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

galaxy upgrade
by Shrum, Donald C 28 May '15

28 May '15

Is there an official upgrade process for galaxy? I'd like to upgrade to the latest version with ldap support. We have a small user base here at FSU but I'd like to avoid just wiping out the existing tools. --Don Florida State University Research Computing Center

2 1

devteam/fastqc (current) vs iuc/fastqc (obsolete?)
by Peter Cock 27 May '15

27 May '15

Hi all, Searching on the main Tool Shed for fastqc gives two conflicting tools, an older version from the IUC, and a newer version from the devteam. If no one objects, I would like to mark the older IUC entry as deprecated, and edit the description to refer to the more up to date devteam entry instead. Regards, Peter -- https://toolshed.g2.bx.psu.edu/view/iuc/fastqc "FastQC wrapper" Containing one tool, "FastQC: Comprehensive QC" (version 0.53) This has an internal tool_dependencies.xml file to install v0.10.1 (rather than using a Tool Shed package). I can't find this tool on the IUC GitHub, https://github.com/galaxyproject/tools-iuc -- https://toolshed.g2.bx.psu.edu/view/devteam/fastqc "Read QC reports using FastQC" Containing one tool, "FastQC" (version 0.63) This has a tool_dependencies.xml pointing at the v0.11.2 package, and previously used the older v0.10.1 package: https://toolshed.g2.bx.psu.edu/view/devteam/package_fastqc_0_10_1 https://toolshed.g2.bx.psu.edu/view/devteam/package_fastqc_0_11_2 This tool's development is here: https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqc

1 0

Can't set value of conditional boolean parameter in tool tests
by Peter Briggs 27 May '15

27 May '15

Hello I've encountered a problem with my tool tests when using a boolean as the "control" parameter within a conditional: it doesn't appear to be possible to change the value from the default "true" or "false" values within the tests. For example if I have a boolean 'bdg2' which controls a conditional block and which defaults to its falsevalue: ... <conditional name="bdg_options"> <param name="bdg2" type="boolean" checked="False" truevalue="-B2" falsevalue="" label="Save pileups in bedGraph?" /> <when value="-B2"> ... and then try to set the value within a test using: <param name="bdg_options|bdg2" value="true" /> then the value remains unchanged from the default when the tests are run. (Similarly if I set checked="True" then the value in the tests is always "True" regardless of the value I try to set.) I've tried various ways of referencing the parameter (e.g. 'bdg_options|bdg2', 'bdg2' and 'bdg_options') but none of these work for me. Am I doing something obviously wrong? (nb this is a different problem from my previous post about setting boolean values in tests - that works fine for booleans which are not conditional control parameters). I've made a small example tool to investigate the issue, the files are here: https://gist.github.com/pjbriggs/c27e4366dfcdd6d96cb2 and using planemo 0.11.1 to run the tests. (On a side note, it also seems that within the <command> section, the values returned for this type of boolean only ever appear to be 'True' or 'False' - but it seems okay to match against the truevalue and falsevalues in the <when> tag.) Thanks for any help, 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

3 5

Tool installation problems within main Tool Shed test framework?
by Peter Cock 26 May '15

26 May '15

Hi all, Looking at https://toolshed.g2.bx.psu.edu/ logged in a peterjc, the "Repositories I Can Change" / "Latest revision: installation errors" listing ought to be empty, but is very long (perhaps all my tools?). The individual tools show things like: https://toolshed.g2.bx.psu.edu/view/peterjc/predictnls/9f2088ca5f6a Test runs 2015-05-07 10:41:19 Automated test environment Time tested: 2015-05-07 10:41:19 System: Linux 3.13.0-36-generic Architecture: x86_64 Python version: 2.7.6 Galaxy revision: v15.03.2-904-g3e80076 Galaxy database version: 128 Tool shed revision: 16935:64266df71fa7 Tool shed database version: 25 Tool shed mercurial version: 3.2.4 Installation errors This repository Error Error getting revision 9f2088ca5f6a of repository predictnls owned by peterjc: An entry for the repository was not found in the database. This tool's prior test runs from back in Januaray (!) passed, so I'm pretty sure this is a systematic problem on the main Tool Shed. The other installation errors seem to be from the same date. I take it since that was a couple of weeks ago that there are still infrastructure problems here? Regards, Peter

