December 2013 - galaxy-dev - lists.galaxyproject.org

sort list of ftp uploaded files
by Ulf Schaefer 18 Dec '13

18 Dec '13

Dear all Is there a way to sort the list of files that a user has uploaded via FTP? Currently they appear on the form of the tool 'Upload File' in random order it seems. There is not much documentation on the <param type="ftpfile" /> tag unfortunately. If the user just selects all files they end up in his/her history in the same random order, which causes a slight inconvenience when using these files as paired multiple input for a workflow. The obvious work-around is to put the files into the history one pair at a time, but this becomes a bit onerous for larger number of files. Thanks a lot for your help. Cheers Ulf ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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Re: [galaxy-dev] How to use Galaxy API?
by Martin Čech 18 Dec '13

18 Dec '13

Hello, by API controller I meant the Python module that takes control over the endpoints of API thus providing logic. You don't need to 'use them' - you can create API requests by many different means by specifying URL (sometimes +params+payload). Look at the extension link I have sent you, that will help you call the API from the browser. M. On Wed, Dec 18, 2013 at 3:15 AM, xlwang <xlwang_0903(a)163.com> wrote: > Hi, > thank you very much for such a quick relpy. > Now, I can connect to galaxy via API. > In addition, please tell me what is API controller?How to use those > modules and where are they in galaxy? > > > > > > At 2013-12-18 12:13:58,"Martin Čech" <marten(a)bx.psu.edu> wrote: > > Hi, > > the best start for using the API, that you found already, is the > documentation that, with a nice introduction, is nicely available here: > https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.… > > Regarding libraries your main controllers of interest are: *libraries*, > *library_contents*, *folders, **folder_contents* - *please beware that > folders API is considered work-in-progress and will probably be deprecated > in future releases.* > > If you want to test how the API behaves you can use something like Postman > extension ( > https://chrome.google.com/webstore/detail/postman-rest-client/fdmmgilgnpjig…) > for chrome or other browser that allows you to nicely simulate API calls. > > As of your error make sure that your local Galaxy, that you are trying to > connect to via API, runs on the 4096 port that you specified for the script > (by default local Galaxy runs at port 8080 - see universe_wsgi.ini for > config changes). > > Thank you for using Galaxy and let us know how it goes! > > Martin, Galaxy Team > > > > On Tue, Dec 17, 2013 at 9:26 PM, xlwang <xlwang_0903(a)163.com> wrote: > >> Hello, >> I want to know how to use Galaxy API(the path is >> /galaxy-dist/scripts/api). I follow the README but get errors. For >> instance, I have generated my_key and use this script: >> ./display.py my_key http://localhost:4096/api/libraries >> I get an error: >> <urlopen error [Errno 111] Connection refused> >> I do not know how it happened. Please tell me how to fix it. Thank you! >> >> In addition, my main purpose is to manage the data library in another >> system. Should I use the api such as library_create_library.py, >> library_upload_from_import_dir.py and so on? >> >> >> >> ___________________________________________________________ >> 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: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > > >

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Bug: Toolbox filters not applied in workflows
by Eric Rasche 18 Dec '13

18 Dec '13

I'm running the stable copy of galaxy and noticed that some custom, administrative tools (and otherwise tools which should be restricted in access due to licensing/etc.) were showing up in normal user's toolboxes inside the workflow editor. I feel that this is a bug, as the tool filters should be applied globally and not just in terms of what tools users are restricted from seeing in the normal toolbox. For me, this presents a problem as I strongly believe any administrative tools that exist should leak as little information as possible--not their entire set of options and associated documentation. Additionally, that sort of information leakage isn't acceptable by my organisation's policies. Do I have my instance misconfigured or is this an actual bug? I have my galaxy configured according to https://wiki.galaxyproject.org/Admin/Config/Access%20Control $ hg head changeset: 11242:9d4cbf2a1c13 branch: stable tag: tip user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Dec 06 16:28:31 2013 -0500 summary: Add missing destination long arg to cli runner's Torque plugin and fix an incorrectly used PBS option in the sample job conf. changeset: 11216:c458a0fe1ba8 parent: 11213:6d633418ecfa parent: 11215:f79149dd3d35 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Nov 04 14:56:57 2013 -0500 summary: Merge security fix for filtering tools from stable/next-stable. $ hg summary parent: 11242:9d4cbf2a1c13 tip Add missing destination long arg to cli runner's Torque plugin and fix an incorrectly used PBS option in the sample job conf. branch: stable commit: 4 modified, 34 unknown update: (current) Thank you, Eric Rasche Programmer II Center for Phage Technology Texas A&M University

