Problems installing Galaxy 18.01
by Peter van Heusden
Hi there
My newly installed Galaxy 18.01 server seems to be unable to install bowtie
(the devteam version). I'm documenting my installation progress at:
http://pvh.wp.sanbi.ac.za/2018/03/18/galaxy-18-01-install/
As noted in the last paragraph:
"My next test was to try and install the bowtie2 tool from the toolshed.
This failed, with the tool status going from New to Error with not much
interesting left in the logs."
The log during the time when I'm trying to install bowtie2 is:
1. [pid: 8856|app: 0|req: 35/48] 10.8.0.2 () {48 vars in 1108 bytes} [Sun
Mar 18 19:14:55 2018] GET
/admin_toolshed/manage_repository?id=f597429621d6eb2b&operation=install =>
generated 650 bytes in 26 msecs (HTTP/1.1 302) 3headers in 269
bytes (1 switches
on core 1)
2. 10.8.0.2 - - [18/Mar/2018:19:14:57 +0000] "GET
/admin_toolshed/manage_repository?id=f597429621d6eb2b&operation=install
HTTP/1.1" 302 - "
https://galaxy.sanbi.ac.za/admin_toolshed/manage_repository?id=f597429621..."
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/65.0.3325.146 Safari/537.36"
3. [pid: 8856|app: 0|req: 37/49] 10.8.0.2 () {48 vars in 1108 bytes} [Sun
Mar 18 19:14:57 2018] GET
/admin_toolshed/manage_repository?id=f597429621d6eb2b&operation=install =>
generated 650 bytes in 24 msecs (HTTP/1.1 302) 3headers in 269
bytes (1 switches
on core 0)
4. galaxy.tools.deps DEBUG 2018-03-18 19:14:59,375 [p:8856,w:2,m:0] [
uWSGIWorker2Core2] Dependency bowtie2 not found.
5. galaxy.tools.deps DEBUG 2018-03-18 19:14:59,376 [p:8856,w:2,m:0] [
uWSGIWorker2Core2] Dependency samtools not found.
6. galaxy.tools.deps DEBUG 2018-03-18 19:15:00,028 [p:8856,w:2,m:0] [
uWSGIWorker2Core3] Dependency bowtie2 not found.
7. galaxy.tools.deps DEBUG 2018-03-18 19:15:00,028 [p:8856,w:2,m:0] [
uWSGIWorker2Core3] Dependency samtools not found.
8. 10.8.0.2 - - [18/Mar/2018:19:14:55 +0000] "GET
/admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12&repository_ids=126c0918b5459666&tool_shed_url=https%3A%2F%
2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - "
https://galaxy.sanbi.ac.za/admin_toolshed/manage_repository?id=f597429621..."
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/65.0.3325.146 Safari/537.36"
9. [pid: 8856|app: 0|req: 38/50] 10.8.0.2 () {48 vars in 1274 bytes} [Sun
Mar 18 19:14:55 2018] GET
/admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12&repository_ids=126c0918b5459666&tool_shed_url=https%3A%2F%
2Ftoolshed.g2.bx.psu.edu%2F => generated 19062 bytes in 7001 msecs (HTTP/
1.1 200) 2 headers in 73 bytes (1 switches on core 2)
10. 10.8.0.2 - - [18/Mar/2018:19:14:57 +0000] "GET
/admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12&repository_ids=126c0918b5459666&tool_shed_url=https%3A%2F%
2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 200 - "
https://galaxy.sanbi.ac.za/admin_toolshed/manage_repository?id=f597429621..."
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/65.0.3325.146 Safari/537.36"
11. [pid: 8856|app: 0|req: 38/51] 10.8.0.2 () {48 vars in 1274 bytes} [Sun
Mar 18 19:14:57 2018] GET
/admin_toolshed/prepare_for_install?changeset_revisions=dc1639b66f12&repository_ids=126c0918b5459666&tool_shed_url=https%3A%2F%
2Ftoolshed.g2.bx.psu.edu%2F => generated 19062 bytes in 5987 msecs (HTTP/
1.1 200) 2 headers in 73 bytes (1 switches on core 3)
12. galaxy.tools.toolbox.base DEBUG 2018-03-18 19:15:14,128 [p:8846,w:1
,m:0] [uWSGIWorker1Core1] Appending to tool panel section: Get Data
13. galaxy.tools.toolbox.base DEBUG 2018-03-18 19:15:14,143 [p:8846,w:1
,m:0] [uWSGIWorker1Core1] Appending to tool panel section: Get Data
14. 10.8.0.2 - - [18/Mar/2018:19:15:11 +0000] "POST
/admin_toolshed/prepare_for_install HTTP/1.1" 200 - "
https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install?changeset_r..."
