- galaxy-dev - lists.galaxyproject.org

View uploaded files
by pieter coussement 15 Mar '17

15 Mar '17

Hi, I just updated galaxy, and now I seem to be unable to view the contents of the files. So i'm able to upload, and can work with them and see the attributes. If however I want to open them ('the eye' on the left), I get an error (as do my collegues) I checked on the full path and the file is there. permission on the file: -rw-r--r-- 1 galaxy galaxy 16 mrt 1 12:10 dataset_140.dat nginx vhost ## # Galaxy ## upstream galaxy_app { server 127.0.0.1:8080; } proxy_next_upstream off; server { client_max_body_size 10G; # ... other server stuff ... location / { proxy_pass http://galaxy_app; proxy_set_header X-Forwarded-Host $host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; } location /static { alias /home/galaxy/Software/galaxy/static; expires 24h; } location /static/style { alias /home/galaxy/Software/galaxy/static/style/blue; expires 24h; } location /static/scripts { alias /home/galaxy/Software/galaxy/static/scripts; } location /favicon.ico { alias /home/galaxy/Software/galaxy/static/favicon.ico; } location /robots.txt { alias /home/galaxy/Software/galaxy/static/robots.txt; } # serve static content for visualization and interactive environment plugins location ~ ^/plugins/(?<plug_type>.+?)/(?<vis_name>.+?)/static/(?<static_file>.*?)$ { alias /home/galaxy/Software/galaxy/config/plugins/$plug_type/$vis_name/static/$static_file; } location /_x_accel_redirect/ { internal; alias /; } location ~ \.php$ { fastcgi_pass 127.0.0.1:9000; include /etc/nginx/conf.d/*.conf; include /etc/nginx/sites-enabled/*; fastcgi_intercept_errors on; error_page 404 /error/404.php; } } I would guess a permission error of some kind but I seem unable to find it. Nginx spits out: 2017/03/01 17:23:39 [error] 28783#0: *1457 open() "/usr/share/nginx/htmltrue/home/galaxy/Software/galaxy/database/files/000/dataset_14 0.dat" failed (2: No such file or directory), client: 172.19.40.126, server: , request: "GET /datasets/32d48e3506ae8cf7/display/?previ ew=True HTTP/1.1", upstream: "http://127.0.0.1:8080/datasets/32d48e3506ae8cf7/display/?preview=True", host: "172.19.32.42", referrer: "http://172.19.32.42/" the file is in home/galaxy/Software/galaxy/database/files/000/dataset_140.dat but the folder /usr/share/nginx/htmltrue does not exists... Any help on this one? Best regards, Pieter -- *ir. Pieter Coussement, PhD* pieter.coussement(a)inbiose.com <mailto:pieter.coussement@inbiose.com> +32 (0) 485 42 79 72 www.inbiose.com <http://www.inbiose.com> Registered address: Inbiose N.V., Technologiepark Zwijnaarde 3 – bus 41, B-9052 Gent, Belgium - rpr gent: 0534 887 593 Confidentiality notice: The information contained in this e-mail, including any attachments, is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify the sender by return e-mail and delete this e-mail, including any attachments. Disclaimer: The author of this e-mail has taken every effort to ensure that the information and advice provided are accurate and up-to-date, based upon the information available at the time of writing. The information and advice can only be binding for Inbiose when this is clearly intended in the message and is contained in the information made available.

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Disk organization for Jetstream Galaxy instance
by David Kovalic 14 Mar '17

14 Mar '17

Hi, When we launch a Galaxy instance on Jetstream, the galaxy user's home dir is set up on the root volume, this has inherent limitations. Is there a good way to change the home dir location to an attached disk? Thanks, David

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Tool dependency installation on older Galaxy installations
by Brian Claywell 14 Mar '17

