>
>> -- Configure the "uwsgi" section of galaxy.yml:
>>
>> The options for various scenarios are given in the "Deployment/uwsgi"
>> section:
>>
>> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#uw
>> s
>>
>>
gi

>>
>> but the required settings seem to be spread out between different
>> sections so (for me) it felt like it took some piecing together to
>> get it to work when I first tried this.
>>
>> (Also I was thrown a little by the "socket" parameter not having a
>> placeholder in sample galaxy.yml.)
>>
>> The core uwsgi options are here:
>>
>>
>> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#co
>> n
>>
>>
figuration-common-to-all-uwsgi-deployment-styles

>>
>> then you need to set other options dependent on:
>>
>> 1. how job submission is handled (e.g. options for the "uwsgi +
>> mules" setup in my case) 2. how you're proxying Galaxy (for Apache or
>> nginx it looks like it's just setting the uwsgi "socket" option,
>> unless you're serving Galaxy from a URL prefix in which case there
>> are a few more options needed - these are covered in the
>> documentation.)
>>
>> -- Fix your job_conf.xml file
>>
>> If you have an existing job_conf.xml file in your config directory
>> then you might need to update that too (specifically the "handlers"
>> section) depending on the job submission handling you've decided to
>> use.
>>
>> -- Use supervisor to manage your uwsgi processes
>>
>> The docs for this are here:
>>
>>
>> https://docs.galaxyproject.org/en/release_18.05/admin/scaling.html#st
>> a
>>
>>
rting-and-stopping

>>
>> Essentially supervisor replaces "run.sh", so this becomes how you
>> start and stop Galaxy (e.g. "supervisorctl start galaxy:" replaces
>> "GALAXY_RUN_ALL=1 sh run.sh --daemon".)
>>
>> I think this is quite straightforward from the docs but again you
>> need to tailor it for how you're handling job submission (e.g the
>> "uwsgi + mules" doesn't need any handlers defining, but it looks like
>> other strategies needs extra stuff defining here).
>>
>> -- Set up the proxying
>>
>> Assuming you're proxing via either Apache or nginx (we're using
>> nginx), these are covered in the relevant sections:
>>
>> https://docs.galaxyproject.org/en/release_18.05/admin/apache.html
>> https://docs.galaxyproject.org/en/release_18.05/admin/nginx.html
>>
>> The main difference I noticed for nginx is that you no longer need to
>> use the "upstream"/"proxy_pass" directives, as nginx can talk
>> directly to uwsgi using a "uwsgi_pass" directive that connects to the
>> socket defined in the "uwsgi" section of galaxy.yml previously.
>>
>> (There's also a "gotcha" if you're nginx configuration also tries to
>> serve "static/scripts/packed", which needs to be removed - this is
>> noted in the "breaking changes" for the 18.05 docs but is easy to
>> miss.)
>>
>> Hopefully this is some help. There's lots of documentation, which is
>> a good thing but which can sometimes make it harder to see where to
>> start.
>>
>> Good luck with the update,
>>
>> Best wishes
>>
>> Peter
>>
>> -- Peter Briggs [hidden email] Bioinformatics Core
>> Facility University of Manchester B.1083 Michael Smith Bldg Tel:
>> (0161) 2751482
>>
>>
>> ________________________________________ From: galaxy-dev
>> [[hidden email]] on behalf of Jochen Bick
>> [[hidden email]] Sent: Monday, July 09, 2018 12:49 PM To:
>> [hidden email] Subject: [galaxy-dev] From Paste
>> to uWSGI
>>
>> Hi all,
>>
>> we would like to update to 18.05 and thereby also update our Paste
>> Server.
>>
>> https://docs.galaxyproject.org/en/latest/admin/scaling.html
>>
>> Is there any tutorial on how to update from Paste to uWSGI?
>>
>>
>> Cheers Jochen
>>
>> -- ETH Zurich *Jochen Bick* Animal Physiology Institute of
>> Agricultural Sciences Postal address: Universitätstrasse 2
>> <https://maps.google.com/?q=Universit%C3%A4tstrasse+2&entry=gmail&sou
>> r
>>
>>
ce=g>

