Re: [galaxy-dev] good practice for Galaxy admin and updates ?

Hi Julie We do something similar, I have described it here: https://galaxyproject.org/admin/ten-simple-steps-galaxy-as-a-service/#rule-10-keep-the-galaxy-software-and-yourself-up-to-date Regards, Hans-Rudolf On 09/03/2018 01:19 PM, julie dubois wrote: Hi Galaxy Community, I manage a

Re: [galaxy-dev] Setting up Galaxy Reports

he stats, but looks very basic and the appropriate style-sheets are probably not found... Any advise on how to set this up properly would be very welcome. Best regards, Christopher On 08/17/2017 04:56 PM, Hans-Rudolf Hotz wrote: Hi Evan I assume you are talking about the 'reports' tool? Have a look he

[galaxy-dev] European Galaxy Days, 19/20 November 2018 in Freiburg, Germany.

Dear all We are happy to announce the European Galaxy Days which will be held 19 and 20 November 2018 in Freiburg, Germany. https://galaxyproject.org/events/2018-europe-dev/ Similar to the events we organized in 2016, 2014 and 2012 the aim is to discuss the status of the Galaxy project,

Re: [galaxy-dev] Expose Command Line in Galaxy

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

Re: [galaxy-dev] MySQL errors and warnings with a fresh install of Galaxy 18-05

Hi Fred Sorry, I don't have an answer I am just wondering: If you start from 'scratch', why don't you use PostgreSQL? Regards, Hans-Rudolf On 06/13/2018 05:41 PM, SAPET, Frederic wrote: Hi, I try to install galaxy 18-05. My database backend is MysqL (5.7.11-4 Percona Server) I start

Re: [galaxy-dev] problem with Visualization 'Scatterplot' in 18.05

On 08/06/18 14:57, Hans-Rudolf Hotz wrote: > > just adding a little bit more information: > > - this problem happens independent of using paste or uwsgi > > - as far as I have tested all visualization plugins (with the > exception of tracks

Re: [galaxy-dev] problem with Visualization 'Scatterplot' in 18.05

'load' not found" Regards, Hans-Rudolf On 06/05/2018 05:14 PM, Hans-Rudolf Hotz wrote: Hi all I am in the process of upgrading our servers to 18.05. And I have encountered an issue with the Visualization tool "Scatterplot, Creates a 2D-scatterplot from tabular datapoints&

[galaxy-dev] problem with Visualization 'Scatterplot' in 18.05

visualization just has an eye (see: 'usegalaxy.eu.png') I hope there is an easy fix for this Regards, Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 40

Re: [galaxy-dev] Galaxy Cleanup

Hi Christopher It depends on the setting of "cleanup_job" ('always', 'onsuccess', 'never'), whether the temporary files are cleaned up or not. Though, to be honest, I don't know, if this setting as any influence, when you 'delete' a job. For the quotas, only dataset in the histories are

Re: [galaxy-dev] Galaxy v17.09 impersonation doesn't work

) allow_user_impersonation = True We use CAS authentication and our database is Postgresql. Our current Galaxy is v15.07 and impersonation works well. I have tried v16.10 before and impersonation didn't work either. Thanks, Ping On Tue, Dec 19, 2017 at 5:12 AM, Hans-Rudolf Hotz <h...@fmi.ch <ma

Re: [galaxy-dev] Galaxy v17.09 impersonation doesn't work

Hi Ping The 'impersonate a user' function works for me with v17.09. I assume, you have set: "allow_user_impersonation = True" in the galaxy.ini file? Do you encounter this problem, for the first time, i.e did it work before using (v17.05 or earlier) and you only have the issues after

Re: [galaxy-dev] Network errors when downloading files

Hi Liam does it happen with every file? on every browser? for every user? what happens when you try to download a file from usegalaxy.org ? to me this sounds like an issue with the proxy settings. Something you need to discuss with your sys admin Regards, Hans-Rudolf On 12/13/2017 09:56