14 Mar '17

We're running an older version of Galaxy (15.07) locally. Is there currently any way to tell what tools in the toolshed (or, worse, what versions of a tool with multiple revisions) won't install their dependencies properly because they rely on Conda dependency management and don't support the old dependency management system any more? Thanks! Cheers, Brian -- Brian Claywell | programmer/analyst Matsen Group | matsen.fredhutch.org <http://matsen.fhcrc.org/> Fred Hutchinson Cancer Research Center

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Newline characters for txt files
by Lawrence, Cris W 14 Mar '17

14 Mar '17

I have observed that when I upload a file with CRLF line endings into Galaxy and then later download it, the endings have changed to UNIX (LF only). I also observed that an uploaded file containing CR only line endings in Galaxy downloads to a file again with LF only line endings. These file types are txt. Just want to confirm - does Galaxy scrub line endings? - Cris

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installation error on venv dependencies.xml
by Linda Bakker 14 Mar '17

14 Mar '17

Hi All, I am having some problems with my tool dependencies to setup a python venv. Dependencies.xml looks like this: When i install my tool from the toolshed, it fails to install the venv dependency with this error message: I am not sure what the problem exactly seems to be. os.py should be a default python package right or do i need to specify it in the dependencies file? Can someone point me in the right direction of what the problem might be. Thanks! with regards , Linda Bakker -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bakker(a)wur.nl

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Search Tool Shed
by Matthias Bernt 09 Mar '17

09 Mar '17

Dear mailing list, What is the expected behavior if I click in the Admin area under "Search Tool Shed" on the "Galaxy Main Tool Shed" button (or any of the Browse .. or Search .. actions that are available via the black triangle submenu)? I remember that a new tab with the corresponding Tool Shed page opened in the browser. This is currently not happening in my installation. What could be the problem? As a work around I can trigger the Browse action via right click and "open link in new tab". As far as I can see this is not a JavaScript problem. Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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Re: [galaxy-dev] Shared Data Library, large number of files
by Hans-Rudolf Hotz 08 Mar '17

08 Mar '17

this sounds more like a browser issue to me which browser do you use? what happens when you use a different browser? and what happens when you just reload the page Hans-Rudolf On 03/01/2017 06:17 PM, D K wrote: > Actually, when I click on the Shared Data-> Data Libraries link I get > only the Galaxy banner and a blank page, so I'm not even seeing the data > libraries themselves. > > If I use the Admin link and then click Data libraries, I can see the > actual libraries. But when I try to enter one of the libraries with lots > of files it hangs. > > > On Wed, Mar 1, 2017 at 9:03 AM, D K <danielfortin86(a)gmail.com > <mailto:danielfortin86@gmail.com>> wrote: > > Hi Hans, > > I'm running 16.10. If I'm not mistaken, the old Data Library > interface is still accessible in the Admin menu isn't it? I have the > same issue when navigating to a Data Library either from the Admin > or Shared Data links. I also tried this in 16.07 with the same > result. If it makes a difference, I'm using PostgreSQL and Apache. > > Dwight > > > > On Tue, Feb 28, 2017 at 11:47 PM, Hans-Rudolf Hotz <hrh(a)fmi.ch > <mailto:hrh@fmi.ch>> wrote: > > Hi Daniel > > Just double checking which version of galaxy are you running? In > other words: are you still using the old Data Library interface? > (if I remember correctly, the old UI was deprecated in 15.10) > We had similar issues with the old UI. > > The new one works fine and is very fast. E.g. we have a 'MISEQ' > folder with more than 100 sub folders and a HISEQ folder with > more than 600 sub folders. Each containing up to 100plus fastq > and text files. > > Regards, Hans-Rudolf > > > > On 03/01/2017 12:13 AM, D K wrote: > > Hi, > > I've noticed that the more files / folders (think hundreds > of folders > each with 20+ fastq files) I add to a Shared Data Library, > the longer > and longer it takes to initially navigate the folder > structure (after > clicking on the specific Shared Data Library). Just opening > up the > Shared Data Library can take several minutes and often the > browser times > out. Is there a way to speed this up? > > If it's relevant, when I add shared data, it's linked rather > than copied > into Galaxy. Any suggestions would be greatly appreciated > > Thanks! > > > ___________________________________________________________ > 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/ > <https://lists.galaxyproject.org/> > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > <http://galaxyproject.org/search/mailinglists/> > > >