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/65.0.3325.146Safari/537.36"
15. [pid: 8846|app: 0|req: 14/52] 10.8.0.2 () {56 vars in 1329 bytes} [Sun
Mar 18 19:15:11 2018] POST /admin_toolshed/prepare_for_install =>
generated 11133 bytes in 2509 msecs (HTTP/1.1 200) 2 headers in 73 bytes
(1 switches on core 1)
16. galaxy.tools.toolbox.base DEBUG 2018-03-18 19:15:15,296 [p:8856,w:2
,m:0] [uWSGIWorker2Core1] Appending to tool panel section: Get Data
17. 10.8.0.2 - - [18/Mar/2018:19:15:15 +0000] "POST
/admin_toolshed/install_repositories HTTP/1.1" 200 - "
https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install" "Mozilla/
5.0 (X11; Linux x86_64) AppleWebKit/537.36(KHTML, like Gecko) Chrome/65.0
.3325.146 Safari/537.36"
18. [pid: 8856|app: 0|req: 39/53] 10.8.0.2 () {54 vars in 1152 bytes} [Sun
Mar 18 19:15:15 2018] POST /admin_toolshed/install_repositories =>
generated 20 bytes in 206 msecs (HTTP/1.1 200) 2 headers in 73
bytes (1 switches
on core 1)
19. 10.8.0.2 - - [18/Mar/2018:19:15:18 +0000] "POST
/admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "
https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install" "Mozilla/
5.0 (X11; Linux x86_64)AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0
.3325.146 Safari/537.36"
20. [pid: 8856|app: 0|req: 40/54] 10.8.0.2 () {54 vars in 1208 bytes} [Sun
Mar 18 19:15:18 2018] POST
/admin_toolshed/repository_installation_status_updates => generated
174 bytes
in 17 msecs (HTTP/1.1 200) 4 headers in 110bytes (1 switches on core 2)
21. 10.8.0.2 - - [18/Mar/2018:19:15:21 +0000] "POST
/admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "
https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install" "Mozilla/
5.0 (X11; Linux x86_64)AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0
.3325.146 Safari/537.36"
22. [pid: 8856|app: 0|req: 41/55] 10.8.0.2 () {54 vars in 1208 bytes} [Sun
Mar 18 19:15:21 2018] POST
/admin_toolshed/repository_installation_status_updates => generated 2 bytes
in 14 msecs (HTTP/1.1 200) 4 headers in 110 bytes (1 switches on core 3)
23. 10.8.0.2 - - [18/Mar/2018:19:15:24 +0000] "POST
/admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "
https://galaxy.sanbi.ac.za/admin_toolshed/prepare_for_install" "Mozilla/
5.0 (X11; Linux x86_64)AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0
.3325.146 Safari/537.36"
24. [pid: 8846|app: 0|req: 15/56] 10.8.0.2 () {54 vars in 1208 bytes} [Sun
Mar 18 19:15:24 2018] POST
/admin_toolshed/repository_installation_status_updates => generated 2 bytes
in 27 msecs (HTTP/1.1 200) 4 headers in 110 bytes (1 switches on core 3)
which doesn't seem terribly informative.
Any ideas?
Thanks!
Peter
1 year, 11 months
FileZilla not working
by Antara Biswas
Dear galaxy team,
I am having trouble since a week uploading data from local computer into FileZilla using FTP for transfer to galaxy server. Error message says- connection refused by server. Please help.
My login id is ab3(a)nibmg.ac.in
Thanks
Antara Biswas
Research Fellow
National Institute of Biomedical Genomics
India
1 year, 11 months
Release of Galaxy 18.01
by Martin Čech
Dear Galaxy Fans,
The release of Galaxy 18.01 is out. Thanks to the Galaxy committers and
you, our community!
Full release notes:
https://docs.galaxyproject.org/en/release_18.01/releases/18.01_announce.html
*Highlights:*
*Performance and User Experience Improvements*
We made Galaxy more lively and responsive. Homepage, published workflows,
published/saved histories, and data libraries should all load much faster
now. Importing data from FTP will also take less of your time.