Re: [galaxy-dev] Dynamic Tool UI based on script

will need once executed. Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy On 24 Nov 2017, at 6:52 pm, Hans-Rudolf Hotz <h...@fmi.ch <mailto:h...@fmi.ch>> wrote: Hi Evan Yes, this is possible with "dynamic_options"

Re: [galaxy-dev] Dynamic Tool UI based on script

University http://web.science.mq.edu.au/~cassidy On 24 Nov 2017, at 6:52 pm, Hans-Rudolf Hotz <h...@fmi.ch <mailto:h...@fmi.ch>> wrote: Hi Evan Yes, this is possible with "dynamic_options" e.g.: 2017 2016 2015 ... ...

[galaxy-dev] broken after upgrade to 17.09 : uploading files via the API

Dear All If I execute the following command: python import_with_dbkey.py *** file.bam hg19sub the bam files will be added to the user's history the code (import_with_dbkey.py) is as follows: import sys sys.path.append('***/bioblend-0.10.0-py2.7.egg')

Re: [galaxy-dev] the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.end...@german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844 -Ursprüngliche Nachricht- Von: Hans-Rudolf Hotz [mailto:h...@fmi.ch] Gesendet: Dienstag, 17. Oktober 2017 16:50 An: Matthias Enders <m.end...@german-seed-alliance

Re: [galaxy-dev] the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

+49 (0)151/ 14247360 Email: m.end...@german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844 -Ursprüngliche Nachricht----- Von: Hans-Rudolf Hotz [mailto:h...@fmi.ch] Gesendet: Dienstag, 17. Oktober 2017 10:33 An: Matthias Enders <m.end...@german-seed-alliance.de>; galaxy-d

[galaxy-dev] the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

Hi Matthias We had a Birds of a Feather session about (the future of) Trackster at the recent galaxy community conference in Montpellier. Though, as far as I know (I might be wrong), this didn't result in any no active development on the Trackster code. What kind of functionality do you

Re: [galaxy-dev] upload file format is data - type not recognized in galaxy

Hi Pavel what happens if you connect your galaxy instance to an empty PostgreSQL database, let galaxy build all the tables and then try to upload files. Regards, Hans-Rudolf On 09/22/2017 10:51 AM, Pavel Fibich wrote: Hello, do you have any idea why my galaxy 16.07 stop recognizing

Re: [galaxy-dev] Monitoring Dashboard for Galaxy

Hi Evan I assume you are talking about the 'reports' tool? Have a look here: https://galaxyproject.org/admin/usage-reports/ https://docs.galaxyproject.org/en/latest/admin/reports.html Additional (system) information about each executed job can be logged by activating plugins in the

Re: [galaxy-dev] galaxy-tours : putting the box next to the preview display

with a little detour via twitter - this is the solution: element: "#current-history-panel > ul.list-items > div:nth-child(1) .dataset-peek table" Many Thanks to William Durand for providing the solution! Hans-Rudolf On 07/27/2017 12:15 PM, Hans-Rudolf Hotz wrote:

[galaxy-dev] galaxy-tours : putting the box next to the preview display

bol. What do I have to write as 'element' in order to get the box pointing to the actual preview data (i.e. the white box)? Thank you very much for your help Regards, Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Bio

Re: [galaxy-dev] Shiny in Galaxy

-Rudolf Hotz <h...@fmi.ch> À: Yvan Le Bras <yvan.le-b...@mnhn.fr>, Md. Rezaul Karim <rezaul.ka...@insight-centre.org>, Mohamed Kassam <k.mam...@gmail.com>, Timothée VIRGOULAY <timothee.virgou...@mnhn.fr>, Valentin CHAMBON <valentin.cham...@mnhn.fr

Re: [galaxy-dev] AD Intergration

9:26:34 -0400] "POST /user/login?use_panels=False HTTP/1.1" 200 - "http://glxlcdcpvm01.nyumc.org:8080/user/login?use_panels=False; "Mozilla/5.0 (Windows NT 10.0; WOW64; rv:53.0) Gecko/20100101 Firefox/53.0" ---