>> / LFW B 58.1 8092 Zurich, Switzerland Office: Eschikon 27 8315
>> Lindau, Switzerland
>>
>> Phone +41 52 354 92 06 <+41%2052%20354%2092%2006>
>> [hidden email] <mailto:[hidden email]>
>> www.ap.ethz.ch
>>
>> ___________________________________________________________ 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/
>> ___________________________________________________________ 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/
> -------------- next part -------------- An HTML attachment was
> scrubbed... URL:
> <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/2018
> 0709/a7d44c29/attachment-0001.html>
>
>  ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________ galaxy-dev mailing
> list [hidden email]
> https://lists.galaxyproject.org/listinfo/galaxy-dev
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>
> ------------------------------
>
> End of galaxy-dev Digest, Vol 145, Issue 3
> ******************************************
> ___________________________________________________________ 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/
>

___________________________________________________________
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/

bar.png (171K) Download Attachment
| Threaded
Open this post in threaded view
|

Re: Expose Command Line in Galaxy

Peter Cock
There is a setting to enable showing the command line string
and full paths on disk via the "i" icon from a history entry, see

https://docs.galaxyproject.org/en/master/admin/options.html#expose-dataset-path

# This option allows users to see the full path of datasets via the
# "View Details" option in the history. This option also exposes the
# command line to non-administrative users. Administrators can always
# see dataset paths.
#expose_dataset_path: false

https://github.com/galaxyproject/galaxy/blob/release_18.05/config/galaxy.yml.sample#L1495

It existed in galaxy.ini too, which has since be replaced by
galaxy.yml

Peter

On Tue, Jul 10, 2018 at 8:19 AM, Matthias Enders
<[hidden email]> wrote:

> Dear Björn,
>
> thanks for the very fast reply. Unfortunately, this part is not visible in our instance. (see screenshot). As you can see in the topmost bar, this is done, while being loged in as admin.
>
> Mit freundlichen Grüßen
>
> Matthias Enders
> -----------------------------------------------------------------------
>
>
> GERMAN SEED ALLIANCE GmbH
> c/o Norddeutsche Pflanzenzucht
> Hans-Georg Lembke KG
> Hohenlieth, 24363 Holtsee
> Tel.: +49 (0)4351/ 736-189
> Fax: + 49 (0)4351/ 736-271
> Mobil: +49 (0)151/ 14247360
>
> Email: [hidden email]
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
>
> -----Ursprüngliche Nachricht-----
> Von: Björn Grüning <[hidden email]>
> Gesendet: Dienstag, 10. Juli 2018 09:15
> An: Matthias Enders <[hidden email]>; [hidden email]
> Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy
> Priorität: Hoch
>
> Hi Matthias,
>
> please have a look at the attached screenshot. Given that you are an admin and click on the info-symbol of the dataset you should see the commandline.
>
> This is with a 18.05 Docker.
> Cheers,
> Bjoern
>
> Am 10.07.2018 um 08:58 schrieb Matthias Enders:
>> Dear Galaxy Community,
>>
>> is there any possibility to expose the command line call, generated
>> within galaxy?
>>
>> We searched the net and found this discussions:
>> https://github.com/galaxyproject/galaxy/issues/3252
>> https://github.com/galaxyproject/galaxy/issues/2954
>>
>> But both are on the exposure to non-admin users. Within our instance
>> we see the command line call nor for admin, neither for normal users!
>>
>> ...
___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Expose Command Line in Galaxy

M_Enders
Dear all,

finally a restart of the container solved the issue with the database/blast.

Regarding the problem with the command line:
For other tools, the command line showed up, but not for blastn, as the wrapper encountered the error before creating the command line (this is my interpretation).

So the error: "An invalid option was selected for database, 'myCoolDatabaseName', please verify." Was produced by the wrapper, which did not find the new database before restarting the galaxy container.

So the real issue here is perhaps more on "How could blast+ be made aware of new integrated databases, without restarting"?

