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

Extract features : error loading field data in usegalaxy
by Gildas Le Corguillé 08 Jan '16

08 Jan '16

Hi, One of my user wanted to import a workflow using the tool "Extract features" provided in the galaxy distrib : tools/filters/gff/extract_GFF_Features.xml On my instance, in the workflow canevas, I get this in red "error loading field data" On usegalaxy.org, I happy to observe that it's the same ... Sorry :) Any idea ? Gildas -- ----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateforme ABiMS (Analyses and Bioinformatics for Marine Science) Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 http://abims.sb-roscoff.fr ------------------------------------------------------------------

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Re: [galaxy-dev] IPython and Rstudio are missing
by Mic 01 Jan '16

01 Jan '16

Hi all, Thank you for your email, I found on the bottom of this site https://wiki.galaxyproject.org/Admin/Config/nginxProxy a configuration for IE, but I am not quite sure whether it is enough. To update the documentation would be really awesome. Thank you in advance. Mic On Tue, Nov 17, 2015 at 12:05 AM, Björn Grüning <bjoern.gruening(a)gmail.com> wrote: > Nate configured it on Galaxy main last week, maybe I can convince him to > update the documentation ... > > > > Hi Mic, > > > > Yes... neither of us use Nginx as our primary proxy, so we never > > wrote the configuration for it. > > > > If you use Nginx I'm assuming you're familiar with its configuration. > > As you can see from the apache route, you really just need a few > > proxy_pass statements. If you can write those, we'd be more than > > happy to include them in our documentation. > > > > Ciao, Eric > > > > > > On 11/16/2015 07:44 AM, Mic wrote: > >> Hi all, Looking at this link > >> ( > http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html > ) > >> > >> > it seem Nginx configuration is missing. > >> > >> How to configure Nginx for IE and Galaxy 15.10? > >> > >> Thank you in advance. > >> > >> Mic > >> > >> On Thu, Nov 12, 2015 at 2:36 AM, Eric Rasche <esr(a)tamu.edu > >> <mailto:esr@tamu.edu>> wrote: > >> > >> Hi Mic, > >> > >> Replying off list as this seems to be a different set of issues > >> than others experience. > >> > >> 1) From your earlier mails it sounded like you had been reading > >> the docs on GIEs, but you asked for then here. Have you read > >> through > >> > http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html > >> > >> > yet? If so, how far did you get? > >> > >> 2) do you have docker installed? what version? ("docker -v" I > >> believe) > >> > >> 3) What release of Galaxy are you on? The instructions are version > >> specific in places. > >> > >> 3) All of the files for GIEs are in > >> config/plugins/interactive_environments. Have you made any changes > >> to your local ipython.ini or rstudio.ini? > >> > >> Any logs from GIEs will appear in your normal Galaxy logs. E.g. > >> paster.log > >> > >> Ciao, Eric > >> > >> 11. nov. 2015 10.05 a.m. skrev Mic <mictadlo(a)gmail.com > >> <mailto:mictadlo@gmail.com>>: > >> > >> Hi all, Is there any log files which could show what did go wrong > >> or is there any documentation how to install IEs? > >> > >> Thank you in advance. > >> > >> Mic > >> > >> On Mon, Nov 9, 2015 at 9:12 AM, Mic <mictadlo(a)gmail.com > >> <mailto:mictadlo@gmail.com>> wrote: > >> > >> Hi Bjoern, Thank you for your email. I tried the attached Annovar > >> output which is tabular separated. Unfortunately, Rstudio and > >> Ipython still did not show up. > >> > >> Thank you in advance. > >> > >> Best wishes, > >> > >> Mic > >> > >> On Sat, Nov 7, 2015 at 9:58 AM, Björn Grüning > >> <bjoern.gruening(a)gmail.com <mailto:bjoern.gruening@gmail.com>> > >> wrote: > >> > >> Hi Mic, > >> > >> please check any other file than a VCF file. Try a txt file for > >> example. > >> > >> Thanks, Bjoern > >> > >> Am 07.11.2015 um 00:54 schrieb Mic: > >>> Hi Eric, I added your line