[galaxy-dev] small issue with the black frame around displayed history item

on. The black frame switches to that history item - though nothing changes in the center panel As I said not a big problem, just a little bit confusing...shall I make Trello card or is there a quick fix possible? Regards Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Fr

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

re a special trick I need 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 rep

Re: [galaxy-dev] disk space does not add up...

Hi Brad have a look at /mnt/galaxy/data/galaxy/galaxy_dist/database/tmp and /mnt/galaxy/data/galaxy/galaxy_dist/database/job_working_directory you might find some stuff to clean up there as wellthough, I doubt it will be 24T Hans-Rudolf On 12/17/2014 01:05 PM, Langhorst, Brad wr

Re: [galaxy-dev] cluster queue job id?

On 01/08/2015 11:20 AM, Anna Terry wrote: Hi Dannon, many thanks, this is helpful. Would also be useful for the destination from the job_conf that was used to be displayed. And maybe the queue and node from the cluster, but appreciate that this may not be achievable due to the large number of

Re: [galaxy-dev] Unable to get data from UCSC

Hi Anna I am just guessing, but it might be worth checking the proxy settings of your local galaxy server. Regards, Hans-Rudolf On 01/13/2015 05:39 PM, Anna Terry wrote: Hi, I am having lots of problems with the get data tools installed on our local galaxy server, I'll start with just one

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 Rega

Re: [galaxy-dev] parallesim

Hi Roberto just double checking: are you using a PostgreSQL database, or are you relying on the built in SQLite? Hans-Rudolf On 02/05/2015 02:26 PM, Roberto Alonso CIPF wrote: Hello, I am trying to use parallelism in Galaxy. I added this entry to the tool xml config: for each sequen

Re: [galaxy-dev] parallesim

rg/Admin/Config/Performance/ProductionServer#Switching_to_a_database_server ) Hans-Rudolf On 02/05/2015 02:44 PM, Roberto Alonso CIPF wrote: Hello, I am using the galaxy built-in database, SQLAlchemy on top of sql lite? May I swith to postgress? Regards On 5 February 2015 at 14:41, Hans-Rudol

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

Hi Edgar Well, if it works, and you get the right numbers, then it is probably correct It is difficult to identify your changes, but I can show you what I have done in order to get all the options to work with our MySQL database. I hope I refer to the same lines in 'jobs.py', don't I?

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 ARCHIVES/users.py_20

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 Ha

Re: [galaxy-dev] Galaxy CloudMan instance - missing link 'display at UCSC' for bed files

Hi Anne Have you also checked: ~/tool-data/shared/ucsc/ucsc_build_sites.txt to make sure the the 'genome' of your bed file is actually listed ? Regards, Hans-Rudolf On 02/13/2015 07:05 PM, Anne Pajon wrote: Dear All, I’ve installed a Galaxy CloudMan instance on amazon for a training co

Re: [galaxy-dev] Galaxy CloudMan instance - missing link 'display at UCSC' for bed files

"CloudMan" specific? Hans-Rudolf Best regards, Anne. On 16 Feb 2015, at 12:30, Hans-Rudolf Hotz wrote: Hi Anne Have you also checked 'universe_wsgi.ini' to make sure it contains: ucsc_display_sites = main Though, this might me stored in config/galaxy.ini in the curr

Re: [galaxy-dev] Galaxy CloudMan instance - missing link 'display at UCSC' for bed files

uclahttp://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks?araTha1 It does contain hg19, the genome of the bed file I am trying to get displayed at UCSC but I still do not have the link to do so… any other ideas where I should look? Many thanks in advance. Best regards, Anne. On 16 Feb 2015, at 08:01, Hans-Rudolf Hot

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

Update/ will be offered by a Galaxy Team member <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 be

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

o. 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 "

Re: [galaxy-dev] Sorting users by last login

Hi Jose First, as a little warning, I would not delete the inactive users as this will destroy the reproducibility. Anyway: are you running the report tools? (see: https://wiki.galaxyproject.org/Admin/UsageReports) There you will find the "Date of last login" tool Regards, Hans-Rudolf On

[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] problems wit upgrading to "latest_15.03" - 'UniverseApplication' object has no attribute 'control_worker'

