- galaxy-dev - lists.galaxyproject.org

cannot extract genomic dna
by Alexandre Maucuer 25 Jul '16

25 Jul '16

Hi, I've installed a Galaxy instance on a local machine under ubuntu 16.04. I am trying to fetch sequences from hg19.2bit I downloaded from ucsc as ~/galaxy/depot/data2/galaxy/hg19$hg19.bit I added: hg19 /depot/data2/galaxy/hg19/hg19.2bit to my twobit.loc file in tool-data directory When running the extract genomic dna, I get the error: "No sequences are available for 'hg19', request them by reporting this error." see also attached screenshot Thanks in advance for your help -- Alexandre Maucuer, Ph.D., INSERM, France

2 2

switching from Apache to "auth_conf" to handle external user authentication via LDAP
by Hans-Rudolf Hotz 25 Jul '16

25 Jul '16

Dear all Our production server uses Apache to handle external user authentication. I have now set up a new test server (16.04) which handles external user authentication via LDAP using the auth_conf file. This works nicely when using an empty database (I have managed to solve all last weeks problems). I have now connected my test server to a copy of the PostgreSQL database used on our production server. I try to log in, and I get: "This account was created for use with an external authentication method, contact...) and the login fails. If I now set external = '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 Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

2 2

activate authentication through LDAP using the auth_conf file
by Hans-Rudolf Hotz 22 Jul '16

22 Jul '16

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 stuck at a very early step: I have started with a fresh checkout of release 16.04 (git clone -b master https://github.com/galaxyproject/galaxy.git) some modifications in galaxy.ini (host, port) and: auth_config_file = config/auth_conf.xml I start galaxy, and I try to login. In the log file I get: galaxy.webapps.galaxy.controllers.user DEBUG 2016-07-22 12:41:50,741 trans.app.config.auth_config_file: ./config/auth_conf.xml galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP authenticate: email is hansrudolf.hotz(a)fmi.ch galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP authenticate: .... This is what I expect...so far so good but further down, I get: galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,742 LDAP authenticate: could not load ldap module According to our sysadmin, "python-ldap" is installed on the machine (running Red Hat 7.2). But I assume, it has to be within the galaxy created virtual env, hasn't-it? Hence I have tried the following cd <galaxy-root> . .venv/bin/activate pip install python-ldap Is this the right way to do it? Doing this, I have been running into the following error: Modules/errors.h:8:18: fatal error: lber.h: No such file or directory #include "lber.h" So I guess I have to tell my sysadmin to install "openldap-devel 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 66 4058 Basel/Switzerland

2 2

Re: [galaxy-dev] Loading tool config file
by Katherine Beaulieu 22 Jul '16

22 Jul '16

On Fri, Jul 22, 2016 at 7:29 AM, Katherine Beaulieu < katherine.beaulieu014(a)gmail.com> wrote: > No I'm really asking about which files in Galaxy, will load those > parameters on the screen. I believe you were the one to give me a link to > adding a new parameter type in Galaxy via the password parameter, but I > haven't quite been able to implement that. The two files I have changed so > far are basic.py and form_builder.py but using these two files it still > only loads a text parameter. > > On Fri, Jul 22, 2016 at 7:26 AM, Peter Cock <p.j.a.cock(a)googlemail.com> > wrote: > >> Hi Katherine, >> >> Are you asking about the XML files which described Galaxy Tools >> by listing all the options to show the user, any help text to show the >> user, and instructions for how to turn the options picked into a >> command line to be executed: >> >> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax >> >> Peter >> >> On Fri, Jul 22, 2016 at 12:09 PM, Katherine Beaulieu >> <katherine.beaulieu014(a)gmail.com> wrote: >> > Dear all, >> > I am looking for the files/functions that get called from the point >> where >> > you click on the tool name to the point where you get an html version of >> > your tool on the screen. Could someone indicate what this path looks >> like? I >> > would be really appreciative! >> > Thanks, >> > Katherine >> > >> > ___________________________________________________________ >> > Please keep all replies on the list by using "reply all" >> > in your mail client. To manage your subscriptions to this >> > and other Galaxy lists, please use the interface at: >> > https://lists.galaxyproject.org/ >> > >> > To search Galaxy mailing lists use the unified search at: >> > http://galaxyproject.org/search/mailinglists/ >> > >

