galaxy-dev April 2013

galaxy-dev@lists.galaxyproject.org

87 participants
164 discussions

Pgp Keys not found error nebc.nerc.ac.uk
by Zeeshan Ali Shah 08 Apr '13

08 Apr '13

I am getting this when install I tried to serach the following keys on other server but could not find it on other pgp key server Err http://nebc.nerc.ac.uk unstable Release.gpg Unable to connect to nebc.nerc.ac.uk:http: Ign http://nebc.nerc.ac.uk unstable Release Ign http://nebc.nerc.ac.uk unstable/bio-linux TranslationIndex Err http://nebc.nerc.ac.uk unstable/bio-linux amd64 Packages Unable to connect to nebc.nerc.ac.uk:http: Err http://nebc.nerc.ac.uk unstable/bio-linux i386 Packages Unable to connect to nebc.nerc.ac.uk:http: Err http://nebc.nerc.ac.uk unstable/bio-linux Translation-en_US Unable to connect to nebc.nerc.ac.uk:http: Err http://nebc.nerc.ac.uk unstable/bio-linux Translation-en Unable to connect to nebc.nerc.ac.uk:http: Ign http://downloads-distro.mongodb.org dist/10gen Translation-en Fetched 316 B in 3s (99 B/s) W: There is no public key available for the following key IDs: 3B4FE6ACC0B21F32 W: GPG error: http://ppa.launchpad.net precise Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 759A8E0E5BA15160 W: There is no public key available for the following key IDs: 3B4FE6ACC0B21F32 W: There is no public key available for the following key IDs: 3B4FE6ACC0B21F32 W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/Release.gpg Unable to connect to nebc.nerc.ac.uk:http: W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/binary-amd64/Pack… Unable to connect to nebc.nerc.ac.uk: http: W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/Packa… Unable to connect to nebc.nerc.ac.uk: http: W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/i18n/Translation-… Unable to connect to nebc.nerc.ac.uk: http: W: Failed to fetch http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/i18n/Translation-… Unable to connect to nebc.nerc.ac.uk: http: -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah

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Galaxy dont work on my Bio-Linux
by BrozPetr＠email.cz 08 Apr '13

08 Apr '13

Hello, please could you help me, how to run galaxy directly from my computer? I am using Bio-Linux (ubuntu distribution) and there is GALAXY already install. When I try to open it, it is state that: "The Galaxy server doesn't seem to be running on your machine. You may need to start it with the command: sudo start galaxy Or else Galaxy may still be starting up (it takes a couple of minutes to get going on the first run)." When I open terminal and write sudo start galaxy it is state that galaxy start/running... But when I trying to open galaxy (just double clic on the icon) it still state problem which I write above. Could you help me please how to fix it?? Thank you very much for your reply! Have a nice day, Petr.

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Re: [galaxy-dev] REST API: upload of dataset to history possible ?
by John Chilton 08 Apr '13

08 Apr '13

On Mon, Apr 8, 2013 at 7:58 AM, Marc Logghe <Marc.Logghe(a)ablynx.com> wrote: > YES!!! > I really could not have found that by myself. Thank you very much. > Great, I am re-responding to galaxy-dev just in case someone else has this problem. > BTW: I have made some additions to blend4j in order to make it compatible to Richard Park's REST API changes regarding the passing of tool parameters. Are these the changes that have made it into Galaxy? If so, if you send me a patch or pull request I would be happy to review it for inclusion into blend4j. Thanks for using blend4j! -John > It allows to pass parameters like this: > WorkflowInputs inputs = new WorkflowInputs(); > inputs.setDestination(new WorkflowInputs.ExistingHistory(history.getId())); > inputs.setWorkflowId(projectWorkflow.getId()); > // Set parameters for params2yaml tool > inputs.setParameters("params2yaml", new ToolParameters("project", "APR000200")); > > Not entirely satisfied with it; might need some api changes but was kind of POC. I also would need some more info from Richard because it is not clear to me if his REST API adjustments allow for multiple parameters. > > Cheers, > Marc > > -----Original Message----- > From: jmchilton(a)gmail.com [mailto:jmchilton@gmail.com] On Behalf Of John Chilton > Sent: Monday, April 08, 2013 2:50 PM > To: Marc Logghe > Subject: Re: [galaxy-dev] REST API: upload of dataset to history possible ? > > Can you retry that with "?" as the db key, admittedly that could use > some more documentation :). The db key is the short identifier > associated with the genome corresponding to the data, "?" indicates > none is specified. > > -John > > On Sun, Apr 7, 2013 at 2:06 PM, Marc Logghe <Marc.Logghe(a)ablynx.com> wrote: >> Thanks John. >> Not sure what I am doing wrong, but in my hands it does not work. No errors but there is no file upload either. >> >> ToolsClient toolsClient = galaxyInstance.getToolsClient(); >> ClientResponse result = toolsClient.fileUploadRequest(history.getId(), "txt", "whatIsAdbKey?", new File("C:\\Users\\mlogghe\\Documents\\bb3d562ec52a9fc5.yml")); >> System.out.println(result.getClientResponseStatus()); >> >> In paster.log I also do not see any evidence that upload_handler is called. >> >> Regards, >> Marc >> >> -----Original Message----- >> From: jmchilton(a)gmail.com [mailto:jmchilton@gmail.com] On Behalf Of John Chilton >> Sent: Thursday, April 04, 2013 3:40 PM >> To: Marc Logghe >> Cc: galaxy-dev(a)lists.bx.psu.edu >> Subject: Re: [galaxy-dev] REST API: upload of dataset to history possible ? >> >> On Tue, Apr 2, 2013 at 5:23 AM, Marc Logghe <Marc.Logghe(a)ablynx.com> wrote: >>> Hi, >>> >>> Is it currently possible to upload an input dataset to a history via the >>> REST API ? >> >> This has been possible since pull request 94: >> https://bitbucket.org/galaxy/galaxy-central/pull-request/94/enable-upload-o…. >> The idea is to use the tools API and to invoke the upload1 tool. I >> imagine this is a little tricky to do with the bioblend Python library >> right now, but the blend4j Java library has a high-level helper >> function (ToolsClient.fileUploadRequest) to make this pretty simple: >> >> https://github.com/jmchilton/blend4j/blob/master/src/main/java/com/github/j… >> >> -John >> >> >>> Or should one use a library dataset instead ? >>> >>> But in the latter case, only an admin can upload data, right ? >>> >>> >>> >>> Thanks, >>> >>> Marc >>> >>> ________________________________________ >>> THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY >>> TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, >>> CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. >>> If the reader of this E-mail message is not the intended recipient, you are >>> hereby notified that any dissemination, distribution or copying of this >>> communication is strictly prohibited. If you have received this >>> communication in error, please notify us immediately at ablynx(a)ablynx.com. >>> Thank you for your co-operation. >>> "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. >>> ________________________________________ >>> >>> >>> ___________________________________________________________ >>> 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/ >> ________________________________________ >> THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. >> If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. >> "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. >> ________________________________________ >> >> >> ___________________________________________________________ >> 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/ > ________________________________________ > THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. > If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. > "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. > ________________________________________ >