.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/path_to_galaxy/galaxy_dist/lib/galaxy/app.py", line 167, in shutdown if self.control_worker: AttributeError: 'UniverseApplication' object has no attribute 'control_worker' Any help apprecia

[galaxy-dev] ignore my previous mail: Re: problems wit upgrading to "latest_15.03" - 'UniverseApplication' object has no attribute 'control_worker'

Please ignore my previous e-mail. The error was actually further up in the logs, and easy to fix. - sorry for filling up your inbox Hans-Rudolf PS: personal memo: don't do four galaxy related things at once. On 04/14/2015 04:47 PM, Hans-Rudolf Hotz wrote: Hi I am in the proce

Re: [galaxy-dev] Job submission failed

Hi Vipin Is this a new problem you encounter since you have done the upgrade to "latest_15.03"? If so, did you experience any troubles during the database schema upgrade to '128'? Regards, Hans-Rudolf On 04/20/2015 08:44 PM, Vipin TS wrote: Hi dev-team, I am experiencing an issue with m

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'

"toolform-upgrade=True", we get: foo__cn__bar__cn__ (using firefox, with linux, Mac, and Windows) Can anybody confirm this (before we fix all affected tools) Thank you very much for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Ins

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] reference in builds.txt

items, And hence independent of the tools used Hans-Rudolf Thanks in advance for your answers. Best regards, Sabrina On 13/05/2015 09:17, Hans-Rudolf Hotz wrote: Hi Sabrina yes, you can add any genome to "builds.txt" (as an example, we have several plasmids added as genomes in our

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. wrote: > Hi all, > > I have uploaded a gff annotation to a shared library and when I try to load > it into trackste

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. wrote: > Hi Hans, > > Actually the older dataset has nothing to do with the actual GFF file > name-wise or other. Trackster tries to load > database/files/004/dataset_

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. wrote: > Nope, the name of the gff file is uniqu

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] GalaxyAdmins Online Meetup this Thursday: Peter Briggs on Galactic Engineering at Manchester

Hi everyone, the online meetup will (hopefully) start in a few minutes at: https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_06_18 Regards, Hans-Rudolf On Jun 15, 2015, at 3:47 PM, Dave Clements wrote: > Hello all, > > The June 2015 online GalaxyAdmins meetup will be this

Re: [galaxy-dev] [SPAM] RE: GalaxyAdmins Online Meetup this Thursday: Peter Briggs on Galactic Engineering at Manchester

-dev-boun...@lists.galaxyproject.org] on behalf of > Hans-Rudolf Hotz [hansrudolf.h...@fmi.ch] > Sent: Thursday, June 18, 2015 4:03 PM > To: Galaxy Dev List > Subject: Re: [galaxy-dev] GalaxyAdmins Online Meetup this Thursday: Peter > Briggs on Galactic Engineering at Manchester > > Hi ev

Re: [galaxy-dev] galaxy.ini

Hi Bryan There should be a "config/galaxy.ini.sample" file. Make a copy "config/galaxy.ini" and modify it. Hans-Rudolf On 07/14/2015 12:35 PM, Bryan Hepworth wrote: Hi For the woefully inept, where in the heck is galaxy.ini stored? I saw the documentation that said change 127.0.0.1 to 0.0

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. Actually,

[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] Galaxy run.sh process crashing

Hi Hans what happens, when you run such a long(ish) on the command line (executed as the same user the galaxy server is running as)? Hans-Rudolf On 08/04/2015 01:12 AM, Hans Vasquez-Gross wrote: Hi, We have been running galaxy for the last year fine on our website to run short running scrip

Re: [galaxy-dev] Sample Tracking Feature in Galaxy

Hi Hakeem I am not an expert on the Sample Tracking, but as far as I remember, you need to log in as an 'admin' in order to get the 'Lab' link in the Galaxy top menu. Regards, Hans-Rudolf On 08/04/2015 01:06 PM, Hakeem Almabrazi wrote: Hi, I am trying to see if we can use Tracking Sample

Re: [galaxy-dev] Sample Tracking Feature in Galaxy

sorry, ignore my suggestion in my previous mail - I was wrong Hans-Rudolf On 08/04/2015 01:42 PM, Hans-Rudolf Hotz wrote: Hi Hakeem I am not an expert on the Sample Tracking, but as far as I remember, you need to log in as an 'admin' in order to get the 'Lab' link in