to ipython.xml and rstudio.xml and > >> restarted Galaxy, but > >>> still Rstudio and Ipython do not appear on my test.vcf > >> file by clicking the > >>> *visualize* icon. > >>> > >>> <test type="isinstance" test_attr="datatype" > >>> result_type="datatype">tabular.Tabular</test> <test > >>> type="isinstance" test_attr="datatype" > >>> result_type="datatype">data.Text</test> *<test type="isinstance" > >>> test_attr="datatype" result_type="datatype">tabular.VCF</test>* > >>> > >>> What did I miss? > >>> > >>> Thank you in advance. > >>> > >>> Mic > >>> > >>> On Sat, Nov 7, 2015 at 1:13 AM, Eric Rasche > >> <esr(a)tamu.edu <mailto:esr@tamu.edu>> wrote: > >>> > >>>> Hi Mic, > >>>> > >>>> I don't believe GIEs are currently activated for > >> anything other than plain > >>>> text and tabular files. You can edit the > >>>> > >> > $GALAXY_ROOT/config/plugins/interactive_environments/ipython/config/ipython.xml > >> > >> (and rstudio/config/rstudio.xml) files to add a line like: > >>>> > >>>> Konsole output <test type="isinstance" test_attr="datatype" > >>>> result_type="datatype">tabular.VCF</test> > >>>> > >>>> and that /should/ let you open VCF files. (I haven't > >> tested that exact > >>>> datatype but I believe that should work). GIEs have > >> been somewhat > >>>> experimental so far, so we haven't felt the need to > >> expand which datatypes > >>>> they apply to lest we overwhelm/surprise users. > >>>> > >>>> Ciao, Eric > >>>> > >>>> > >>>> > >>>> > >>>> On 11/06/2015 02:56 AM, Mic wrote: > >>>>> Hello, Last week, I cloned Galaxy from Github. I uploaded a > >> VCF file from my > >>>>> computer. I also installed the following additional > >> software: > >>>>> > >>>>> /apt-key adv --keyserver keyserver.ubuntu.com > >> <http://keyserver.ubuntu.com> > >>>>> <http://keyserver.ubuntu.com> --recv-keys E084DAB9/ /echo > >>>>> 'deb > >> http://cran.r-project.org/bin/linux/ubuntu trusty/' >> > >>>>> /etc/apt/sources.list/ /apt-get -qq update && apt-get > >>>>> install > >> --no-install-recommends -y > >>>>> libcurl4-openssl-dev libxml2-dev/ /apt-get install > >>>>> apt-transport-https python-dev > >> libc-dev pandoc > >>>>> pkg-config liblzma-dev libbz2-dev libpcre3-dev/ /apt-get > >>>>> install libblas-dev liblapack-dev gfortran > >> libzmq3-dev curl/ > >>>>> /apt-get install libfreetype6-dev libpng-dev > >> net-tools procps r-base > >>>>> libreadline-dev / /pip install distribute --upgrade/ /pip > >>>>> install scipy sklearn-pandas bioblend > >> matplotlib patsy pysam khmer > >>>>> ggplot mpld3 sympy rpy2/ /pip install pyzmq ipython==2.4 > >>>>> jinja2 tornado > >> pygments numpy biopython > >>>>> scikit-learn pandas/ > >>>>> > >>>>> However, clicking the /visualize/ icon no iPython > >> and RStudio are > >>>>> visible. Galaxy is in my home folder installed > >> //home/lorencm/galaxy./ > >>>>> > >>>>> What am I missing? > >>>>> > >>>>> Thank you in advance. > >>>>> > >>>>> Mic > >>>>> > >>>>> > >>>>> > >> ___________________________________________________________ > >>>>> 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/ > >>>>> > >>>> > >>>> -- Eric Rasche Programmer II > >>>> > >>>> Center for Phage Technology Rm 312A, BioBio Texas A&M > >>>> University College Station, TX 77843 404-692-2048 > >>>> <tel:404-692-2048> esr(a)tamu.edu <mailto:esr@tamu.edu> > >>>> > >>>> > >>> > >>> > >>> > >>> > >> ___________________________________________________________ > >>> 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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Incorrect User Disk Usage
by Ping Luo 14 Dec '15

14 Dec '15

Hello, We have a galaxy user who has only one history which occupied 239.9GB disk space. However, total disk usage, as showing at the top right corner, is 925.6GB. I have done dataset cleanup and run set_user_disk_usage, but the total is still the same. Actually, running set_user_disk_usage.py had added up about 90G to the somewhat 840G total disk space showning in his account. Anybody knows what could be wrong? Thanks, Ping