Re: [galaxy-dev] AD Intergration

always keep the mailing list in the loop! in order for others to help or learn On 06/08/2017 07:27 PM, John Chen wrote: Hans-Rudolf This is the error I get when I start the Galaxy server. ... xml.etree.ElementTree.ParseError: mismatched tag: line 8, column 105 This is very

Re: [galaxy-dev] AD Intergration

Hi John I am trying to integrate AD with Galaxy. My auth_config.xml look like the below, but galaxy won't start with those setting. what error do you get in the log? activedirectory This should be "ldap", shlouldn't-it? Regards, Hans-Rudolf

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

Re: [galaxy-dev] python subprocess OSError when running bwa-mem

put such path setting scripts into run.sh? yes, at least for samtools, I guess this is currently the best option. Regards, Hans-Rudolf Best, Georgios On 05/22/2017 08:11 AM, Hans-Rudolf Hotz wrote: Hi Georgios I am just guessing here, but the error looks familiar: Do you have samtools

Re: [galaxy-dev] python subprocess OSError when running bwa-mem

Hi Georgios I am just guessing here, but the error looks familiar: Do you have samtools installed? and is it in $PATH? (for a similar case, see: https://biostar.usegalaxy.org/p/19938/ ) Regards, Hans-Rudolf On 05/19/2017 10:03 AM, Georgios Nikolis wrote: Dear all, we are currently working

Re: [galaxy-dev] LDAP group data synchronization

Hi Matthias This is great! Thank you very much for sharing this with the community. I hope I will find time to test this with our server soon. Regards, Hans-Rudolf On 03/30/2017 01:24 PM, Matthias Bernt wrote: Dear galaxy-dev, as a follow-up to my own question I have just implemented a

Re: [galaxy-dev] deprecated 'page' tag in tool xml - more than deprecated?

-Rudolf On 03/28/2017 03:59 PM, Hans-Rudolf Hotz wrote: Dear All As part of our move to upgrade from v. 16.04 to 17.01, I have noticed that the 'page' tag in the tool xml file doesn't work anymore. I know, the 'page' tag has been deprecated for a while, however, we have many old but important tools

Re: [galaxy-dev] Convert BED to Feature Location Index breaks when "preserve_python_environment = legacy_only"

...and indeed adding it to the "whitelist" (~/galaxy_dev/8090/galaxy/lib/galaxy/tools/_init__.py solves the problem. I can keep 'preserve_python_environment = legacy_only' I have made a pull request. Hans-Rudolf On 03/27/2017 04:38 PM, Hans-Rudolf Hotz wrote: Hi All I am in t

[galaxy-dev] Convert BED to Feature Location Index breaks when "preserve_python_environment = legacy_only"

nvironment = always' in "galaxy.ini" it works. Looks like more tools need to be added to the "whitelist" ? Regards, Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstr

Re: [galaxy-dev] Shared Data Library, large number of files

or Shared Data links. I also tried this in 16.07 with the same result. If it makes a difference, I'm using PostgreSQL and Apache. Dwight On Tue, Feb 28, 2017 at 11:47 PM, Hans-Rudolf Hotz <h...@fmi.ch <mailto:h...@fmi.ch>> wrote: Hi Daniel Just do

Re: [galaxy-dev] Shared Data Library, large number of files

to a Data Library either from the Admin or Shared Data links. I also tried this in 16.07 with the same result. If it makes a difference, I'm using PostgreSQL and Apache. Dwight On Tue, Feb 28, 2017 at 11:47 PM, Hans-Rudolf Hotz <h...@fmi.ch <mailto:h...@fmi.ch>> wrote: Hi Dani

Re: [galaxy-dev] AD/LDAP Integration

Hi I have no solution for you so far. However, I recommend to have a closer look at the entries in the 'galaxy_user' table for the users which work, and the users which don't work. In particular, check for 'email' and 'username' whether they are exactly the same as in your accounts provider.