3 3

Re: [galaxy-dev] Loading tool config file
by Katherine Beaulieu 22 Jul '16

22 Jul '16

No I have not sorry. On Fri, Jul 22, 2016 at 7:43 AM, Mohamed Kassam <k.mamoud(a)gmail.com> wrote: > Hello Katherine, > it is Mohamed from the NIHS. > So have you find a way to incluse the password tahg in the xml file ? > > Mohamed > > 2016-07-22 13:34 GMT+02:00 Katherine Beaulieu < > katherine.beaulieu014(a)gmail.com>: > >> >> >> On Fri, Jul 22, 2016 at 7:29 AM, Katherine Beaulieu < >> katherine.beaulieu014(a)gmail.com> wrote: >> >>> No I'm really asking about which files in Galaxy, will load those >>> parameters on the screen. I believe you were the one to give me a link to >>> adding a new parameter type in Galaxy via the password parameter, but I >>> haven't quite been able to implement that. The two files I have changed so >>> far are basic.py and form_builder.py but using these two files it still >>> only loads a text parameter. >>> >>> On Fri, Jul 22, 2016 at 7:26 AM, Peter Cock <p.j.a.cock(a)googlemail.com> >>> wrote: >>> >>>> Hi Katherine, >>>> >>>> Are you asking about the XML files which described Galaxy Tools >>>> by listing all the options to show the user, any help text to show the >>>> user, and instructions for how to turn the options picked into a >>>> command line to be executed: >>>> >>>> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax >>>> >>>> Peter >>>> >>>> On Fri, Jul 22, 2016 at 12:09 PM, Katherine Beaulieu >>>> <katherine.beaulieu014(a)gmail.com> wrote: >>>> > Dear all, >>>> > I am looking for the files/functions that get called from the point >>>> where >>>> > you click on the tool name to the point where you get an html version >>>> of >>>> > your tool on the screen. Could someone indicate what this path looks >>>> like? I >>>> > would be really appreciative! >>>> > Thanks, >>>> > Katherine >>>> > >>>> > ___________________________________________________________ >>>> > Please keep all replies on the list by using "reply all" >>>> > in your mail client. To manage your subscriptions to this >>>> > and other Galaxy lists, please use the interface at: >>>> > https://lists.galaxyproject.org/ >>>> > >>>> > To search Galaxy mailing lists use the unified search at: >>>> > http://galaxyproject.org/search/mailinglists/ >>>> >>> >>> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > >

1 0

Loading tool config file
by Katherine Beaulieu 22 Jul '16

22 Jul '16

Dear all, I am looking for the files/functions that get called from the point where you click on the tool name to the point where you get an html version of your tool on the screen. Could someone indicate what this path looks like? I would be really appreciative! Thanks, Katherine

2 1

BLAST only using single core
by Shane Sturrock 21 Jul '16

21 Jul '16

Previously, the BLAST wrapper was able to use multiple cores but recently users have started complaining it has got really slow and when I look at the cluster a job is only using a single core. I don’t want jobs split across multiple cluster nodes, but each node has 16 cores so it would be good if they could be used. I’m still using the older 16.01 release and this has been upgraded repeatedly over the last few years so I’m still using the universe_wsg.ini file (sym linked to config/galaxy.ini) and I don’t have a job_conf.xml set up. I’m using drmaa to drive an LSF cluster. BLAST is the main issue here so I was wondering if there’s a way to pass the -num_threads flag without breaking everything until I can build up a new server? Dr. Shane Sturrock NZGL BioIT Admin nzgl(a)biomatters.com

2 4

Galaxy, Docker Containers, and Installing tools not in Toolshed
by Yip, Miu ki 21 Jul '16

21 Jul '16

Hello Galaxy Team, We're from the Bioinformatics Shared Resources at Cold Spring Harbor Lab and we're trying to create a new flavour of Galaxy for local use in the lab using docker containers. We want to add tools that are specific for our lab, such as importing files from our system, onto this flavour of Galaxy using Docker containers. Is there a recommended way to do this? I've taken a look at the README from: https://github.com/bgruening/docker-galaxy-stable I have been able to successfully create an instance of Galaxy where the homepage is different and tools are imported from the Tool Shed. However, I cannot figure out how to install tools onto Galaxy that are not from the Tool Shed. I have tried creating a container, putting the tools into the tools folder, changing the tool conf and the integrated tool panel xml file. Then committing the container and creating a new image. From the new image, I tried creating another container and running it. This does not create a Galaxy instance with the new tool. (This also does not seem like the best way to go about something like this.) Thank you for your help. Best, Miuki Yip