*Web Server and Configuration*
The default web server used by Galaxy has changed from Paste to uWSGI and
the default configuration file for Galaxy is now config/galaxy.yml instead
of config/galaxy.ini. To minimize the impact of this change on existing
Galaxy instances, if a Galaxy has a galaxy.ini file configured, it will
continue to use Paste by default unless additional steps are taken by the
administrator
*Dataset Collection Usability*
This release has significantly improved the usability of Galaxy dataset
collections. Dozens of improvements to collections have been made, some of
the key highlights include:
* Data library folders can now be sent to histories as a dataset collection.
* Failed dataset collection elements can now be fixed using job re-running
* Collections now appear with state and progress bars in the history panel
and contained datasets are hidden by default
* We added intuitive workflow post job actions for dataset collections
* The web interface now supports collections with arbitrary nesting and size
* More robust nametag discovery and propagation when using collections
*Client Architecture*
The architecture for the client code that powers the Galaxy user interface
has been significantly overhauled. The code base has been converted to ES6,
Yarn now powers the build and dependency management of the code, Prettier
is now used to ensure consistent code formatting, and the VueJS framework
has been integrated.
*New BAM datatypes*
Previously Galaxy only supported coordinate sorted BAM files by default
(the bam datatype). In addition, this release of Galaxy now supports three
new types of BAM:
* qname_sorted.bam, that ensures that the file is queryname sorted (e.g.
SO:queryname);
* qname_input_sorted.bam, that can be used to describe the output of
aligners which generally keep mate pairs adjacent
* unsorted.bam, that makes no assumptions about the sort order of the file.
*Experimental Job Caching*
Galaxy can now be configured to allow users the option of skipping
duplicated jobs if one with identical parameters has been previously
executed and simply reuse the previously generated outputs.
Thanks for using Galaxy!
http://galaxyproject.org
1 year, 11 months
tool dependencies
by Matthias Bernt
Hi all,
I tried to install velvetoptimizer (for the assembly tutorial in the GTN).
It lists velvetoptimiser as requirement in the main xml and the
tool_dependencies.xml (listing the installation steps). Now there seems
to be a conda package perl-velvetoptimiser.
What would be the steps to to update the tool (I would happily create a
PR)? Is the tool_dependencies.xml intended to be kept and I just need to
update the names of the requirements (I guess the name in the
tool_dependencies.xml does not matter)?
Furthermore the tool_dependencies.xml includes the package_velvet which
is listed as missing dependency in the management pages. Shouldn't this
be ignored if there is a conda package?
Last question: Is it possible to update an installed package by editing
the xml files? It seemed to me that changes do not have an effect.
Cheers,
Matthias
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt(a)ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
1 year, 11 months
March Galaxy News: GCCBOSC oral presentations due in 2 weeks, plus lots more
by Dave Clements
Hello all,
The March 2018 Galaxy News
<https://galaxyproject.org/galaxy-updates/2018-03/> brings more news than
usual, with much of it about upcoming meetings, including GCCBOSC, and
continental meetings in Europe and Africa.
- *Lots* of GCCBOSC 2018 news
<https://galaxyproject.org/galaxy-updates/2018-03/#gccbosc-2018>:
- Abstract submission, registration & housing are open
<https://galaxyproject.org/galaxy-updates/2018-03/#abstract-submission-reg...>
- *Oral presentation abstracts due March 16
<https://easychair.org/conferences/?conf=gccbosc2018>*
- Training Schedule set
<https://galaxyproject.org/galaxy-updates/2018-03/#training-schedule-set>
- 17 topics in 22 sessions over two days covering the full
spectrum of open source bioinformatics
- We are pleased to announce two of the keynote speakers
<http://localhost:8080/galaxy-updates/2018-03/#keynote-speakers>:
- Fernando Pérez, of the Berkeley Institute for Data Science,
University of California Berkeley and Project Jupyter
- Tracy K. Teal, of the Carpentries and the *Journal for Open
Scource Software*
- Sponsors
<https://galaxyproject.org/galaxy-updates/2018-03/#gccbosc-2018-sponsors>
:
- F1000Research
<https://galaxyproject.org/galaxy-updates/2018-03/#f1000research>
- Technology Association of Oregon
<https://galaxyproject.org/galaxy-updates/2018-03/#technology-association-...>
- Call for sponsors
<https://galaxyproject.org/galaxy-updates/2018-03/#call-for-sponsors>
- *Continental* community meetings:
- *Europe, 14-16 March, Freiburg*
<https://galaxyproject.org/galaxy-updates/2018-03/#elixir-galaxy-community...>
- *Africa, 3-5 April, Cape Town*
<https://galaxyproject.org/galaxy-updates/2018-03/#galaxy-africa-3-5-april...>
- Apply for a Conference Fellowship
<https://galaxyproject.org/galaxy-updates/2018-03/#conference-fellowships>
*by 10 March*.