Re: [galaxy-dev] display at UCSC does not work

udolf On 09/05/2016 11:44 AM, Hans-Rudolf Hotz wrote: Hi I am trying to set up the possibility to display data sets with the UCSC genome browser for our new galaxy installation. After clicking on "display at UCSC main", I get the UCSC genome browser, opening in the right assembly

Re: [galaxy-dev] Connection to mariaDB generates tables, but does not migrate information

Hi Evan Although, this is a MySQL to PostgreSQL migration, you might find some ideas and tricks for you case as well: https://wiki.galaxyproject.org/Community/Log/2015/MySQL2PostgreSQL Regards, Hans-Rudolf On 12/19/2016 06:46 PM, Nate Coraor wrote: Hi Evan, Migration only refers to the

[galaxy-dev] MySQL versus PostgreSQL - was: History is not accessible by user

On 12/01/2016 12:08 PM, Maximilian Friedersdorff wrote: >PS: and a completely unrelated piece of advice: Once you have fixed >this issue, I strongly recommend switching to PostgreSQL. > I gather SQLAlchemy prefers this! What kind of issues can I expect when using MySQL? As far as

Re: [galaxy-dev] Datasets incorrectly flagged as deleted

Hi Lance I don't remember seeing the problem you describe with our servers. If I do your query, I get: ... count --- 55 (1 row) looking at the actual ids, they are all in the lower three digits range and many years old. Regards, Hans-Rudolf On 11/30/2016 08:20 PM, Lance

Re: [galaxy-dev] History is not accessible by user

Hi Max This does look bizarre indeed. I have no answer, and I can just recommend a few things to test: - delete your cookies - how do you authenticate your users? can you log in as someone else? what happens if you set 'require_login = False' - what happens if you simplify your

Re: [galaxy-dev] Moving Galaxy Install From One Server To Another

Hi Evan Well, in theory, this is a simple task, since Galaxy mostly works with relative paths. Of course, it all depends on how sophisticated your installation is and how different the old and the new 'machine' is (eg same OS?) So my advice is: just do it or rather try it. - make a copy

Re: [galaxy-dev] Budgeting a production Galaxy instance

Hi Vladimir It is difficult to give you a good number, as it depends on a lot of factors, like: - how "active" are your anticipated '50 active user'? more than 1 job/workflow a day or just 1 job/workflow a month? - do you have to set up a system in order to give the galaxy users access

Re: [galaxy-dev] Odd error, solution not understood

Hi Scott click on the question mark next to 'database' in your history item and set the "Database/Build" to the genome you need. Regards, Hans-Rudolf On 09/13/2016 09:11 PM, Scott Szakonyi wrote: Hi all, I'm getting the following error when attempting to do a trackster visualization:

Re: [galaxy-dev] Converting an internal user to an external user

Hi Ryan Are you doing external authentication via apache? if so, I suggest to change the value in the 'external' column from 'f' to 't' in the galaxy_user table. also, check, whether the e-mail used is really the same as the one coming from your external authentication system. However, be

[galaxy-dev] display at UCSC does not work

it to work, even if I have "require_login = True"? Thank you very much for your help Regards, Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 40

Re: [galaxy-dev] Docker on Windows 10

Hi Jochen I would definitively go for the native docker for Windows and not using docker tool box. Though, this is based on my experience using native docker for Mac versus docker tool box. Maybe someone else on the list has experience with running Bjoern's docker images on windows? Yes,

Re: [galaxy-dev] Docker on Windows 10

Hi Jochen try starting docker with: docker run -i -t -p 8080:80 -v E:\galaxy_storage\:/export/ bgruening/galaxy-stable /bin/bash This will provide an interactive session. You can then start Galaxy (and other stuff like the required PostgreSQL server) with startup > log 2>&1 & and have

Re: [galaxy-dev] how to create users through Galaxy API?

