- galaxy-dev - lists.galaxyproject.org

Customising the Galaxy FTP Upload interface for import from Linux
by Peter Cock 29 Aug '16

29 Aug '16

Hello all, RE: https://wiki.galaxyproject.org/Admin/Config/UploadviaFTP We're in the process of setting up a new Galaxy server integrated into our cluster, where all the accounts will map to a Linux user and jobs on the cluster will run as that user. Because many of the users will have their input data already on the shared Linux file system, we have re-used the FTP upload functionality as an easy way to directly get files into Galaxy. 1. On Linux copy data to the /mnt/shared/pretend_ftp_upload folder, 2. On Galaxy import these files via the "FTP" upload. This seems to work fairly well, but to make it smoother we'd ideally like to edit the Galaxy UI to replace the "FTP" text. Has anyone done this before, or is there a better way - ideally could we let users browse their Linux account's home folder? Thanks, Peter

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Galaxy migration to docker environment
by Matthias De Smet 29 Aug '16

29 Aug '16

Hi all, We’re looking to migrate our Galaxy instance from a VM based solution to a docker based solution. Therefore, we need to move all our user and reference data. What is the best possible solution to migrate all data and change the path of said data in the database? Thanks! M

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Putting it all together - toolshed tool + conda dependency
by Steve Cassidy 28 Aug '16

28 Aug '16

Hi all, I’m making baby steps towards having a repeatable installation for my tools. But I’m now stuck, so help would be appreciated. I have a tool that works and is in the test toolshed (alveoimport in Data Sources). It depends on my python package which is now part of bioconda (pyalveo, version 0.6). I can run my tool via planemo, which works I think because I have pyalveo installed in a local venv. If I try to run the docker image (derived from bgruening/galaxy-stable but with the testtoolshed added) I am able to install my tool, but it doesn’t pick up the dependency, so it doesn’t work. I tried running with planemo turning on conda dependency resolution (following https://pypi.python.org/pypi/planemo/) planemo serve --galaxy_branch release_16.01 --conda_dependency_resolution . It seems to have a go, but fails: galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Building dependency shell command for dependency 'pyalveo' galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Find dependency pyalveo version 0.6 galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x105bef5d0> (isnull? True) galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x105bef5d0> (isnull? True) galaxy.tools.deps WARNING 2016-08-25 17:32:22,451 Failed to resolve dependency on 'pyalveo', ignoring So, what’s the easiest route to a Galaxy deployment with my tool installed. The Docker route would be best I think, but what do I have to add to bgruening/galaxy-stable to have conda find my dependencies. Thanks in advance, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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Loading a GUI on galaxy
by Lijo John 28 Aug '16

28 Aug '16

Hello All, I want to know, whether it is possible to embed graphical user interface like that of WEKA VisualizePanel tool in galaxy ? I am able to load the GUI on a local instance of galaxy. But when i am trying to access the galaxy server through a remote connection, this GUI is not able to load on remote desktop. Any comments or suggestions would be of great interest ! -- Regards, Lijo John

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Re: [galaxy-dev] Workflow Compatibility
by Katherine Beaulieu 26 Aug '16

26 Aug '16

On Fri, Aug 26, 2016 at 10:42 AM, Katherine Beaulieu < katherine.beaulieu014(a)gmail.com> wrote: > Hi Peter, > I think I did not explain myself well. I meant that if I have a tool that > takes multiple file paths and outputs multiple Galaxy datasets to the > history, would this tool be workflow compatible, meaning capable of being a > part of any workflow? From the behaviour I am getting now I am assuming it > isn't but I just wanted to confirm that this isn't supported functionality. > > On Fri, Aug 26, 2016 at 10:34 AM, Peter Cock <p.j.a.cock(a)googlemail.com> > wrote: > >> Hi Katherine, >> >> Are you asking about compatibility staying on the same Galaxy >> instance, or the harder problem of compatibility sharing workflows >> between Galaxy servers? >> >> Taking data from input Galaxy datasets should be fine, anything else >> may not be portable. Even the relatively simple case of using >> datafiles referenced via an example.loc file (e.g. BLAST databases) >> would require the entries in the example.loc file be synchronised >> between Galaxy instances, and the associated data files too. >> >> Peter >> >> >> On Fri, Aug 26, 2016 at 1:27 PM, Katherine Beaulieu >> <katherine.beaulieu014(a)gmail.com> wrote: >> > Hi Everyone, >> > Would anyone be able to tell me the conditions which would make a tool >> > non-workflow compatible? I have a tool that imports files from a third >> party >> > application and auto-detects the file format. There is also the option >> to >> > upload multiple files at once so the tool always uploads at least two >> files. >> > From what I have described can anyone see why this tool would not be >> able to >> > send one of its files to the next tool in the chain, ex. a text >> manipulation >> > tool? >> > 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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Upgrade to Galaxy 16.07, import dumps problem
by D K 26 Aug '16