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Visualization issue
by Scott Szakonyi 14 Dec '15

14 Dec '15

Hi all, If I try to build a new track browser from a custom build, I'm not able to see any of the datasets in my build after clicking add datasets and selecting my workflow from history. Am I doing something wrong, or is there a problem? I've been able to recreate this on both my local server and usegalaxy.org. Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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workflow export name attribute changes
by Jorrit Boekel 14 Dec '15

14 Dec '15

Hi all, I noticed something strange in my (latest) galaxy-dist. I have around 10-20 workflows, which are in certain cases very similar for e.g. slightly different experimental setups with the same output. I then usually copy the first wf and adapt a few steps to fit the second one. Anyway, they are on a testserver and I export them to import in my production instance. There I noticed that sometimes in (always the same 3) workflows, the export to json changes the ‘name’ attribute of the workflow. So when importing them in production, the wf has a different name. I haven’t been able to pinpoint where the problem lies, but the new name is very similar to the old one. I therefore believe that it may be that I have copied the workflow and the name of the source-wf is hanging around in some db table somewhere. Unlikely as it sounds. To be more specific it doesn’t show up when I do bioblend: workflows.show_workflow(id=x), but only when export_workflow_json(). It only happens in 3 of my workflows and I have surely copied more of them. Easy enough to workaround though, and kind of hoping this is a glitch in my setup only but wanted to let you know. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

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IOError kills collections
by Alexander Vowinkel 10 Dec '15

10 Dec '15

Hi, when I run a tool on a big collection with cloudman, I get the following error in at least one of the tasks: Traceback (most recent call last): File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/runners/drmaa.py", line 151, in queue_job fh = file( ajs.job_file, "w" ) IOError: [Errno 11] Resource temporarily unavailable: '/mnt/galaxy/tmp/job_working_directory/000/714/galaxy_714.sh' What can I do here? Also now the collection of the results is missing the result of this collection element, correct? How can I 'repair' my collection? Thanks, Alexander

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Picard installation dependency issues
by Scott Szakonyi 01 Dec '15

01 Dec '15

Hi all, I'm installing the latest revision of Picard tools (efc56ee1ade4). Picard installs successfully, and the tools are appearing in the appropriate menu, but several packages that install with Picard are reporting dependency issues, and I'm concerned that not all the tools will work appropriately. The tools reporting issues are: - package_cairo_1_12_14 (last lines of long warning/error sequence) - /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib: file not recognized: Is a directory collect2: ld returned 1 exit status make[3]: *** [libcairo.la] Error 1 make[2]: *** [all] Error 2 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 - package_pixman_0_32_4 - /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' collect2: ld returned 1 exit status make[2]: *** [clip-test] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 - package_readline_6_2 - Error downloading from URL ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz: <urlopen error ftp error: [Errno 110] Connection timed out> Is anyone else having issues with these packages? Any suggestions for resolving these problems? Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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Question about contributing a Visualization plugin to Galaxy
by Greg Von Kuster 30 Nov '15

30 Nov '15

Hello Galaxy-devs, I’m preparing to contribute a Visualization plug-in to the Galaxy code via a PR, and I’m hoping someone can privide the details for how to prepare the Javascript files that will be included in the PR. 1) What is the process for compressing the Javascript files? 2) Looking at the code base, it seems that 3rd party Javascript libraries are kept in ~/static/scripts. Should all of the 3rd party libraries that are used by my plugin be added here as part of the PR? Thanks very much, Greg Von Kuster

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Last day to submit your abstract! BIB-SCB: III Bioinformatics and Computational Biology
by Dave Clements 30 Nov '15

