- galaxy-dev - lists.galaxyproject.org

param name="type"
by Jorrit Boekel 17 Dec '14

17 Dec '14

Hi all, Just a heads-up, I had a tool.xml file in which a command line was called with a parameter called —type. I therefore set <param name=“type” type=“select > etc etc. to do: command —type $type Big mistake. This lead to errors as soon as the tool was modified in the workflow (set as runtime triggered an error for me), due to the fact that the workflow module type was not one of tool, data input, data collection, but was instead the value of the type param which was currently filled in. Now I know not to do this, hope you already did. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

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When do tool tests run on main & test toolsheds?
by Peter Briggs 16 Dec '14

16 Dec '14

Hello all When do the tool tests run on the main and test toolsheds? In Greg's blog about the toolshed: http://gregvonkuster.org/galaxy-tool-shed-certifying-repositories-install-t… it's implied that the tests run daily for both, but it doesn't look like any tests have run for tools that I've pushed to either toolshed over the last few days. I wondered if was because my tests are broken somehow, but the links to "Latest revision: missing tool tests" etc don't bring anything up either. I'm interested because I'd like to check that the tests run on the test toolshed before I push the tool to the main toolshed - so any advice or suggestions appreciated. Best wishes, Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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How galaxy workflow work ?
by Weiyan Shen 15 Dec '14

15 Dec '14

Hi , As we know galaxy tools work with the python,perl,and other tools script in galaxy-dist/tools,but are there any workflow scripts will be created when we edit or import it to run and where they saved? Are there some details about how galaxy workflow work? Thank you very much.

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server datacache.g2.bx.psu.edu unreachable
by Sarah Maman 15 Dec '14

15 Dec '14

Hello, The server datacache.g2.bx.psu.edu <rsync://datacache.g2.bx.psu.edu/indexes/oviAri1> isn't reachable since 2/3 days, so we can't access to banks provided by Galaxy Project (https://wiki.galaxyproject.org/Admin/UseGalaxyRsync) Could you please give us some informaiton to solve this problem? The error message is the following : /*En essayant d'accéder à l'URL http://datacache.g2.bx.psu.edu/ l'erreur suivante a été rencontrée :*/ /*La connexion 128.118.250.10 a échouée.*/ /*Le système a retourné : *//*(111) Connection refused */ / /Thanks in advance for your help, Sarah Maman -- --*-- Sarah Maman INRA - GenPhySE - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - CS 52 627 - 31326 Castanet Tolosan cedex 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--

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Assertion errors when starting Galaxy
by Lance Parsons 12 Dec '14

12 Dec '14

After updating my local instance of Galaxy to latest_2014.10.06 I get a number of similar errors relating to DisplayApplications. It seems that others have run into this problem as well (see http://dev.list.galaxyproject.org/Assertion-errors-when-starting-Galaxy-td4…) but as of yet I haven't figured out the cause (or a workaround or solution). An example is below: galaxy.datatypes.registry ERROR 2014-12-11 10:57:01,183 Error loading display application (./display_applications/igv/vcf.xml): Filename and id attributes required for dynamic_links Traceback (most recent call last): File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/registry.py", line 576, in load_display_applications display_app = DisplayApplication.from_file( config_path, self ) File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", line 170, in from_file return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry ) File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", line 183, in from_elem for link in DynamicDisplayApplicationBuilder( dynamic_links, rval, datatypes_registry.build_sites ): File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", line 91, in __init__ assert filename is not None, 'Filename and id attributes required for dynamic_links' AssertionError: Filename and id attributes required for dynamic_links Note: Cross posted on Galaxy Biostars site: https://biostar.usegalaxy.org/p/9944/ -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Strange issue with datatypes in Galaxy version of last week
by Lukasse, Pieter 12 Dec '14

12 Dec '14

Hi, Apparently a new datatypes bug has been introduced in the Galaxy version of last week: I have a tool that generates a csv file. Tool configuration is like this: <outputs> <data name="simOut" format="msclust.csv" label="${tool.name} on ${on_string} - SIM file"/> The datatypes has this entry: <datatype extension="msclust.csv" type="galaxy.datatypes.tabular:Tabular" mimetype="text/csv" display_in_upload="true" subclass="true"/> At first Galaxy output seems fine: [cid:image001.png@01CF4847.DE4A1A70] But when I download the file, the downloaded file name will be : Galaxy40-[MsClust_on_data_1_-_SIM_file]- When I go to "edit attributes" and just click "save", then upon downloading again, the file name is correct... Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv . Anyone faced this issue? Thanks and regards, Pieter. Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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Nginx + HTTPS
by Nicholas Kline 11 Dec '14