Mit freundlichen Grüßen

Matthias Enders
-----------------------------------------------------------------------


GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

Email: [hidden email]

Firmensitz Köln
Amtsgericht Köln, HRB 73844

-----Ursprüngliche Nachricht-----
Von: Peter Cock <[hidden email]>
Gesendet: Dienstag, 10. Juli 2018 12:11
An: Matthias Enders <[hidden email]>
Cc: Björn Grüning <[hidden email]>; [hidden email]
Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy

There is a setting to enable showing the command line string and full paths on disk via the "i" icon from a history entry, see

https://docs.galaxyproject.org/en/master/admin/options.html#expose-dataset-path

# This option allows users to see the full path of datasets via the # "View Details" option in the history. This option also exposes the # command line to non-administrative users. Administrators can always # see dataset paths.
#expose_dataset_path: false

https://github.com/galaxyproject/galaxy/blob/release_18.05/config/galaxy.yml.sample#L1495

It existed in galaxy.ini too, which has since be replaced by galaxy.yml

Peter

On Tue, Jul 10, 2018 at 8:19 AM, Matthias Enders <[hidden email]> wrote:

> Dear Björn,
>
> thanks for the very fast reply. Unfortunately, this part is not visible in our instance. (see screenshot). As you can see in the topmost bar, this is done, while being loged in as admin.
>
> Mit freundlichen Grüßen
>
> Matthias Enders
> ----------------------------------------------------------------------
> -
>
>
> GERMAN SEED ALLIANCE GmbH
> c/o Norddeutsche Pflanzenzucht
> Hans-Georg Lembke KG
> Hohenlieth, 24363 Holtsee
> Tel.: +49 (0)4351/ 736-189
> Fax: + 49 (0)4351/ 736-271
> Mobil: +49 (0)151/ 14247360
>
> Email: [hidden email]
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
>
> -----Ursprüngliche Nachricht-----
> Von: Björn Grüning <[hidden email]>
> Gesendet: Dienstag, 10. Juli 2018 09:15
> An: Matthias Enders <[hidden email]>;
> [hidden email]
> Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy
> Priorität: Hoch
>
> Hi Matthias,
>
> please have a look at the attached screenshot. Given that you are an admin and click on the info-symbol of the dataset you should see the commandline.
>
> This is with a 18.05 Docker.
> Cheers,
> Bjoern
>
> Am 10.07.2018 um 08:58 schrieb Matthias Enders:
>> Dear Galaxy Community,
>>
>> is there any possibility to expose the command line call, generated
>> within galaxy?
>>
>> We searched the net and found this discussions:
>> https://github.com/galaxyproject/galaxy/issues/3252
>> https://github.com/galaxyproject/galaxy/issues/2954
>>
>> But both are on the exposure to non-admin users. Within our instance
>> we see the command line call nor for admin, neither for normal users!
>>
>> ...
___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Expose Command Line in Galaxy

Peter Cock
Thanks for getting back to us - this was actually my guess from the
original email - that it was not a blastn error message, but a Galaxy
message before ever calling BLAST.

My guess is you are seeing this issue, or something like it, with
having to restart Galaxy to reload the *.loc files?

https://github.com/galaxyproject/galaxy/issues/3171

Peter

On Tue, Jul 10, 2018 at 12:22 PM, Matthias Enders
<[hidden email]> wrote:

> Dear all,
>
> finally a restart of the container solved the issue with the database/blast.
>
> Regarding the problem with the command line:
> For other tools, the command line showed up, but not for blastn, as the wrapper encountered the error before creating the command line (this is my interpretation).
>
> So the error: "An invalid option was selected for database, 'myCoolDatabaseName', please verify." Was produced by the wrapper, which did not find the new database before restarting the galaxy container.
>
> So the real issue here is perhaps more on "How could blast+ be made aware of new integrated databases, without restarting"?
>
> Mit freundlichen Grüßen
>
> Matthias Enders
___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Expose Command Line in Galaxy