30 Nov '15

Hi All, and especially any Spanish speakers out there, I meant to pass this on sooner ... There's a bioinformatics / computational biology symposium in Barcelona on 18 December. At the end of the day there will also be a Galaxy session, where users and developers can, not only share > information and code, but also plan how to coordinate for future Galaxy > workshops and other activities. Chairs of this session are Toni Espinosa > (UAB) and Gonzalo Vera (CRAG). If you are interested in participating in the Spanish Galaxy Community, then I encourage you to attend. See below for details. Thanks, Dave C From: BIB comunicació <comunicacio(a)bioinformaticsbarcelona.eu> Date: Wed, Nov 25, 2015 at 9:48 AM Subject: [Socis-BIB] Last days to submit your abstract! BIB-SCB:IIIBioinformatics and Computational BiologySymposium, 18th December 2015 To: Llista de distribució socis BIB <socis.bib(a)bsc.es> Dear all, This is a reminder of the invitation to the *III Bioinformatics and Computational Biology Symposium* jointly organised by the *Societat Catalana de Biologia* (SCB) and *Bioinformatics * *Barcelona Association* (BIB), which will take place at the *Institut d'Estudis Catalans the 18th of December, 2015*. We could confirm four excellent keynote speakers that will shed light on different aspects of our local bioinformatics, as well as other initiatives in Europe, from which we can learn. Beyond these talks, the Symposium also relies on short talks (10’ presentation + 5’ questions) given by PhD students and postdocs. Therefore, we want to particularly encourage them to participate and to submit and share their work with us. Keynote Speakers: *Arcadi Navarro (ICREA, UPF)* *Modesto Orozco (IRB, BSC, UB)* *David Carrera (BSC, UPC)* *Tim Hubbard (King’s College, London)* Please, do not forget that this year we will organise, at the end of the day, a Galaxy session, where users and developers can, not only share information and code, but also plan how to coordinate for future Galaxy workshops and other activities. Chairs of this session are Toni Espinosa (UAB) and Gonzalo Vera (CRAG). This symposium is sponsored by <http://atos.net/> Additional information can be found in the attached PDF and registration through http://www.iec.cat/jornades/bioinformatica2015.asp IMPORTANT DATES: - Registration opens: 3rd of November 2015 * - Deadline of abstracts:* *30th of November 2015* - Selection of abstracts for oral presentation: 5th of December 2015 - Meeting day: 18th of December 2015 Please, share the event information with your contacts. Please, save this day in your agenda… we hope to see you all there! David Torrents (Chair) for the organisation team… -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Re: [galaxy-dev] Error installing tools from toolshed
by Nicola Soranzo 30 Nov '15

30 Nov '15

Hi Scott, the mercurial mirror is not up to date unfortunately, see this previous discussion: http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-t… Cheers, Nicola On 20/11/15 13:13, Scott Szakonyi wrote: > Hi Nicola, > > I'm not entirely sure which version... but I am still using the > mercurial mirror, which says I'm up to date. Would this be a wise > time, then, to change over to the Git repository directly? > > Thanks! > > Scott > > On Thu, Nov 19, 2015 at 8:15 PM, Nicola Soranzo <nsoranzo(a)tiscali.it > <mailto:nsoranzo@tiscali.it>> wrote: > > Hi Scott, > which Galaxy release are you using? > This is a bug which should be fixed in an updated release_15.07 > git branch. > > Cheers, > Nicola > > ---- Scott Szakonyi ha scritto ---- > > > Hello all, > > I'm having issues installing Trimmomatic and Picard tools from the > toolshed. The errors are of the following form (Trimmomatic used > for the example). > > Trimmomatic 0.32 package shows an installation error. > > Error details: > File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 142, in install_and_build_package_via_fabric > tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict ) > File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 136, in install_and_build_package > dir = tmp_dir > File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__ > self.gen.throw(type, value, traceback) > File "/vectorbase/web/Galaxy/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py", line 142, in _setenv > yield > File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 100, in install_and_build_package > initial_download=True ) > File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step > initial_download=initial_download ) > File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 685, in execute_step > dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) > File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 223, in url_download > extraction_path = archive.extract( install_dir ) > File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract > os.chmod( absolute_filepath, unix_permissions ) > > [Errno 2] No such file or directory: '/data/galaxy/tmp/tmp-toolshed-mtdeqJvts/Trimmomatic-0.32/Trimmomatic-0.32/' > > I've tried several version of the tool with no success. Any > thoughts? I've searched project website but haven't come up with > anything definitive. > > Thanks for any help you can offer, > > -- > Scott B. Szakonyi > Research Programmer > *Center for Research Computing* > 107 Information Technology Center > Notre Dame, IN 46556 > http://crc.nd.edu <http://crc.nd.edu/> > > > > > -- > Scott B. Szakonyi > Research Programmer > > *Center for Research Computing* > 107 Information Technology Center > Notre Dame, IN 46556 > http://crc.nd.edu <http://crc.nd.edu/>

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