11 Dec '14

Hello. I am trying to configure our local production Galaxy server to always use HTTPS on nginx. When I visit http://localhost I see the main galaxy webpage where I can sign in. However, when I enter my administrator credentials and click Login, the page tries to redirect to HTTPS but then displays an 'unable to connect' error. What changes do I need to make to my nginx.conf file so that our galaxy server always uses HTTPS. My nginx.conf file is included below. Thanks :) ################## # nginx.conf ################## user www-data; worker_processes 4; pid /run/nginx.pid; events { worker_connections 768; # multi_accept on; } http { ## # Basic Settings ## sendfile on; tcp_nopush on; tcp_nodelay on; keepalive_timeout 65; types_hash_max_size 2048; # server_tokens off; # server_names_hash_bucket_size 64; # server_name_in_redirect off; include /etc/nginx/mime.types; default_type application/octet-stream; ## # Logging Settings ## access_log /var/log/nginx/access.log; error_log /var/log/nginx/error.log; ## # Gzip Settings ## 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)"; ## # nginx-naxsi config ## # Uncomment it if you installed nginx-naxsi ## #include /etc/nginx/naxsi_core.rules; ## # nginx-passenger config ## # Uncomment it if you installed nginx-passenger ## #passenger_root /usr; #passenger_ruby /usr/bin/ruby; ## # Virtual Host Configs ## include /etc/nginx/conf.d/*.conf; #include /etc/nginx/sites-enabled/*; ## # Galaxy ## upstream galaxy_app { # As defined in galaxy config file universe_wsgi.ini server localhost:8080; server localhost:8081; server localhost:8082; server localhost:8083; server localhost:8084; server localhost:8085; server localhost:8086; server localhost:8087; server localhost:8088; server localhost:8089; } server { # Maximum upload size that can be handled by POST requests through nginx. # Disabled because using FTP instead of web interface. #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; # If using SSL, makes Galaxy aware of what type of URL it should generate for external sites like Biomart. proxy_set_header X-URL-SCHEME https; } # nginx is more efficient at serving static content. # expires 24h is for caching purposes. location /static { alias /home/galaxy/galaxy-dist/static; expires 24h; } location /static/style { alias /home/galaxy/galaxy-dist/static/june_2007_style/blue; expires 24h; } location /static/scripts { alias /home/galaxy/galaxy-dist/static/scripts/packed; } location /favicon.ico { alias /home/galaxy/galaxy-dist/static/favicon.ico; } location /robots.txt { alias /home/galaxy/galaxy-dist/static/robots.txt; } # Use nginx to send files (downloads) instead of Galaxy. location /_x_accel_redirect/ { internal; alias /; } } }

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order of tools installed from toolshed
by Wolfgang Maier 10 Dec '14

10 Dec '14

Dear all, I'm currently testing a software package we developed for installation from the testtoolshed. Things seem to work fine mostly, but there is one thing I don't know how to solve (if it can be solved). Our package consists of 14 individual tools, which I uploaded as 14 separate repositories together with a repository suite definition that's taking care of installing all tools. Now, somewhat naively as it seems, I expected the order of repository declarations in the suite definition file to determine the order of the tools in the Galaxy Tools Bar, but, instead, they are added in seemingly random order. So I'm looking for a way to predefine the final order of the tools so that it makes sense for a typical workflow. Any advice how to address this? Thanks for your help, Wolfgang

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Unable to add tools from tool shed
by Ryan G 10 Dec '14

10 Dec '14

I'm following the guide on https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial to add a tool from the tool shed. The tutorial uses 'bwa_base', but I don't see that. So instead, I'm using 'bwa_mem'. I choose 'Preview and Install', then 'Install to Galaxy'. I then select to have it installed in 'NGS: Mapping' tool panel, then click Install. The page then shows two tools: bwa_mem, and package_bwa_0_7_7. Both of which show 'Error' as the status. Clicking on 'bwa_mem' shows some information with "This repository is not installed correctly (see the Repository Installation Error below)...." What does this mean? And how do I fix it?

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"Repository dependency definitions" broken on Test Tool Shed
by Peter Cock 10 Dec '14

10 Dec '14

Hi all, The "Repository dependency definitions" link is working on the Main Tool Shed, but fails with the following exception on the Test Tool Shed: URL: http://testtoolshed.g2.bx.psu.edu/repository/browse_repository_dependencies File '/var/opt/galaxy/toolshed_data/test_toolshed/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/var/opt/galaxy/toolshed_data/test_toolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/var/opt/galaxy/toolshed_data/test_toolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/var/opt/galaxy/toolshed_data/test_toolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/toolshed_data/test_toolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/toolshed_data/test_toolshed/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/var/opt/galaxy/toolshed_data/test_toolshed/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/var/opt/galaxy/toolshed_data/test_toolshed/lib/galaxy/webapps/tool_shed/controllers/repository.py', line 765 in browse_repository_dependencies return self.repository_dependencies_grid( trans, **kwd ) File '/var/opt/galaxy/toolshed_data/test_toolshed/lib/galaxy/web/framework/helpers/grids.py', line 306 in __call__ kwargs=kwargs ) File '/var/opt/galaxy/toolshed_data/test_toolshed/lib/galaxy/web/framework/webapp.py', line 772 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/var/opt/galaxy/toolshed_data/test_toolshed/lib/galaxy/web/framework/webapp.py', line 787 in fill_template_mako return template.render( **data ) File '/var/opt/galaxy/toolshed_data/test_toolshed/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/var/opt/galaxy/toolshed_data/test_toolshed/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/var/opt/galaxy/toolshed_data/test_toolshed/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/var/opt/galaxy/toolshed_data/test_toolshed/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/var/opt/galaxy/toolshed_data/test_toolshed/database/compiled_templates/community/base.mako.py', line 66 in render_body __M_writer(unicode(next.body())) File '/var/opt/galaxy/toolshed_data/test_toolshed/database/compiled_templates/community/grid_base.mako.py', line 91 in render_body __M_writer(unicode(self.load())) File '/var/opt/galaxy/toolshed_data/test_toolshed/database/compiled_templates/community/grid_base.mako.py', line 120 in render_load __M_writer(unicode( h.dumps( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/var/opt/galaxy/toolshed_data/test_toolshed/database/compiled_templates/community/grid_base.mako.py', line 303 in render_get_grid_config value = column.get_value( trans, grid, item ) File '/var/opt/galaxy/toolshed_data/test_toolshed/lib/tool_shed/grids/repository_grids.py', line 1505 in get_value required_repository_metadata_id = trans.security.encode_id( required_repository_metadata.id ) AttributeError: 'NoneType' object has no attribute 'id' Regards, Peter

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