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Rg: Galaxy Version
by Anamika Singh 08 Mar '17

08 Mar '17

Dear galaxy team, I am using galaxy platform (old version) in Linux OS which was not installed by me. I would like to know 'how to check what is the galaxy version installed currently in my system. Regards -- Anamika

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tool problems (data_manager_fetch_ncbi_taxonomy & ggplot2)
by Matthias Bernt 08 Mar '17

08 Mar '17

Dear mailing list, I'm experimenting with the tools available at the Tool Shed and ran into problems with two of the tools. 1. data_manager_fetch_ncbi_taxonomy If I run the data manager I get an error in the browser: "Uncaught exception in exposed API method" The terminal shows the following stack trace: Traceback (most recent call last): File "/home/berntm/galaxy/lib/galaxy/web/framework/decorators.py", line 282, in decorator rval = func( self, trans, *args, **kwargs ) File "/home/berntm/galaxy/lib/galaxy/webapps/galaxy/api/tools.py", line 98, in build return tool.to_json(trans, kwd.get('inputs', kwd)) File "/home/berntm/galaxy/lib/galaxy/tools/__init__.py", line 1853, in to_json tools = self.app.toolbox.get_loaded_tools_by_lineage( self.id ) File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 492, in get_loaded_tools_by_lineage tool_lineage = self._lineage_map.get( tool_id ) File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/factory.py", line 38, in get lineage = ToolShedLineage.from_tool_id( self.app, tool_id ) File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/tool_shed.py", line 70, in from_tool_id return ToolShedLineage( app, tool_version ) File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/lineages/tool_shed.py", line 53, in __init__ self.tool_version_id = tool_version.id File "/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/attributes.py", line 237, in __get__ return self.impl.get(instance_state(instance), dict_) File "/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/attributes.py", line 578, in get value = state._load_expired(state, passive) File "/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/state.py", line 474, in _load_expired self.manager.deferred_scalar_loader(self, toload) File "/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/loading.py", line 610, in load_scalar_attributes (state_str(state))) DetachedInstanceError: Instance <ToolVersion at 0x7fc7180b5310> is not bound to a Session; attribute refresh operation cannot proceed Any ideas whats going on - and how to fix this? 2. The second tool is ggplot2_2_2_1. Here mingchen0919 is listed as owner in the Tool Shed -- so I do not know if this mailing list is the correct address. If not: how do I find contact information to the owner of a tool in the ToolShed? Otherwise, the problem is missing dependencies: In package_fontconfig_2_11_1 (which is a dependency of ggplot) I get """ configure: error: in `/home/berntm/galaxy/database/tmp/tmp-toolshed-mtdBsL0ig/fontconfig-2.11.1': configure: error: The pkg-config script could not be found or is too old. Make sure it is in your PATH or set the PKG_CONFIG environment variable to the full path to pkg-config. Alternatively, you may set the environment variables FREETYPE_CFLAGS and FREETYPE_LIBS to avoid the need to call pkg-config. See the pkg-config man page for more details. To get pkg-config, see <http://pkg-config.freedesktop.org/>. See `config.log' for more details """ Is pkg-config supposed to be installed on the computer running galaxy? Or should this be installed within galaxy? In addition on the terminal the following error appears after the pkg-config error: """ Exception happened during processing of request from ('127.0.0.1', 42534) Traceback (most recent call last): File "/home/berntm/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 331, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 654, in __init__ self.finish() File "/usr/lib/python2.7/SocketServer.py", line 713, in finish self.wfile.close() File "/usr/lib/python2.7/socket.py", line 283, in close self.flush() File "/usr/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe """ Thank you very much for your help. Best regards, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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March 2017 News of the Galaxy
by Dave Clements 07 Mar '17

07 Mar '17

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