1 0

Data visualization
by Keith Suderman 24 May '15

24 May '15

Greetings, I am looking for information, tips, and pointers on writing a component for visualizing text data in Galaxy. In particular I would like to use Brat (http://brat.nlplab.org/embed.html) which can be embedded in web pages/apps. The “Implementation Details” section on the Learn/Visualization page (https://wiki.galaxyproject.org/Learn/Visualization#Implementation_Details) hints at exactly what I want to do: - use AJAX to fetch JSON data. - use a Javascript client to draw the data I can do both of the above steps, I am just not sure how to wire Brat into Galaxy. All of the documentation I can find about visualization covers installing existing Genome visualization tools and nothing about how to adapt an existing Javascript client to work in Galaxy. I am hoping someone can sketch out the basic steps I need to accomplish before I spend too much time grepping through the Galaxy code base. Cheers, Keith ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY

2 3

Data Visualization
by Keith Suderman 23 May '15

23 May '15

Greetings, I am looking for information, tips, and pointers on writing a component for visualizing text data in Galaxy. In particular I would like to use Brat (http://brat.nlplab.org/embed.html) which can be embedded in web pages/apps. The “Implementation Details” section on the Learn/Visualization page (https://wiki.galaxyproject.org/Learn/Visualization#Implementation_Details) hints at exactly what I want to do: - use AJAX to fetch JSON data. - use a Javascript client to draw the data I can do both of the above steps, I am just not sure how to wire Brat into Galaxy. All of the documentation I can find about visualization covers installing existing Genome visualization tools and nothing about how to adapt an existing Javascript client to work in Galaxy. I am hoping someone can sketch out the basic steps I need to accomplish before I spend too much time grepping through the Galaxy code base. Cheers, Keith ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY

1 0

Re: [galaxy-dev] galaxy-dev Digest, Vol 107, Issue 22
by Gurp, Thomas van 22 May '15

22 May '15

Unsubscribe Verstuurd vanaf mijn iPhone > Op 22 mei 2015 om 18:01 heeft "galaxy-dev-request(a)lists.galaxyproject.org" <galaxy-dev-request(a)lists.galaxyproject.org> het volgende geschreven: > > Send galaxy-dev mailing list submissions to > galaxy-dev(a)lists.galaxyproject.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.galaxyproject.org/listinfo/galaxy-dev > or, via email, send a message with subject or body 'help' to > galaxy-dev-request(a)lists.galaxyproject.org > > You can reach the person managing the list at > galaxy-dev-owner(a)lists.galaxyproject.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-dev digest..." > > > HEY! This is important! If you reply to a thread in a digest, please > 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread you are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. > > Today's Topics: > > 1. Re: connecting composite data elements to a display > application (Brian Haas) > 2. Re: connecting composite data elements to a display > application (Daniel Blankenberg) > 3. Re: connecting composite data elements to a display > application (Brian Haas) > 4. Re: samtools index tool (Eleanor Morgan) > 5. Re: samtools index tool (Peter Cock) > 6. Re: Web processes and SSL (John Chilton) > 7. Re: error executing test (John Chilton) > 8. Re: error executing test (Roberto Alonso CIPF) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 May 2015 13:48:11 -0400 > From: Brian Haas <bhaas(a)broadinstitute.org> > To: galaxy-dev(a)lists.galaxyproject.org > Subject: Re: [galaxy-dev] connecting composite data elements to a > display application > Message-ID: > <CAJCu8qObPm71Ht1QYnmLvcZB966Vp26cq8of4FxmXF7xq2uukQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > The following slides show how my 'hack' works: > > ftp://ftp.broadinstitute.org/pub/users/bhaas/tmp/FI-web.pptx > > It's definitely suboptimal, but at the very least, I've got something that > works and meets my immediate needs. > > I'm still *very* interested in following up with an alternative that > somehow leverages a galaxy API or well-supported mechanism for doing this. > > best, > > ~brian > > > On Thu, May 21, 2015 at 7:18 AM, Brian Haas <bhaas(a)broadinstitute.org> > wrote: > >> Hi Bjoern, >> >> My galaxy/database/files/000/dataset_1_files/ directory contains a bunch >> of files that I want to load into a genome viewer, including the target >> fasta file, .fai, several bam and .bam.bai files, and some bed files among >> a few others. I'm looking to wire up an IGV-web application (a pure >> javascript version of IGV) to access and display these files. The IGV-web >> app just needs the URLs to access these files. I have a tool built into >> galaxy that generates these files and stores them as the composite data >> type, and I'm trying to add in the visualization capability such that one >> can click on a hyperlink provided in the finished job panel in order to >> access the igv-web view. >> >> Again, the general issue is just - how to best enable an external >> application to access the extra_files of a composite data set? >> >> Ideally, it would involve configuration of some >> >> galaxy/display_applications/display.xml >> >> file to indicate how the URL should be constructed. The final url could >> be simply: >> >> http://MyWebServer/my_web_app.cgi?data_base_url=http://galaxyURL >> >> where data_base_url just gives the base URL to where my files would exist >> on galaxy, and since I know ahead of time the names of the files to expect >> in that directory, my web app can just reconstruct the URLs to the various >> files (fa, bam, bed, etc.). >> >> Alternatively, the url could provide a list of urls to all of the required >> resources - with the requirement that the .bam.bai files can be accessed by >> simply putting a .bai on the end of the bam url for each bam, and likewise >> for .fai for fasta files. >> >> >> many thx, >> >> ~brian >> >> >> >> >> On Thu, May 21, 2015 at 4:56 AM, Bjoern Gruening < >> bjoern.gruening(a)gmail.com> wrote: >> >>> Hi Brian, >>> >>> sorry to be so late to this adventure ... >>> Can you give me a few more details about your web-application? >>> >>> Have you considered to use the VIS framework from Galaxy or the >>> interactive environment framework? >>> This will give you more control over your datasets, because it's build-in >>> into Galaxy and would open up your webapp also for other servers. >>> >>> Cheers, >>> Bjoern >> -- >> -- >> Brian J. Haas >> The Broad Institute >> http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> > > > > -- > -- > Brian J. Haas > The Broad Institute > http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> >