M_Enders

Dear Peter,

 

up to our galaxy admin, we make use of the  Data Manager, so this seems not to be the issue here?:

 

 

 

Mit freundlichen Grüßen

 

Matthias Enders

-----------------------------------------------------------------------

 

 

GERMAN SEED ALLIANCE GmbH

c/o Norddeutsche Pflanzenzucht

Hans-Georg Lembke KG

Hohenlieth, 24363 Holtsee

Tel.: +49 (0)4351/ 736-189

Fax: + 49 (0)4351/ 736-271

Mobil: +49 (0)151/ 14247360

 

Email: [hidden email]

 

Firmensitz Köln

Amtsgericht Köln, HRB 73844

 

-----Ursprüngliche Nachricht-----
Von: Peter Cock <[hidden email]>
Gesendet: Dienstag, 10. Juli 2018 13:27
An: Matthias Enders <[hidden email]>
Cc: Björn Grüning <[hidden email]>; [hidden email]
Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy
Priorität: Hoch

 

Thanks for getting back to us - this was actually my guess from the original email - that it was not a blastn error message, but a Galaxy message before ever calling BLAST.

 

My guess is you are seeing this issue, or something like it, with having to restart Galaxy to reload the *.loc files?

 

https://github.com/galaxyproject/galaxy/issues/3171

 

Peter

 

On Tue, Jul 10, 2018 at 12:22 PM, Matthias Enders <[hidden email]> wrote:

> Dear all,

> 

> finally a restart of the container solved the issue with the database/blast.

> 

> Regarding the problem with the command line:

> For other tools, the command line showed up, but not for blastn, as the wrapper encountered the error before creating the command line (this is my interpretation).

> 

> So the error: "An invalid option was selected for database, 'myCoolDatabaseName', please verify." Was produced by the wrapper, which did not find the new database before restarting the galaxy container.

> 

> So the real issue here is perhaps more on "How could blast+ be made aware of new integrated databases, without restarting"?

> 

> Mit freundlichen Grüßen

> 

> Matthias Enders


___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Expose Command Line in Galaxy

Peter Cock
Is there anything in the Admin's interface to let you reload the BLAST *.loc files?

If yes, did you try it but it didn't work?

What version of Galaxy do you have?

Peter

On Tue, Jul 10, 2018 at 3:11 PM, Matthias Enders <[hidden email]> wrote:

Dear Peter,

 

up to our galaxy admin, we make use of the  Data Manager, so this seems not to be the issue here?:

 

 

 

Mit freundlichen Grüßen

 

Matthias Enders



___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Expose Command Line in Galaxy

M_Enders

Dear Peter,

 

yes we did reload the Blast *.loc files using the admin interface. Our Version is 18.05 (based on the Galaxy – Docker image).

 

Mit freundlichen Grüßen

 

Matthias Enders

-----------------------------------------------------------------------

cid:image001.png@01D03960.8254BEE0

 

GERMAN SEED ALLIANCE GmbH

c/o Norddeutsche Pflanzenzucht

Hans-Georg Lembke KG

Hohenlieth, 24363 Holtsee

Tel.: +49 (0)4351/ 736-189

Fax: + 49 (0)4351/ 736-271

Mobil: +49 (0)151/ 14247360

 

Email: [hidden email]

 

Firmensitz Köln

Amtsgericht Köln, HRB 73844

 

Von: Peter Cock <[hidden email]>
Gesendet: Mittwoch, 11. Juli 2018 16:01
An: Matthias Enders <[hidden email]>
Cc: Björn Grüning <[hidden email]>; [hidden email]
Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy

 

Is there anything in the Admin's interface to let you reload the BLAST *.loc files?

 

If yes, did you try it but it didn't work?

 

What version of Galaxy do you have?

 

Peter

 

On Tue, Jul 10, 2018 at 3:11 PM, Matthias Enders <[hidden email]> wrote:

Dear Peter,

 

up to our galaxy admin, we make use of the  Data Manager, so this seems not to be the issue here?:

 

 

 

Mit freundlichen Grüßen

 

Matthias Enders

 


___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Expose Command Line in Galaxy

Peter Cock
Good. So is everything resolved now?

