October 2015 - galaxy-dev - lists.galaxyproject.org

Login problem with Galaxy instance
by Makis Ladoukakis 05 Nov '15

05 Nov '15

Hi I have some experience with setting up Galaxy instances but I came across a very peculiar issue when trying to setup the newest version. While I am able to register as a new user when I try to login I get redirected to the home page without being logged in. In the galaxy.ini is I disabled user_activation as I don't want a confirmation e-mail for new registrations, altered the host to 0.0.0.0 for network use and changed the port (which i opened up through the apache webserver) Am I missing something? Any help would be appreciated. Kind regards, Efthymios Ladoukakis

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installable revisions for repository suite definitions
by Aaron Petkau 04 Nov '15

04 Nov '15

Hello, I'm running into some issues with maintaining multiple installable revisions for a repository suite and I'm not sure if there's something I've missed. I have a local toolshed where I'm maintaining my tools, and I have a repository suite definition, defining a number of dependencies. So, I have: suite_X (mercurial revision 0): Dependency A Dependency B I updated "suite_X" and changed the dependencies: suite_X (mercurial revision 1): Dependency A Dependency B Dependency C I would like to have both mercurial revision 0 and 1 installable in Galaxy, but only revision 1 (the latest) is showing up as installable. I found documentation at https://wiki.galaxyproject.org/RepositoryRevisions but this seems to only cover a repository containing a single tool, not a suite of tools. Is there something I'm doing wrong or some setting I have to change here? My toolshed is running with Galaxy tag "v15.07". Thanks, Aaron

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support for newer versions of Torque
by Malcolm Tobias 04 Nov '15

04 Nov '15

I'm having trouble "scrambling my eggs". I'm trying to build PBS support into Galaxy on a cluster running Torque >5.0. The problem seems to be with pbs_python 4.4.0 which doesn't build against newer versions of Torque. I was able to download 4.6.0 and was able to build it from: ftp://ftp.surfsara.nl/pub/outgoing/pbs_python.tar.gz but I'm not sure how to integrate that build with Galaxy. It seems if 4.6.0 was available from: http://eggs.galaxyproject.org/pbs_python/ I'd have a chance. Any thoughts? Cheers, Malcolm -- Malcolm Tobias 314.362.1594

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Developing package wrappers
by Tiago Rodrigues Antao 02 Nov '15

02 Nov '15

Hi, I am afraid that I might be overlooking something obvious but... I am trying to add a few tools to the RAD-Seq portfolio of Galaxy. For that effect I am designing a few package wrappers. My problem is to understand the best practice to develop wrappers for dependencies of external tools. For normal tools, that is quite easy: one uses the galaxy/tool/XXX to do all development and testing. But for dependency wrappers, the only solution that I have found is to upload the wrapper to a toolshed and installing it via the admin interface... This is cumbersome. Is there any way to test/develop a package wrapper so that I can test tool_dependencies.xml without uploading it to a toolshed and installing it from there? Thanks, Tiago

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Re: [galaxy-dev] Good entry bugs/entry points to start developing for Galaxy
by Eric Rasche 31 Oct '15

31 Oct '15

30. okt. 2015 10.45 p.m. skrev Damian Birchler <damian(a)damianbirchler.net>: > > Thanks Eric and Bjoern for your quick replies. > > I think I'll have a look at issue "Join two Datasets" (join1) does not > preserve column headers #524, which I believe you tagged as beginner > friendly, Eric? Ah, yes, I migrated that one from trello. Peter Cock (@peterjc) is the original author of that issue, and I'm sure if yoi have questions on the underlying issue he'll be able to help. > > Should I note down somewhere that I'm looking at this? Just comment on the card! It's an easy way for us to keep in touch and whenever you solve the bug github can associate it with your pull request and close it :-) > > Cheers, > Damian > > On 2015-10-30 22:04, Eric Rasche wrote: > > Hi Damian, > > > > > > 30. okt. 2015 9.43 p.m. skrev Damian Birchler > > <damian(a)damianbirchler.net>: > >> > >> Hi list > >> > >> I'm looking to get involved in Galaxy as a developer and I was > >> wondering > >> whether you could point me to one (a few) bugs that you consider > >> having > >> a go at would be a good entry point into developing for Galaxy. > >> > >> I know Python and a bit of Javascript (not familiar with Javascript > >> libraries, though) and almost nothing of bioinformatics - altought I'm > >> eager to learn more about just that. > > > > Great! That's excellent news. > > > > We're currently migrating some of our issues to github from trello. > > You might be interested in those tagged beginner-friendly > > https://github.com/galaxyproject/galaxy/labels/beginner-friendly > > > > Generally whoever tagged one of those as beginner friendly should be > > able to provide guidance and answer questions you might have. > > > >> > >> Unfortunately I couldn't access the Trello card mentioned at > >> https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md under > >> before you begin with "with links to smaller issues we believe would > >> make the best entry points for new developers" - if I access this link > >> nothing happens for quite a while and then Firefox asks me whether I > >> want to kill an unresponsive script. > > > > Heh, that happens to me with trello too, it does not play nicely with > > my out of date work desktop. > > > >> > >> Thanks, > >> Damian > > > > Ciao, > > Eric > >> ___________________________________________________________ > >> 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] Good entry bugs/entry points to start developing for Galaxy
by Eric Rasche 30 Oct '15