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 wou

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 from

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

. Filutowska wrote: Dnia 2015-09-21, pon o godzinie 13:55 +0200, Hans-Rudolf Hotz pisze: 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? Yes, I always

Re: [galaxy-dev] Sharing galaxy on CentOS7/Slurm/HPC/Proftp/Postgres/Apache/LDAP setup configurations

Hi Sven Nice resource - thank you very much for sharing! Please allow me to suggest that you copy or link your documents to the 'Galaxy Community Log Board': https://wiki.galaxyproject.org/Community/Logs This makes sharing and especially finding your documents much easier Regards, Hans-Ru

[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

[galaxy-dev] using Bioblend with external authentication

very much for any 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

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-Rud

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

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 Galaxy installation does not work anymore - well, this is also the case on usegalaxy.org. We can easily s

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 P

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

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

reduced to ~30 minutes and at about 2000 jobs to go, the waiting time was about 10 minutes and 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

Re: [galaxy-dev] Happy new year!

...and also very special greetings to all Galaxy Admins! All the Best for the New Year Hans-Rudolf PS: the next Galaxy Admin Web Meetup will on Thursday February 18th. Please let me know, if you want to present your local Galaxy installation - how you solved or not-solved any specific

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 'dy

[galaxy-dev] RedHat versus CentOs

y much 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 "reply all&

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 serv

Re: [galaxy-dev] Filtering dynamic options in tool with tagset

Hi Matthias I don't think you can do that...I would delegate the filtering to the 'list_files' function, i.e. by calling: list_files(archive_source,query) Regards, Hans-Rudolf On 01/27/2016 10:07 AM, Matthias De Smet wrote: Hi All, I’m trying to implement a tool that get a list of optio

Re: [galaxy-dev] Filtering dynamic options in tool with tagset

ghtforward wau to get the same results. same for me :( Hans-Rudolf Matthias Op 27 jan. 2016, om 10:20 heeft Hans-Rudolf Hotz het volgende geschreven: Hi Matthias I don't think you can do that...I would delegate the filtering to the 'list_files' function, i.e

Re: [galaxy-dev] RedHat versus CentOs

Dear All As promised here is the summary of the 9 replies I have received: CentOS 6 : 6 CentOS 7 : 1 Scientific Linux 6: 2 Regards, Hans-Rudolf On 01/20/2016 02:20 PM, Hans-Rudolf Hotz wrote: Dear All Our production Galaxy server has been running smoothly

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] Bypassing Data Managers?

oing it just for the FASTA files but should still use Data Managers for index generation? Thank you! Ray On Thu, Feb 18, 2016 at 3:54 PM, Hans-Rudolf Hotz wrote: 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 f

Re: [galaxy-dev] 18 February GalaxyAdmins Meetup: Ansible, Python Wheels

quick reminder: the meetup will start in ~30 minutes the link is: https://connect.johnshopkins.edu/galaxyadmins201602 Hans-Rudolf On 02/11/2016 02:03 PM, Hans-Rudolf Hotz wrote: Hello all, The next GalaxyAdmins online meetup is next week, on Thursday, February 18 at 5PM CET (see your local

Re: [galaxy-dev] cleanup

Hi Philipp Since the new galaxy version, I am unable to perform a cleanup anymore. From the galaxy root directory I want to start the script cleanup_datasets.py with the following line: $ python cleanup_datasets.py /export/galaxy-central/config/galaxy.ini -d -60 -1 I get the error message:

Re: [galaxy-dev] cleanup

utomatically installed with python... Cheers, Philipp -Original message- *From:* Hans-Rudolf Hotz *Sent:* Monday 22nd February 2016 17:09 *To:* Rathert, Philipp, Dr. ; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] cleanup Hi Philipp > Sinc

Re: [galaxy-dev] Lost prostgresql database

Hi Amos Since the PostgreSQL database stores much more than the links to and previews of the individual datasets, you need to restore it from your PostgreSQL backup file. Hans-Rudolf On 02/25/2016 08:53 PM, Raphenya, Amogelang wrote: Hi All, Our server hard drive failed and we lost the d

Re: [galaxy-dev] Lost prostgresql database

u have just a few very valuable datasets that have to be recovered, I would look at the file dates (guided by the automatically incremented dataset numbers), sizes, and look at the data to check the contents (everything will be named *.dat as the extension, other than complex datatypes). Peter On F

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, Hans

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.