Hi Peter I guess it is here: https://docs.galaxyproject.org/en/master/api_doc.html Regards, Hans-Rudolf On 08/29/2016 05:27 PM, Peter Cock wrote: Hi Martin, I'd like to look into creating new users via the API (where we can control the email address and username format for integration

Re: [galaxy-dev] problems with 'action type="metadata" name="dbkey"' in tool xml

! -John On Tue, Aug 16, 2016 at 9:02 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote: Hi Nicola and others on the list It looks like it has something to do with the 'conditional' I took the rnaStar xml file, and reduced it to the bare bones, just to reproduce the issue (see atta

Re: [galaxy-dev] problems with 'action type="metadata" name="dbkey"' in tool xml

if it's a regression in Galaxy. Cheers, Nicola On 16/08/16 11:29, Nicola Soranzo wrote: Hi Hans, see my comment below. On 16/08/16 09:51, Hans-Rudolf Hotz wrote: Dear All I am trying to move our Galaxy installation to new hardware and at the same time to a new version (the original is "

[galaxy-dev] problems with 'action type="metadata" name="dbkey"' in tool xml

t;False"/> but it results in the same kind of error: Thank you very much for any help/comments Regards, Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maul

Re: [galaxy-dev] Removing job in error state

Hi Ryan If the "Stop Jobs" option on the Admin page does not work, you can go for the direct way by manually interacting with the PostgreSQL database: Change the state to "error" in the 'job' table, eg: update job set state='error' where id=12772; As always, be very careful when you

Re: [galaxy-dev] Galaxy history UI suggestion

Hi Bongsoo The 'View all histories' tool (the function to the right of the 'History options' wheel) is a good alternative to the 'Saved Histories' page. Regards, Hans-Rudolf On 08/02/2016 10:26 PM, Bongsoo Park wrote: Hello, In the saved histories, the selected page goes to the first

Re: [galaxy-dev] activate authentication through LDAP using the auth_conf file

to get it to build. Good luck! -Dannon On Fri, Jul 22, 2016 at 7:07 AM Hans-Rudolf Hotz <h...@fmi.ch <mailto:h...@fmi.ch>> wrote: Dear all I am looking into authentication through LDAP using the auth_conf file (we are currently using Apache to handle this). And it looks li

[galaxy-dev] activate authentication through LDAP using the auth_conf file

in order to have 'lber.h' on the system? Or do I have to do something else? Thank you very much for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse

Re: [galaxy-dev] default number of concurrent jobs

u just get "job_conf.xml.sample_advanced" and "job_conf.xml.sample_basic", so I assume it is not really using any of those two. However in the "job_conf.xml.sample_basic" there is a comment saying "". But the number of workers in there is set to 4. So why 5? Any

Re: [galaxy-dev] default number of concurrent jobs

Hi Ulf Have a look at the "job_conf.xml" file, see also: https://wiki.galaxyproject.org/Admin/Config/Jobs Regards, Hans-Rudolf On 07/14/2016 01:35 PM, Ulf Schaefer wrote: Hi all I installed an out-of-the-box Galaxy instance on my local machine as per the instructions

Re: [galaxy-dev] Docker for Mac

nd demonstration purposes so far. haven’t tried to access it over our network, but don’t see a reason why it should not work. Hans-Rudolf > Cheers, > > Philipp > > From: Hans-Rudolf Hotz [mailto:hansrudolf.h...@fmi.ch > <mailto:hansrudolf.h...@fmi.ch>] > Sent:

Re: [galaxy-dev] Docker for Mac

Hi Philipp I have successfully used "Docker for Mac (beta)” on 10.11.5, but I have always used the traditional location for the image to fetch from: https://index.docker.io/u/bgruening/galaxy-stable/ (i.e just following the excellent

[galaxy-dev] will start in 10 minutes - Re: GalaxyAdmins Meetup This Thursday

ur before the meetup. GalaxyAdmins is a discussion group for Galaxy community members that administer Galaxy installations. Hope to see you (online) on Thursday, Dave Clements and Hans-Rudolf Hotz -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject

Re: [galaxy-dev] How to replace 'BioMart Central server' in the "Get Data" tools ?

