- galaxy-dev - lists.galaxyproject.org

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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Re: [galaxy-dev] cognoma
by Casey Greene 19 Jul '16

19 Jul '16

Thank you for your interest in the cognoma project [ http://dev.list.galaxyproject.org/cognoma-td4669691.html ]. As it turns out, we have heard of Galaxy. It would be hard to be in computational biology and unaware of Galaxy. We appreciate the galaxy project's contributions to web-based workflows in bioinformatics. For the use case and target audience that we aim to serve, galaxy seemed less suited than alternative light weight and modular approaches. Of course, we appreciate your enthusiasm for galaxy and cognoma! If you feel passionately that galaxy is the right framework, the easiest way to demonstrate that is by delivering a galaxy-cognoma solution. Thanks! Casey

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jupyter + apache proxy + SSL
by Nikolay Aleksandrov Vazov 19 Jul '16

19 Jul '16

Hi, I am trying to set up galaxy server with IE jupyter with apache proxy and SSL enbled. Does anybody have a similar setup? I am using == galaxy.ini dynamic_proxy_manage=False ('True' gives the same error) dynamic_proxy=node dynamic_proxy_session_map=database/session_map.sqlite #dynamic_proxy_bind_port=8800 #dynamic_proxy_bind_ip=0.0.0.0 dynamic_proxy_external_proxy=True dynamic_proxy_prefix=gie_proxy == httpd.conf ProxyPass /gie_proxy/jupyter/ipython/api/kernels ws://localhost:8800/gie_proxy/jupyter/ipython/api/kernels VirtualHost _default_:80> RewriteEngine on ReWriteCond %{SERVER_PORT} !^443$ RewriteRule ^/(.*) https://%{HTTP_HOST}/$1 [NC,R,L] </VirtualHost> It works fine with HTTP but not HTTPS and, naturally, I get jquery.js:10261 Mixed Content: The page at 'https://mydomain.xx/' was loaded over HTTPS, but requested an insecure XMLHttpRequest endpoint 'http://mydomain.xx/gie_proxy/jupyter/ipython/login?next=%2Fgie_proxy%2Fjupy…'. This request has been blocked; the content must be served over HTTPS. Is there a way to modify the container config such that it runs on a https, or is there a galaxy configuration routine I can use? Thank you Nikolay =============== Nikolay Vazov, PhD Department for Research Computing, University of Oslo

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cognoma
by Calvin Morrison 19 Jul '16

19 Jul '16

Hi guys, a recruiter hit me up recently and mentioned a local hackathon.. I took a look at their big biologist machine learning online service idea, but it sounded awfully fimiliar. Looks like the greenlab out of UPenn hasn't heard of galaxyproject, but I'm not doing a very good job explaining how galaxy could be leveraged to do exactly what I want... just seems like awful duplication on their part when expanding galaxy would be preferable. see my issue on it: https://github.com/cognoma/cognoma/issues/18#issuecomment-233335587 Their website: https://github.com/cognoma/cognoma/ A current doc outlining the project: https://docs.google.com/document/d/1QoLZwTmMhvu_tv3SO4bA3-XomV1y5BR0CWhh833… Any ideas I can spin them to help convince them that galaxy probably does almost everything they need, aside from integrating their tools? Calvin

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Implementing iRODS with Galaxy
by Katherine Beaulieu 18 Jul '16

18 Jul '16

Hi there, I have developed a tool that does the importing and exporting to Galaxy. Please see the attached link to the github repos for the two tools. Please keep in mind that this tool is still in development. As well, it has only been tested on a local instance of Galaxy and the authentication with iRODS has not quite been worked on. If you have any suggestions please let me know. https://github.com/AAFC-MBB/Galaxy/tree/dev/wrappers/irods_pull https://github.com/AAFC-MBB/Galaxy/tree/dev/wrappers/irods_push

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Suggestion for Structural Variant Analysis onto Galaxy Main
by Wong, Orlando 15 Jul '16

15 Jul '16

Hello Galaxy dev I would like to suggest the idea of adding structural variant analysis tools for large structural variations for detecting long insertions, inversions or translocations on to the Galaxy Main. Currently, there are tools for detecting small variants, less than 50 bp for small indels. There are some of these structural variant analysis tools available on the Galaxy toolshed, but none are available on Galaxy Main or any of the other public galaxy servers listed on the wiki. I think it would be a great addition to Galaxy main, if it is possible. Thank you!

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planemo shed_create bug? on planemo/server docker image
by Steve Cassidy 15 Jul '16

15 Jul '16

I’m just getting my head around tool dependencies and in doing so trying to push my tools to a local toolshed which I can handily run with the planemo/server docker image via Kitematic. That toolshed is set up with an admin user planemo(a)test.com<mailto:planemo@test.com> so I have a stanza in my .planemo.yml: shed_username: "stevecassidy" sheds: http://localhost:32768/: key: "" email: "planemo(a)test.com<mailto:planemo@test.com>" password: "planemo" Now I try to create a repository in the toolshed with planemo: $ planemo shed_create --shed_target http://localhost:32768/ Repository created cd '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git rev-parse HEAD cd '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git diff --quiet Repository [alveoimport] does not exist in the targeted Tool Shed. Note the conflicting messages here. The repository is created (and I can confirm that it is there) but then I get the message that the repo does not exist in the Toolshed. After a bit of digging it turns out that this is because the repo is owned by the user ‘planemo’ rather than my username as declared in .planemo.yml. If I add —owner plane to the command then it works fine. So I’m not sure if this is a bug in the shed_create code or a weird interaction with the setup on planemo/server. Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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