26 Aug '16

Hi Galaxy-devs, I just tried upgrading to 16.07 from 16.01 and get this error when starting up: > Traceback (most recent call last): > File "./scripts/paster.py", line 26, in <module> > serve.run() > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py", > line 1061, in run > invoke(command, command_name, options, args[1:]) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py", > line 1067, in invoke > exit_code = runner.run(args) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py", > line 223, in run > result = self.command() > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py", > line 639, in command > app = loadapp( app_spec, name=app_name, relative_to=base, > global_conf=vars) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 292, in loadapp > return loadobj(APP, uri, name=name, **kw) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 317, in loadobj > return context.create() > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 755, in create > return self.object_type.invoke(self) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 274, in invoke > filtered = context.next_context.create() > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 755, in create > return self.object_type.invoke(self) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 191, in invoke > return fix_call(context.object, context.global_conf, > **context.local_conf) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", > line 94, in fix_call > val = callable(*args, **kw) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/buildapp.py", > line 39, in app_factory > return paste_app_factory( global_conf, **kwargs ) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/buildapp.py", > line 76, in paste_app_factory > webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/web/framework/webapp.py", line > 115, in add_ui_controllers > module = import_module( module_name ) > File "/opt/rh/python27/root/usr/lib64/python2.7/importlib/__init__.py", > line 37, in import_module > __import__(name) > File > "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py", > line 16, in <module> > from galaxy.util.json import dumps > ImportError: cannot import name dumps Any suggestions? Thanks!

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The new Galaxy release July 2016 Galaxy Release (v 16.07) is out!
by Jennifer Hillman-Jackson 26 Aug '16

26 Aug '16

July 2016 Galaxy Release (v 16.07) <https://wiki.galaxyproject.org/News/2016_07_GalaxyRelease> The Galaxy Committers team <https://github.com/galaxyproject/galaxy/blob/dev/doc/source/project/organiz…> is pleased to announce the *July 2016 (v16.07) release of Galaxy <https://docs.galaxyproject.org/en/master/releases/16.07_announce.html>*. *Reminders* - Python 2.6 is no longer supported. Details: 16.01 release announcement <https://wiki.galaxyproject.org/News/2016_01_GalaxyRelease> - The Galaxy source is no longer hosted on Bitbucket. Details: 16.04 release announcement <https://github.com/galaxyproject/galaxy/blob/dev/doc/source/releases/16.04_…> . *Highlights <https://docs.galaxyproject.org/en/master/releases/16.07_announce.html#highl…>* [image: Inline image 1] *Get Galaxy <http://getgalaxy.org/>* [image: Inline image 2] On behalf of the Galaxy Core and Contributor team <https://wiki.galaxyproject.org/GalaxyTeam> (and community), *Thanks for using Galaxy!* -- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org

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Workflow Compatibility
by Katherine Beaulieu 26 Aug '16

26 Aug '16

Hi Everyone, Would anyone be able to tell me the conditions which would make a tool non-workflow compatible? I have a tool that imports files from a third party application and auto-detects the file format. There is also the option to upload multiple files at once so the tool always uploads at least two files. From what I have described can anyone see why this tool would not be able to send one of its files to the next tool in the chain, ex. a text manipulation tool? Thanks, Katherine

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Loading GUI on galaxy
by Lijo John 26 Aug '16

26 Aug '16

Hello, I want to know, whether it is possible to embed graphical user interface like that of WEKA VisualizePanel tool in galaxy ? I am able to do it on a local instance of galaxy. But when i am trying to access the server (in which galaxy is installed) this GUI is not able to load on remote desktop. John

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Re: [galaxy-dev] Parameter Storing in Database
by Katherine Beaulieu 25 Aug '16

25 Aug '16

On Thu, Aug 25, 2016 at 2:25 PM, Katherine Beaulieu < katherine.beaulieu014(a)gmail.com> wrote: > Hi Peter, > No actually I meant in what file is the table job_parameter getting filled > during execution? > Katherine > > On Fri, Aug 5, 2016 at 3:00 PM, Peter van Heusden <pvh(a)sanbi.ac.za> wrote: > >> You mean the stuff for the tool-data tables? As I understand it, it is >> loaded in: >> >> lib/galaxy/tools/data/__init__.py >> >> There's a ToolDataTableManager and a TabularToolDataTable (with >> associated TabularToolDataField). >> >> Peter >> >> On Fri, 5 Aug 2016 at 20:46 Katherine Beaulieu < >> katherine.beaulieu014(a)gmail.com> wrote: >> >>> Would anyone be able to tell me in what file the storing of tool >>> parameters into the database occurs? >>> 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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