- Upcoming events
<https://galaxyproject.org/galaxy-updates/2018-03/#upcoming-events> (on
four continents)
- New:
- Galactic Blog post from Arun Decano: Coding in the Winter
Wonderland: Galaxy Admin Training
<https://galaxyproject.org/galaxy-updates/2018-03/#new-galactic-blog-entry...>
- 133 publications
<https://galaxyproject.org/galaxy-updates/2018-03/#publications>
(including
5 highlighted ones)
- Openings in 6 groups on 2 continents
<https://galaxyproject.org/galaxy-updates/2018-03/#whos-hiring>
- Public Galaxy Server News
<https://galaxyproject.org/galaxy-updates/2018-03/#public-galaxy-server-news>
(a new server and two updated ones)
- ToolShed contributions
<https://galaxyproject.org/galaxy-updates/2018-03/#toolshed-contributions>
- Releases
<https://galaxyproject.org/galaxy-updates/2018-03/#releases> of
Planemo, Pulsar, and galaxy-lib.
- And other news
<https://galaxyproject.org/galaxy-updates/2018-03/#other-news> too
See the newsletter <https://galaxyproject.org/galaxy-updates/2018-03/> for
more.
Hope to see you in Freiburg, Cape Town, and Portland!
Dave C
--
https://gccbosc2018.sched.com/
https://galaxyproject.org/
https://usegalaxy.org/
1 year, 11 months
Re: [galaxy-dev] Shiny in Galaxy
by Yvan Le Bras
Dear Mohamed,
Following exchanges with Hans and french colleagues as William from the carpem project (university hospital Georges Pompidou), we have finalized a first gie shiny template for Galaxy-E project. You can refer to the GitHub repo for details, don't hesitate to ask more info...https://github.com/65MO/Galaxy-E/tree/master/GIE
Cheers,.Yvan
Envoyé depuis mon smartphone Samsung Galaxy.
-------- Message d'origine --------De : Mohamed Kassam <k.mamoud(a)gmail.com> Date : 14/03/2018 09:59 (GMT+01:00) À : Hans-Rudolf Hotz <hrh(a)fmi.ch> Cc : Yvan Le Bras <yvan.le-bras(a)mnhn.fr>, "Md. Rezaul Karim" <rezaul.karim(a)insight-centre.org>, Timothée VIRGOULAY <timothee.virgoulay(a)mnhn.fr>, Valentin CHAMBON <valentin.chambon(a)mnhn.fr>, Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Objet : Re: [galaxy-dev] Shiny in Galaxy
Dear all
I am contacting about the shiny integration into the Galaxy framewrok.
Now, we are running a shiny app outside the Galaxy framework and we are pointing a link in the Galaxy tools that allow the user to open another browser for the use of the shiny app.
Howerver we would like to integrate directly the shiny into Galaxy framewrok, and I would like to know if someone find a solution for doing that.
Best regards
Mohamed
2017-07-11 13:57 GMT+02:00 Hans-Rudolf Hotz <hrh(a)fmi.ch>:
Hi Yvan
Yes, after an additional week in the South of France, we traveled back safely last weekend.
I use the free version of the shiny server. In addition to what you already have mentioned, we run into another 'feature' of the free version: you cannot set the R path. You need to set the R path in the environment of the user, the shiny server is running as.
I am currently not using IE, since I cannot use Docker in our production environment. Hence the detour via an html page linking to the extra shiny server. Maybe this will change with Singularity in the future......
Using IE is definitively the way forward.
Regards, Hans-Rudolf
On 07/06/2017 10:58 PM, Yvan Le Bras wrote:
Hi Hans, Hi everyone,
I hope your return trip from GCC has been safe! Unfortunately, I didn't take time during gcc to see you Quick and dirty solution... Can we go further on this Shiny / Galaxy integration idea ? It seems that the Shiny licence can be a problem but it appears to me, if I don't make a mistake, that using the open source version of Shiny (without ssl and identification) on Galaxy through IE can be sufficent... no ?
Cheers,
Yvan
----- Mail d'origine -----
De: Hans-Rudolf Hotz <hrh(a)fmi.ch>
À: Yvan Le Bras <yvan.le-bras(a)mnhn.fr>, Md. Rezaul Karim <rezaul.karim(a)insight-centre.org>, Mohamed Kassam <k.mamoud(a)gmail.com>, Timothée VIRGOULAY <timothee.virgoulay(a)mnhn.fr>, Valentin CHAMBON <valentin.chambon(a)mnhn.fr>
Cc: Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org>
Envoyé: Mon, 29 May 2017 09:39:10 +0200 (CEST)
Objet: Re: [galaxy-dev] Shiny in Galaxy
Hi Yvan and list
This is great news!