Thank you very much for your help Hans-Rudolf On 11/17/2015 08:40 AM, Hans-Rudolf Hotz wrote: Hi As you probably know, the central BioMart server is currently unavailable (see: http://www.biomart.org/notice.html). Hence, the "Get Data -> BioMart Central server" tool in our local G

Re: [galaxy-dev] [SPAM] RE: GalaxyAdmins Meetup THIS THURSDAY: Galaxy on Mobile Devices; and Tools, Tools, Tools!

...@lists.galaxyproject.org] on behalf of Hotz, Hans-Rudolf [hansrudolf.h...@fmi.ch] Sent: Monday, April 18, 2016 10:06 AM To: galaxy-dev@lists.galaxyproject.org Cc: Hans-Rudolf Hotz Subject: [galaxy-dev] GalaxyAdmins Meetup THIS THURSDAY: Galaxy on Mobile Devices; and Tools, Tools, Tools! Hello all, The next <ht

Re: [galaxy-dev] Problem with LDAP authentication

Hi Scott what happens when you remove all galaxy related cookies or try accessing Galaxy from another desktop/laptop? Regards, Hans-Rudolf On 04/07/2016 03:29 AM, Scott Szakonyi wrote: Hi all, I'm having some difficulties with logging into my production website. I get the following error

Re: [galaxy-dev] "Edit settings" button in Trackster is no longer working (15.10)

On Mon, Mar 21, 2016 at 9:01 AM, Hans-Rudolf Hotz <h...@fmi.ch <mailto:h...@fmi.ch>> wrote: Hi all Since we upgraded our Galaxy installation from 15.05 to 15.10 (plus the recent security fix, changeset: 17161:3f95c21b1a85), the "Edit

Re: [galaxy-dev] shed_tool_conf.xml

On 03/22/2016 12:56 PM, Peter Cock wrote: I would try validating the broken XML file (e.g. using an online tool, or an XML aware editor). That might be enough to find the error and fix it by hand. I don't know if there is a clever way to regenerate the file instead... probably a lot of

[galaxy-dev] "Edit settings" button in Trackster is no longer working (15.10)

up anymore. This happens with different browsers on mac and linux. On the console I get: "TypeError: a.browser is undefined" Has anyone else seen this problem? Or is there even already a fix available? Thank you very much for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bi

Re: [galaxy-dev] Load tools without service interruption

Hi Floreline It depends on the 'source' of the tool: If you add the tool via Tool Shed, then there is no need to restart the Galaxy server. However, if you add a tool manually (i.e. by adding a line to tool_conf.xml) you need to restart the server - at least that is my current knowledge.

Re: [galaxy-dev] Galaxy External Authentication and API access

Hi Lance just double checking: Have you implemented this fix: https://github.com/galaxyproject/galaxy/pull/1003 (https://gist.github.com/8d0412367371127e90ad) This solved our problem with the 'View all histories' nicely - though we still have problems with 'Impersonate a user' Regards,

Re: [galaxy-dev] cleanup

tically installed with python... Cheers, Philipp -----Original message- *From:* Hans-Rudolf Hotz <h...@fmi.ch> *Sent:* Monday 22nd February 2016 17:09 *To:* Rathert, Philipp, Dr. <philipp.rath...@ibc.uni-stuttgart.de>; galaxy-dev@lists.galaxyproject.org *Sub

Re: [galaxy-dev] Bypassing Data Managers?