3 5

Re: [galaxy-dev] errors when updating tools
by Sarah DIEHL 21 Jul '16

21 Jul '16

Hi Nikolay, I set it to 50000 and the request goes through, but I still only see an empty list for "Monitoring installing tool shed repositories". I suppose something is wrong with my existing version of cuffdiff, since I can't update or repair it also. I had issues with galaxy messing up entries in the tool install database before. Maybe the existing entry is screwing up the installation of the new version. Best regards, Sarah ---- Sarah Diehl HPC System Administrator UNIVERSITÉ DU LUXEMBOURG LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE Campus Belval | Biotech II 6, avenue du Swing L-4371 Belvaux T +352 46 66 44 5360 sarah.diehl(a)uni.lu<mailto:sarah.diehl@uni.lu> http://lcsb.uni.lu<http://lcsb.uni.lu/> ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. ----- From: Nikolay Aleksandrov Vazov <n.a.vazov(a)usit.uio.no<mailto:n.a.vazov@usit.uio.no>> Date: Thursday 21 July 2016 13:36 To: Sarah DIEHL <sarah.diehl(a)uni.lu<mailto:sarah.diehl@uni.lu>> Subject: Re: errors when updating tools I am not very familiar with ToolShed and I don't know what "encoded_repo_info_dicts" actually does. Do you remember what your previous values were? The apache option worked for me. Try to set 50000 instead. Nikolay =============== Nikolay Vazov, PhD Department for Research Computing, University of Oslo ________________________________ From: Sarah DIEHL <sarah.diehl(a)uni.lu<mailto:sarah.diehl@uni.lu>> Sent: 21 July 2016 13:05 To: Nikolay Aleksandrov Vazov; galaxy-dev(a)lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org> Subject: Re: errors when updating tools Hi Nikolay, thanks a lot for the hint. I looked up the apache option and everywhere it says that something is wrong if you have to change that ;-). I did it anyway and I can see in the logs that a very long request appears that doesn't look right (see attached file) and afterwards I just get an empty page.

1 0

errors when updating tools
by Sarah DIEHL 21 Jul '16

21 Jul '16

Hi, I just updated our Galaxy from 15.10 to 16.04. I also wanted to update the tools installed, but I'm (again) getting a whole bunch of different errors. Some of the updated tools rely on package_cairo_1_12_14, which fails, because it cannot find some of it's dependencies (see package_cairo_errors.jpg): > Error installing tool dependency fontconfig version 2.11.1: Unable to locate required tool shed repository named package_fontconfig_2_11_1 owned by iuc with revision 2ce32675340e. > Error installing tool dependency freetype version 2.5.2: Unable to locate required tool shed repository named package_freetype_2_5_2 owned by iuc with revision 3b09e7916896. In the main overview of the repository I also see the message "Dependency was not resolved by any resolver module." (see package_cairo_resolver.jpg). Is this related and something I should worry about? I did not touch the resolver configuration, I left the line in galaxy.ini commented. I also don't understand why it tries to install a different revision of a package repo that's already installed. I'm having similar errors for some other packages. Furthermore, when I try to "Get Updates" for cuffdiff, I get an internal server error (see cuffdiff_update_error.txt). The same for macs2 (see macs2_update_error.jpg). When I try to install the newest version of cuffdiff from the toolshed, after I click "Install to Galaxy", I get a "Request-URI Too Large" error (from apache I guess). The last message before it fails in the Galaxy log is "Building repository dependency relationships...". I'm a bit reluctant to update any package repositories I have installed, since in the past this lead to dependencies breaking. Also uninstalling and reinstalling usually doesn't help, since the database keeps the records and once it's messed up it stays messed up. I checked on the galaxy-stable docker image and there everything works fine, so I guess it's related to my Galaxy instance, not the package/tool repositories. Any help on how to solve this is greatly appreciated! Best regards, Sarah ---- Sarah Diehl HPC System Administrator UNIVERSITÉ DU LUXEMBOURG LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE Campus Belval | Biotech II 6, avenue du Swing L-4371 Belvaux T +352 46 66 44 5360 sarah.diehl(a)uni.lu<mailto:sarah.diehl@uni.lu> http://lcsb.uni.lu<http://lcsb.uni.lu/> ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

2 2