Peter

On Wed, Jul 11, 2018 at 3:08 PM, Matthias Enders <[hidden email]> wrote:

Dear Peter,

 

yes we did reload the Blast *.loc files using the admin interface. Our Version is 18.05 (based on the Galaxy – Docker image).

 

Mit freundlichen Grüßen

 

Matthias Enders



___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Expose Command Line in Galaxy

M_Enders

Dear Peter,

 

the reloading of the blast *.loc files did not solve the Problem. Actually only a complete restart of the container solved the problem for us.

 

Mit freundlichen Grüßen

 

Matthias Enders

-----------------------------------------------------------------------

cid:image001.png@01D03960.8254BEE0

 

GERMAN SEED ALLIANCE GmbH

c/o Norddeutsche Pflanzenzucht

Hans-Georg Lembke KG

Hohenlieth, 24363 Holtsee

Tel.: +49 (0)4351/ 736-189

Fax: + 49 (0)4351/ 736-271

Mobil: +49 (0)151/ 14247360

 

Email: [hidden email]

 

Firmensitz Köln

Amtsgericht Köln, HRB 73844

 

Von: Peter Cock <[hidden email]>
Gesendet: Mittwoch, 11. Juli 2018 16:12
An: Matthias Enders <[hidden email]>
Cc: Björn Grüning <[hidden email]>; [hidden email]; [hidden email]
Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy

 

Good. So is everything resolved now?

 

Peter

 

On Wed, Jul 11, 2018 at 3:08 PM, Matthias Enders <[hidden email]> wrote:

Dear Peter,

 

yes we did reload the Blast *.loc files using the admin interface. Our Version is 18.05 (based on the Galaxy – Docker image).

 

Mit freundlichen Grüßen

 

Matthias Enders

 


___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Expose Command Line in Galaxy

Peter Cock
You may have found a new Galaxy bug then :(

Could you log an issue here:

https://github.com/galaxyproject/galaxy/issues

(From what you've said, I don't think that this is a problem in the
BLAST+ wrappers themselves)

Peter

On Wed, Jul 11, 2018 at 3:20 PM, Matthias Enders <[hidden email]> wrote:

Dear Peter,

 

the reloading of the blast *.loc files did not solve the Problem. Actually only a complete restart of the container solved the problem for us.

 

Mit freundlichen Grüßen

 

Matthias Enders


___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Expose Command Line in Galaxy

M_Enders

Dear Peter,

 

we will re-create this problem with a new database in our instance, (to be sure on the reproducibility) and then raise an issue.

 

Mit freundlichen Grüßen

 

Matthias Enders

-----------------------------------------------------------------------

cid:image001.png@01D03960.8254BEE0

 

GERMAN SEED ALLIANCE GmbH

c/o Norddeutsche Pflanzenzucht

Hans-Georg Lembke KG

Hohenlieth, 24363 Holtsee

Tel.: +49 (0)4351/ 736-189

Fax: + 49 (0)4351/ 736-271

Mobil: +49 (0)151/ 14247360

 

Email: [hidden email]

 

Firmensitz Köln

Amtsgericht Köln, HRB 73844

 

Von: Peter Cock <[hidden email]>
Gesendet: Mittwoch, 11. Juli 2018 16:42
An: Matthias Enders <[hidden email]>
Cc: Björn Grüning <[hidden email]>; [hidden email]; [hidden email]
Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy

 

You may have found a new Galaxy bug then :(

 

Could you log an issue here:

 

https://github.com/galaxyproject/galaxy/issues

 

(From what you've said, I don't think that this is a problem in the

BLAST+ wrappers themselves)

 

Peter

 

On Wed, Jul 11, 2018 at 3:20 PM, Matthias Enders <[hidden email]> wrote:

Dear Peter,

 

the reloading of the blast *.loc files did not solve the Problem. Actually only a complete restart of the container solved the problem for us.

 

Mit freundlichen Grüßen

 

Matthias Enders


___________________________________________________________
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/