Hi Ray If you already have the reference data (as you have written in your first e-mail), then I suggest you manually add those files (file paths) to ~/tool-data/bowtie2_indices.loc ~/tool-data/bowtie_indices.loc This way you prevent duplication of your reference data Regards, Hans-Rudolf

Re: [galaxy-dev] Python ValueError: too many values to unpack

Hi Matthias Make sure 'listing' is a list of (displayName,value,boolean) Though, there might be other errors as well Regards, Hans-Rudolf I am not sure, whether this On 01/26/2016 01:22 PM, Matthias De Smet wrote: Hi all, I’m trying to develop a tool that lets you select a file on the

[galaxy-dev] RedHat versus CentOs

help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland ___ Please keep all replies on the list by using "reply all" in your m

Re: [galaxy-dev] tool development

Hi Matthias Have you considered "Data Libraries"? A cron job can query your LIMS and use the API to create "Data Libraries". Then the user can select which datasets she/he wants to import. And back to your original question: Yes, it is possible to create interactive tools. Check out the

[galaxy-dev] Galaxy job scheduler slows down, when too many jobs are in the queue

nd eventually it went down to zero again. Has anyone else seen such a behavior before? Thank very much for any help or suggestions Regards, Hans-Rudolf PS: I now modifying the script, with a call to the database to check whether all jobs have been done, before making the call to upload

Re: [galaxy-dev] Does anybody know if ts (a task scheduler) is supported under Galaxy.

Hi Shane, please allow me to jump in late - since you are looking for a simple solution: why not rely just on the built in job scheduler? Have a look at ~/config/job_conf.xml.sample_advanced Even on a single box, you can set up different queues with individual restrictions. Hans-Rudolf

Re: [galaxy-dev] API key change manually

Hi Mic You said, you had migrated your "Galaxy installation to Postgresql"? So why did you lose your API key? - I assume by 'loosing' you mean: is no longer valid, don't you? Have you forgot to migrate the "api_keys" table? All the keys are stored there. Hans-Rudolf On 11/17/2015 02:10

Re: [galaxy-dev] using Bioblend with external authentication

On 10/22/2015 04:09 PM, Dannon Baker wrote: My guess is that it has to do with the prefix there. Is the Galaxy API at galaxy-dev.fmi.ch/galaxy/api <http://galaxy-dev.fmi.ch/galaxy/api> or galaxy-dev.fmi.ch/api <http://galaxy-dev.fmi.ch/api>? On Thu, Oct 22, 2015 at 6:41 AM Hans-Ru

[galaxy-dev] using Bioblend with external authentication

ny help with this Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland ___ Please keep all replies on the list by using "

[galaxy-dev] tomorrow's GalaxyAdmins Online Meetup: Galaxy at Analome with David Kovalic

and how it supports ongoing bioinformatics projects while at the same time providing opportunities for social good. Second, we gonna have "News from the Galaxy project": Galaxy Wiki Replacement: Options, thoughts, and questions I hope many of you will join us Dave and Hans-Rudol

Re: [galaxy-dev] Need urgent help: ItemOwnershipException: History is not owned by user

Hi Zuzanna This sort of rings a bell...can you give some more details: - Have you always used external authentication? or do you get this problem after switching to external authentication? - what do you mean by "new LDAP users"? - Are you sure, you get the "correct information" back

Re: [galaxy-dev] [Galaxy-dev] user authentication (NIS)

PLEASE don't cross-post. See my answer to the same question you posted here: https://biostar.usegalaxy.org/p/13725/ Hans-Rudolf On 08/12/2015 11:01 AM, Floreline TOUCHARD wrote: Hi, I read the doc about external authentication but I'm not sure to understand all of it (I'm a newbie). I

[galaxy-dev] if you consider switching from MySQL to PostgreSQL....

every PostgreSQL expert would smash her/his head to the desk while reading it), but it worked. Regards, Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

Re: [galaxy-dev] Reasons to choose psql over mysql or not

Hi Eric Well, there is no official statement besides the one you have quoted below, but anyone in the Galaxy team I have spoken to recently told me to move to PostgreSQL. And that's why, I've been through the painful process of migrating our MySQL database to a PostgreSQl database.

Re: [galaxy-dev] Adding packages for bedtools and ucsc-utils for Trackster?