In my limited spare time, I am currently playing with shiny as well. My
current 'quick and dirty' trick goes like this:
The galaxy tool creates a new shiny app and the output of the galaxy
tool is a html page with the URL to the shiny app. I hope, I will have
something ready to show/discuss at GCC
Regards, Hans-Rudolf
On 05/26/2017 04:13 PM, Yvan Le Bras wrote:
Dear Mohamed, Karim, galaxy-dev list,
A rapid e-mail to inform you that we plan to work on this task in the
upcoming weeks with Thimothée and Valentin, copied. We have had some
exchanges with Eric (Rasche) and Björn (Grüning) and it seems that using
the Galaxy "interactive environment" functionality is a good way to
proceed. Don't hesitate to give us more informations to collaborate on
it...
Wishing you a good week end.
Cheers,
Yvan
-------- Message d'origine --------
De : "Md. Rezaul Karim" <rezaul.karim(a)insight-centre.org>
Date : 26/05/2017 15:45 (GMT+01:00)
À : Mohamed Kassam <k.mamoud(a)gmail.com>
Cc : Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org>
Objet : Re: [galaxy-dev] Shiny in Galaxy
+1
On May 26, 2017 2:44 PM, "Mohamed Kassam" <k.mamoud(a)gmail.com
<mailto:k.mamoud@gmail.com>> wrote:
Dear all,
I have a shiny application working in my RStudio, but I would like
to integrate it to Galaxy that the users can call my application via
Galaxy .
Thanks in Advance,
Mohamed
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
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https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/ <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:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/
1 year, 11 months
Re: [galaxy-dev] Shiny in Galaxy
by Yvan Le Bras
Dear Mohamed, Karim, galaxy-dev list,
A rapid e-mail to inform you that we plan to work on this task in the upcoming weeks with Thimothée and Valentin, copied. We have had some exchanges with Eric (Rasche) and Björn (Grüning) and it seems that using the Galaxy "interactive environment" functionality is a good way to proceed. Don't hesitate to give us more informations to collaborate on it...
Wishing you a good week end.
Cheers,
Yvan
-------- Message d'origine --------
De : "Md. Rezaul Karim" <rezaul.karim(a)insight-centre.org>
Date : 26/05/2017 15:45 (GMT+01:00)
À : Mohamed Kassam <k.mamoud(a)gmail.com>
Cc : Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org>
Objet : Re: [galaxy-dev] Shiny in Galaxy
+1
On May 26, 2017 2:44 PM, "Mohamed Kassam" <k.mamoud(a)gmail.com> wrote:
Dear all,
I have a shiny application working in my RStudio, but I would like to integrate it to Galaxy that the users can call my application via Galaxy .
Thanks in Advance,
Mohamed
___________________________________________________________
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/
1 year, 11 months
Error during FASTQ preview
by Previti
Dear all,
I've recently had following error occur on our local Galaxy instance.
Every time I want to preview a fastq file it gives this:
Content Encoding Error
The page you are trying to view cannot be shown because it uses an
invalid or unsupported form of compression.
Please contact the website owners to inform them of this problem.
Any idea how to solve this...? This is the first time I'm seeing it....I
tried changing the data type multiple times (fastq, fastq.gz,
fastqsanger...etc) but this doesn't get rid of it.
Best regards,
Christopher Previti
--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661
christopher.previti(a)dkfz.de <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>
Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537
Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.
1 year, 11 months
API Access and User Impersonation
by John Letaw
Hi all,
We have a system in place that sends jobs to a compute cluster based on the real user name, as opposed to something like ‘galaxyuser’. Galaxy workflows are created and invoked using bioblend code, so the users don’t have to go in and manually set workflow inputs. However, this means each user needs admin access in order to create these workflows via API.
Additionally, we have one or two actual admin users that are charged with fixing the occasional workflow problem that pops up. The ability to impersonate users is super helpful in this situation, as you might imagine. So, I’m stuck in this situation where I’d rather not have MOST users with impersonate access. I don’t know of any way to do this, do you? With our setup, can anyone recommend an alternate configuration that would close this security hole? How hard is it to feed a list on email address to the user impersonation config variable?
Thanks,
John
1 year, 11 months