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"Skip automated testing of tools in this revision" setting?
by Peter Cock 18 Dec '13

18 Dec '13

Hi Dave & Greg, Could you double check how the "Skip automated testing of tools in this revision" setting is being used on the Test Tool Shed? e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/ee10017fcd… Test runs Automated test environment Not tested Licensing issues restrict automated tool dependency installation. 2013-11-29 17:19:34 Automated test environment Not tested Licensing issues restrict automated tool dependency installation. (Ticked) Skip automated testing of tools in this revision That all looks fine, and it is listed under "Latest revision: skip tool tests". However, this tool is also listed under "Latest revision: failing tool tests". Regards, Peter

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How to use Galaxy API?
by xlwang 17 Dec '13

17 Dec '13

Hello, I want to know how to use Galaxy API(the path is /galaxy-dist/scripts/api). I follow the README but get errors. For instance, I have generated my_key and use this script: ./display.py my_key http://localhost:4096/api/libraries I get an error: <urlopen error [Errno 111] Connection refused> I do not know how it happened. Please tell me how to fix it. Thank you! In addition, my main purpose is to manage the data library in another system. Should I use the api such as library_create_library.py, library_upload_from_import_dir.py and so on?

2 1

Trinity in local
by Jorge Braun 17 Dec '13

17 Dec '13

hi mates, I have problems to run trinity in local galaxy, because there is no executable script. any ideas? thank you very much

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Count intervals in one file overlapping intervals in another file
by Javier Simon-Sanchez 17 Dec '13

17 Dec '13

Hello, I just noticed that when using the above mentioned option, it is not possible to set a minimum overlap required. This option can be run in the command line version of BEDtools and I think is crucial. Could you please implement it in Galaxy? Thanks a lot. ------------------------------------- Javier Simón-Sánchez, PhD Research Scientist MRC-Holland Willem Schoutenstraat 6 1057 DN, Amsterdam The Netherlands

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cloudlaunch - Can't ssh or ping
by greg 16 Dec '13

16 Dec '13

Hi guys, I just did a cloud launch of MSG by going here: https://usegalaxy.org/cloudlaunch I downloaded the pem file as instructed and I can access the galaxy admin page now. However when I try to ssh into it: $ ssh -i Downloads/cloudman_keypair.pem ubuntu(a)ec2-54-196-189-227.compute-1.amazonaws.com ssh: connect to host ec2-54-196-189-227.compute-1.amazonaws.com port 22: Operation timed out And the same problem when I use the IP address. I also can't ping the above address nor the IP address. It just says request time out. Thanks, Greg

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cloud launch question
by greg 13 Dec '13

13 Dec '13

Hi guys, When I go here: https://usegalaxy.org/cloudlaunch and enter my amazon security credentials It lists two instances under the "Instances in your account" dropdown. Where is it getting these from? And how can I clear them out and get a fresh start. (I think I may have made them over a year ago but I no longer need them.) Thanks, Greg

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'Lost connection to MySQL server during query' error
by David Hoover 13 Dec '13

13 Dec '13

My recent Galaxy update has broken the feature that solves the 'Lost connection to MySQL server during query' error. I've set the variable database_engine_option_pool_recycle = 14400 to fix this. It used to work, but now periodically loading the page gives a gray warning page, which after reloading the URL goes to Galaxy. Is there something different that we need to do now? David Hoover Helix Systems Staff

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