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

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, P

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 'man

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

2016 at 9:01 AM, Hans-Rudolf Hotz 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 settings" button in Trackster is no longer wo

Re: [galaxy-dev] Troubleshooting BAM file upload issues

Hi Amelia Does this happen with "Auto-detect" or do you pre-set the data type to 'bam' ? Regards, Hans-Rudolf On 03/22/2016 07:28 PM, Amelia Ireland wrote: I'm setting up a Galaxy instance on a new server and am having some issues with BAM file uploads. I'm using the BAM files supplied wit

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 m

Re: [galaxy-dev] Allow users to see the job queue?

Hi Ray Are you running the reports tool? https://wiki.galaxyproject.org/Admin/UsageReports you can inform your user about this page, and then, they can check the "All unfinished jobs" page. This is probably the easiest way - though you need to consider, that all users can see each other job

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] Removing stale references from a history

Hi Scott Can you explain a little bit more what you mean by "file references that are no longer valid in one of his histories"? What happens when your user tries to delete the affected history item? Regards, Hans-Rudolf On 05/16/2016 06:21 PM, Scott Szakonyi wrote: Hello, Due to some p

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 Galax

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

thanks M. On Wed, Jun 8, 2016 at 4:53 AM Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote: Hi all Please allow me to come back to this old problem: On usegalaxy.org <http://usegalaxy.org>, the tool is now pointing to http://www.ensembl.org/biomart/martview (see also:

[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] 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 recip

Re: [galaxy-dev] Docker for Mac

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: Wednesday, June 29, 2016 3:50 PM > To: Ra

[galaxy-dev] Swiss German Galaxy Tour/Day 2016 - Freiburg (Germany), 20/21 October

Dear all After the big success of the “Swiss German Galaxy Tour” in 2014, we are going to organize a similar event again in October this year. This time we meet for two days in Freiburg (Germany): https://wiki.galaxyproject.org/Events/SG2016 It is our great pleasure to announce that Dannon Bak

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 (https://wiki.galaxy

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

;. You 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?

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

evel 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 M

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

box here to get it to build. Good luck! -Dannon On Fri, Jul 22, 2016 at 7:07 AM Hans-Rudolf Hotz 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 like, I am

[galaxy-dev] switching from Apache to "auth_conf" to handle external user authentication via LDAP

f' in the galaxy_user table, it works Since manually modifying the database is a bad thing, I just want to double check, whether this is the right way to do it? If so, I will add a line or two to the wiki Many thanks for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinfo

Re: [galaxy-dev] switching from Apache to "auth_conf" to handle external user authentication via LDAP

that would result from doing this. It seems like it is going to be the right thing to do in your case (but no promises :)). If it works, it would be super awesome if you update the wiki - thanks for taking the time to do that! -John On Mon, Jul 25, 2016 at 9:00 AM, Hans-Rudolf Hotz wrote: Dea

Re: [galaxy-dev] This job failed for reasons that could not be determined.

Hi Ulf I don't think the two things are connected which each other. In the logs of our local installation we see once in a while, lines like: File "/usr/lib64/python2.6/socket.py", line 303, in flush self._sock.sendall(buffer(data, write_offset, buffer_size)) error: [Errno 32] Broken p

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 page

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 direct

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

tswith" keep="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

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

ot sure 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 ori

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

15.10). It works in both cases. Each time, the right dbkey is picked up. Hans-Rudolf On 08/16/2016 01:47 PM, Hans-Rudolf Hotz wrote: Hi Nicola Many thanks for your comments/suggestions. I've just tested the rnaStar wrapper, and it works as well. I will try to dig deeper Hans-Rudolf

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

eport Hans! -John On Tue, Aug 16, 2016 at 9:02 AM, Hans-Rudolf Hotz 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 attachment: rg_rn

Re: [galaxy-dev] Galaxy migration to docker environment

Hi Matthias You don't need to change the path. All data sets are stored in relative paths in the PostgreSQL database. Hence, in a setup without local modifications all you need to do: - copy the 'database/files/' folder - make sure your new Galaxy installation points to the old PostgreSQL d

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 with

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 acc

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,

[galaxy-dev] display at UCSC does not work

ay to get 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 Maulbeerstr

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

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] 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 t

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 of

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