30 Oct '15

Hi Damian, 30. okt. 2015 9.43 p.m. skrev Damian Birchler <damian(a)damianbirchler.net>: > > Hi list > > I'm looking to get involved in Galaxy as a developer and I was wondering > whether you could point me to one (a few) bugs that you consider having > a go at would be a good entry point into developing for Galaxy. > > I know Python and a bit of Javascript (not familiar with Javascript > libraries, though) and almost nothing of bioinformatics - altought I'm > eager to learn more about just that. Great! That's excellent news. We're currently migrating some of our issues to github from trello. You might be interested in those tagged beginner-friendly https://github.com/galaxyproject/galaxy/labels/beginner-friendly Generally whoever tagged one of those as beginner friendly should be able to provide guidance and answer questions you might have. > > Unfortunately I couldn't access the Trello card mentioned at > https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md under > before you begin with "with links to smaller issues we believe would > make the best entry points for new developers" - if I access this link > nothing happens for quite a while and then Firefox asks me whether I > want to kill an unresponsive script. Heh, that happens to me with trello too, it does not play nicely with my out of date work desktop. > > Thanks, > Damian Ciao, Eric > ___________________________________________________________ > 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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Good entry bugs/entry points to start developing for Galaxy
by Damian Birchler 30 Oct '15

30 Oct '15

Hi list I'm looking to get involved in Galaxy as a developer and I was wondering whether you could point me to one (a few) bugs that you consider having a go at would be a good entry point into developing for Galaxy. I know Python and a bit of Javascript (not familiar with Javascript libraries, though) and almost nothing of bioinformatics - altought I'm eager to learn more about just that. Unfortunately I couldn't access the Trello card mentioned at https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md under before you begin with "with links to smaller issues we believe would make the best entry points for new developers" - if I access this link nothing happens for quite a while and then Firefox asks me whether I want to kill an unresponsive script. Thanks, Damian

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Uploading files to Galaxy with nginx proxy server
by McCully, Dwayne (NIH/NIAMS) [C] 30 Oct '15

30 Oct '15

Hello Everyone, Uploading a file does not complete with a listing of the file in the history section. The file upload does reach 100 percent. Files are successfully being upload but not displayed. I'm getting the below error In my pastore.log file. galaxy.tools ERROR 2015-10-30 11:00:53,471 Checking parameter files failed. 'UploadDataset' object has no attribute 'from_html' galaxy.tools ERROR 2015-10-30 11:00:53,589 tools::to_json() - Skipping parameter expansion for files. Traceback (most recent call last): File "/home/niamsgalaxy/galaxy/lib/galaxy/tools/__init__.py", line 2550, in iterate tool_dict = input.to_dict(trans, other_values=other_values) TypeError: to_dict() got an unexpected keyword argument 'other_values' Any hints would be appreciated. Dwayne

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Uploading files to Galaxy with nginx proxy server
by McCully, Dwayne (NIH/NIAMS) [C] 30 Oct '15

30 Oct '15

Hello Everyone, Uploading a file does not complete with a listing of the file in the history section. The file upload does reach 100 percent. I'm getting the below error In my pastore.log file. galaxy.tools ERROR 2015-10-30 11:00:53,471 Checking parameter files failed. 'UploadDataset' object has no attribute 'from_html' galaxy.tools ERROR 2015-10-30 11:00:53,589 tools::to_json() - Skipping parameter expansion for files. Traceback (most recent call last): File "/home/niamsgalaxy/galaxy/lib/galaxy/tools/__init__.py", line 2550, in iterate tool_dict = input.to_dict(trans, other_values=other_values) TypeError: to_dict() got an unexpected keyword argument 'other_values' Any hints would be appreciated. Dwayne

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toolshed and proxy
by Floreline TOUCHARD 30 Oct '15

30 Oct '15

Hi, I've got an issue with the toolshed : I can't open it. I installed my galaxy instance on a server protected by a firewall and proxy. The toolshed url (https://toolshed.g2.bx.psu.edu) is open for this server. The wget command works (I can download the index.html file). Firefox is configured with the proxy just as my server (http_proxy). But when I try to access the toolshed, I have a "page not found" error. I installed Firebug for details on the error output. Here is the url Galaxy tries to access : https://toolshed.g2.bx.psu.edu/repository/browse_valid_categories?galaxy_ur… <servername>:<port> Any ideas ? Where should I start my investigations ? Thanks in advance ! F.T

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