On 06/18/2015 09:06 AM, Peter van Heusden wrote: Hi there I'm trying to visualise some of our genome data using Trackster. Initial input is 790,000 lines of GFF3. When I try and create the visualisation, I get errors from two tools: Convert GFF to Interval Index on data 3 -- an out of memory

Re: [galaxy-dev] Trackster bug

I am not really familiar about the linking of the datasets in the database (especially, when it comes down to visualization), but as a last suggestion: Have you tried using a new visualization ? Hans-Rudolf On Jun 10, 2015, at 12:36 PM, C. Ch. tuto...@hotmail.com wrote: Nope, the name of

Re: [galaxy-dev] Trackster bug

Hi Cristian This problem sounds familiar. Have the new and the old file the same name? If so, try renaming your new gff file. Hans-Rudolf On Jun 10, 2015, at 10:34 AM, C. Ch. tuto...@hotmail.com wrote: Hi all, I have uploaded a gff annotation to a shared library and when I try to load

Re: [galaxy-dev] Trackster bug

just double checking:and what about the 'name' in the History panel? Hans-Rudolf On Jun 10, 2015, at 11:43 AM, C. Ch. tuto...@hotmail.com wrote: Hi Hans, Actually the older dataset has nothing to do with the actual GFF file name-wise or other. Trackster tries to load

Re: [galaxy-dev] reference in builds.txt

Hi Sabrina yes, you can add any genome to builds.txt (as an example, we have several plasmids added as genomes in our Galaxy server). Just make sure the dbkey (e.g. hg19) you gonna add is unique. If you also intend to use the built in visualization tools, make sure to add the corresponding

Re: [galaxy-dev] optional tool arguments

Hi Ryan I guess you can work with filters, see: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set Regards, Hans-Rudolf On 04/28/2015 06:28 PM, Ryan G wrote: Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2 fastq files as input. If 1

[galaxy-dev] follow up question regarding the 'toolform-upgrade'

-- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland ___ Please keep all replies on the list by using reply all in your mail client. To manage your

[galaxy-dev] GalaxyAdmins Online Meetup on 16 April

Hi all Just a heads-up/reminder: The second GalaxyAdmins (https://wiki.galaxyproject.org/Community/GalaxyAdmins) meetup of 2015 will be on Thursday, April 16. Hans-Rudolf ___ Please keep all replies on the list by using reply all in

[galaxy-dev] storing set max value in trackster for wig file display

Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland ___ Please keep all replies on the list by using reply all in your mail client

[galaxy-dev] REMINDER: GalaxyAdmins Online Meetup on 19 February

https://wiki.galaxyproject.org/GalaxyTeam, and Hans-Rudolf Hotz https://wiki.galaxyproject.org/HansrudolfHotz will lead a short discussion on /GalaxyAdmins direction/. Thanks to everyone for letting us know what dates and times worked best for you. This time and day of the week worked

Re: [galaxy-dev] Adding options to a tool

Hi Scott and just double checking, in case you do have an 'old' Galaxy installation: after modifying the xml file (I assume you are talking about tophat_wrapper.xml?): Have you re-loaded the tool? click on 'Reload a tool's configuration' on the administration menu and select the tool

Re: [galaxy-dev] Tools to download SRA datasets from GEO

Hi Are you looking for any special GEO data, which is not mirrored at the ENA? If not, you can probaly use the Get Data - EBI SRA tool, which is part of the installation. Also, have you looked at the toolshed? e.g. https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit Regards,

Re: [galaxy-dev] galaxy report page - server error solution?

Hi again for jobs.py I have modified the same lines as you, plus line 285 (group_by) for users.py I have modified the same lines as you Hans-Rudolf On 02/05/2015 04:20 PM, Fernandez Edgar wrote: Actually, here’s what I came up with : diff users.py

[galaxy-dev] Hovering over a history dataset lights up the other datasets....?

to do? Thanks for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland ___ Please keep all replies on the list by using