1 0

error executing test
by Roberto Alonso CIPF 22 May '15

22 May '15

Hello, I am designing some test and I have a problem, it works under the Galaxy web environment, but it doesn't work when I try to use it as a test case. Indeed I am trying other tests and they fail as well. My test *./run_tests.sh -framework -id parallelism_bam_filter_reads* says the next: ====================================================================== ERROR: filter reads ( parallelism_bam_filter_reads ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 268, in test_tool self.do_it( td ) File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 55, in do_it raise e RunToolException: Error creating a job for these tool inputs - {u'type': u'error', u'data': {u'input': u'History does not include a dataset of the required format / build'}} And the other test *./run_tests.sh -framework -id compare_bam_as_sam* ====================================================================== ERROR: compare_bam_as_sam ( compare_bam_as_sam ) > Test-1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 268, in test_tool self.do_it( td ) File "/home/ralonso/galaxy/test/functional/test_toolbox.py", line 37, in do_it stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) File "/home/ralonso/galaxy/test/base/interactor.py", line 38, in stage_data_in_history upload_wait() File "/home/ralonso/galaxy/test/base/interactor.py", line 279, in wait while not self.__history_ready( history_id ): File "/home/ralonso/galaxy/test/base/interactor.py", line 297, in __history_ready return self._state_ready( state, error_msg="History in error state." ) File "/home/ralonso/galaxy/test/base/interactor.py", line 356, in _state_ready raise Exception( error_msg ) Exception: History in error state. -------------------- >> begin captured logging << -------------------- Besides than it tries to migrate the database each time I try a test case and it takes too long. I have seen that you can use --db postgres but it doesn't work, I think this option should be user with --dockerize (that is not my case). would you have any idea of what is going on? Best regards -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574 E-Mail: ralonso(a)cipf.es

2 2

Web processes and SSL
by Scott Szakonyi 22 May '15

22 May '15

Hello all, In our situation we're required to serve Galaxy via SSL. I encountered problems trying to do this with Paste processes. It appears that when Apache load balancing sends an incoming request to one of the load balanced processes, it's no longer under SSL. Running uWSGI is not a preferred option, as our computing infrastructure is not set up to support RedHat 7. Thus, I either need to understand how to configure SSL to work with the load balanced Paste processes, or run with another setup. So, if anyone in the community has experience with getting SSL to work with the Paste processes, or with setting up some other sort of SSL friendly configuration, I'd appreciate it if you would share your experience. -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

2 1

Re: [galaxy-dev] samtools index tool
by Eleanor Morgan 22 May '15

22 May '15

Hi all, Excuse me for the newbie question. I am developing a local instance of galaxy to use primarily for teaching purposes. I would like to index bam files produced in galaxy in order to view them in IGV. I can't seem to find the samtools index tool in the toolshed. I can run samtools on the command line and generate indexes, but can find no way to add this functionality to the tool panel so that I can do it in Galaxy. I also can't find this functionality in the tool panel (under Samtools or BAM tools) on usegalaxy.org. Am I missing something? Do I need to write my own tool? Regards, Eleanor Eleanor Morgan Senior Scientific Officer | School of Biomedical Sciences | Faculty of Health Sciences Curtin University Tel | +61 8 9266 7516 Mob | +61 408 004 369 Fax | +61 8 9266 2342 Email | e.morgan(a)curtin.edu.au<mailto:e.morgan@curtin.edu.au> Web | biomed.curtin.edu.au [cid:ED62B336-732F-4D99-ABF8-AFACA1E1C7E3] Curtin University is a trademark of Curtin University of Technology. CRICOS Provider Code 00301J (WA), 02637B (NSW)

2 1