galaxy-dev July 2016

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49 participants
69 discussions

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/ >> > >

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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/ >> > >

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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

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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

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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

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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.

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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. -----

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Uploads not working in local Galaxy installation
by Adrià Cereto i Massagué 21 Jul '16

21 Jul '16

Hello, I've been trying to get working a local galaxy installation, using nginx with the upload module as a proxy. It all seems to work, except uploading files to Galaxy, where I get a "GET /_upload/ HTTP/1.1" 404 and nothing else Ic an find in the logs. There must be some misconfiguration somewhere, but I can't sport it. Could you help me? Here's my nginx.conf: user galaxy; > worker_processes 10; > pid /run/nginx.pid; > > events { > worker_connections 768; > } > http { > gzip on; > gzip_http_version 1.1; > gzip_vary on; > gzip_comp_level 4; > gzip_proxied any; > gzip_types text/plain text/css application/x-javascript text/xml > application/xml text/javascript application/json; > gzip_buffers 16 8k; > gzip_disable "MSIE [1-6].(?!.*SV1)"; > upstream galaxy_app { > server localhost:8080; > } > server { > client_max_body_size 10G; > location / { > proxy_pass http://galaxy_app; > proxy_set_header X-Forwarded-Host $host; > proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; > } > location /_x_accel_redirect/ { > internal; > alias /; > } > location ~ > ^/plugins/visualizations/(?<vis_name>.+?)/static/(?<static_file>.*?)$ { > alias > /home/galaxy/galaxy/config/plugins/visualizations/$vis_name/static/$static_file; > > expires 24h; > } > location /static { > alias /home/galaxy/galaxy/static; > expires 24h; > } > location /static/style { > alias /home/galaxy/galaxy/static/june_2007_style/blue; > expires 24h; > } > location /static/scripts { > alias /home/galaxy/galaxy/static/scripts/packed; > expires 24h; > } > location /favicon.ico { > alias /home/galaxy/galaxy/static/favicon.ico; > expires 24h; > } > location /robots.txt { > alias /home/galaxy/galaxy/static/robots.txt; > expires 24h; > } > location /_upload { > upload_store /home/galaxy/galaxy/database/tmp/upload_store; > upload_pass_form_field ""; > upload_set_form_field "__${upload_field_name}__is_composite" > "true"; > upload_set_form_field "__${upload_field_name}__keys" "name > path"; > upload_set_form_field "${upload_field_name}_name" > "$upload_file_name"; > upload_set_form_field "${upload_field_name}_path" > "$upload_tmp_path"; > upload_pass_args on; > upload_pass /_upload_done; > } > location /_upload_done { > set $dst /api/tools; > if ($args ~ nginx_redir=([^&]+)) { > set $dst $1; > } > rewrite "" $dst; > } > location /plugins { > alias /home/galaxy/galaxy-dist/config/plugins; > } > } > } > And here's my galaxy.ini: [server:handler0] > port = 8090 > host = 127.0.0.1 > use_threadpool = true > threadpool_workers = 10 > > [server:handler1] > port = 8091 > host = 127.0.0.1 > use_threadpool = true > threadpool_workers = 10 > > [server:handler2] > port = 8092 > host = 127.0.0.1 > use_threadpool = true > threadpool_workers = 10 > > [server:handler3] > port = 8093 > host = 127.0.0.1 > use_threadpool = true > threadpool_workers = 10 > > [server:main] > port = 8080 > host = 0.0.0.0 > use_threadpool = True > threadpool_workers = 30 > threadpool_kill_thread_limit = 10800 > > [filter:gzip] > > [filter:proxy-prefix] > prefix = /galaxy > > [app:main] > paste.app_factory = galaxy.web.buildapp:app_factory > database_connection = postgresql://galaxy:not_the_actual_password@localhost > /galaxy?host=/var/run/postgresql > nginx_x_accel_redirect_base = /_x_accel_redirect > nginx_upload_store = database/tmp/upload_store > nginx_upload_path = /_upload > tool_dependency_dir = dep_dir > use_nglims = False > nglims_config_file = tool-data/nglims.yaml > static_enabled = True > debug = False > use_interactive = False > id_secret = ValarDohaerys > admin_users = adria.cereto(a)ctns.cat, galactus(a)galaxy.gal > allow_user_impersonation = True > allow_user_dataset_purge = True > new_user_dataset_access_role_default_private = True > expose_user_name = True > master_api_key = heavysplatling > track_jobs_in_database = True > enable_job_recovery = True > > [galaxy_amqp] > > [uwsgi] > processes = 44 > stats = 127.0.0.1:9191 > socket = 127.0.0.1:4001 > pythonpath = lib > threads = 12 > logto = /home/galaxy/uwsgi.log > master = True Thank you in advance, Adrià -- *Adrià Cereto i Massagué* Centre for Omic Sciences (COS) www.omicscentre.com Servei de Recursos Científics i Tècnics (SRCiT) Universitat Rovira i Virgili Av. Universitat, 1. 43204 Reus (Catalonia) Tel: +34 977 77 69 32 <%2B34%20977%2077%2014%2009> Extensió URV: 4838 Languages: Català, Español, English, Français, Deutsch, Português Important Notice <http://www.gnu.org/philosophy/no-word-attachments.html>

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Fwd: New galaxy parameter type
by Martin Čech 20 Jul '16

20 Jul '16

forwarding to the list ---------- Forwarded message --------- From: Katherine Beaulieu <katherine.beaulieu014(a)gmail.com> Date: Fri, Jul 15, 2016 at 3:45 PM Subject: Re: [galaxy-dev] New galaxy parameter type To: Martin Čech <marten(a)bx.psu.edu> Thanks Peter, I will look into that. The reason I am asking is because of what Mohammed asked earlier as well. I developed two tools which allow you to import and export information from a program called irods but you need to be able to authenticate with irods to be able to do so. Thanks again for always being helpful! On Fri, Jul 15, 2016 at 3:10 PM, Martin Čech <marten(a)bx.psu.edu> wrote: > Katherine please disregard my answer, I probably misread your question. :) > M. > > On Fri, Jul 15, 2016 at 3:05 PM Peter Cock <p.j.a.cock(a)googlemail.com> > wrote: > >> Did you mean parameter as in input field shown >> to the user? Like a combobox or text field? >> >> Since this happened to come up earlier today, here's >> a rejected pull request which added a password >> parameter - that ought to give you a rough idea: >> >> https://github.com/galaxyproject/galaxy/pull/393 >> >> Peter >> >> On Fri, Jul 15, 2016 at 7:46 PM, Katherine Beaulieu >> <katherine.beaulieu014(a)gmail.com> wrote: >> > Hi everyone, >> > I am looking to implement a new parameter type for galaxy tool >> development. >> > Does anyone know what would be involved in doing something like this or >> > perhaps what files would need to be edited? >> > >> > >> > ___________________________________________________________ >> > 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/ > >

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Issue creating cluster
by Cameron Buckley 19 Jul '16

19 Jul '16

Hi Galaxy Dev, I'm currently trying to create a cluster following this guide: http://vlsci.github.io/lscc_docs/tutorials/gvl_launch/gvl_launch/ I did this a couple of weeks ago and worked fine. However, I terminated my instance on NectarCloud this morning and have been unsuccessful in creating a new cluster (see screenshot below - problem getting security groups?). I'm unsure if this should be directed to NectarCloud support instead? [cid:image001.jpg@01D1E261.EC545570] Any information would be great. Regards, Cam

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galaxy-dev July 2016