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How to show alert message to user when running a tool in galaxy
by BingXin Lu 08 Apr '13

08 Apr '13

Dear all, I have added a tool in galaxy. After clicking 'Execute', this tool will query an external database for some information to ensure that there are no conflict records in the database. So sometimes an alert message should be sent to user if there are wrong records in the database. But I have not found out an efficient way to implement this in galaxy. I am wondering if it is possible to give some warning message to users when running a tool in galaxy and how to do it if it is feasible. I implemented the tool with an xml file and a python file. I am wondering calling javascript from the python code to give user error information. But it seems infeasible and I do not know where to start. Do you have any ideas? Thank you very much! Best regards, --Bingxin

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REST API: upload of dataset to history possible ?
by Marc Logghe 07 Apr '13

07 Apr '13

Hi, Is it currently possible to upload an input dataset to a history via the REST API ? Or should one use a library dataset instead ? But in the latter case, only an admin can upload data, right ? Thanks, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________

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PBS_Python Unable to submit jobs
by Ganote, Carrie L 05 Apr '13

05 Apr '13

Hi Galaxy dev, My setup is a bit non-standard, but I'm getting the following error: galaxy.jobs.runners.pbs WARNING 2013-04-04 13:24:00,590 (75) pbs_submit failed (try 1/5), PBS error 15044: Resources temporarily unavailable Here is my setup: Torque3 is installed in /usr/local/bin and I can use it to connect with (Default) server1. Torque4 is installed in /N/soft/ and I can use it to connect to server2. I'm running trq_authd so torque4 should work. I can submit jobs to both servers from the command line. For server2, I specify the path to qsub and the servername (-q batch@server2). In Galaxy, I used torquelib_dir=/N/soft to scramble pbs_python. My path is pointing at /N/soft first so 'which qsub' returns torque4. If I just use pbs:///, it will submit a job to server1 (shouldn't work, because /N/soft/qsub doesn't work from the commandline, since the default server1 is running torque3). If I use pbs://-l vmem=100mb,walltime=00:30:00/, it won't work (the server string in pbs.py becomes "-l vmem=100mb,walltime=00:30:00" intsead of "server1") If I use pbs://server2/, I get the Resources temp unavail error above. The server string is server2, and I put the following in pbs.py: whichq = os.popen("which qsub").read() stats = os.popen("qstat @server2").read() These return the correct values for server2 using the correct torque version4. I'm stumped as to why this is not making the connection. It's probably something about the python implementation I'm overlooking. Thanks for any advice, Carrie Ganote

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core dump after trying to view data
by Jason Evans 05 Apr '13

05 Apr '13

Hello Galaxy Buddies, I am having a problem with run.sh core dumping. It happens when I try to view data (click on the eye) for a large text file of results. It doesn't happen when viewing data of a smaller size and it executes jobs fine. Here is the server's output. Starting server in PID 30831. serving on http://127.0.0.1:8000 127.0.0.1 - - [05/Apr/2013:15:08:26 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.11) Gecko/20121116 Firefox/10.0.11" 127.0.0.1 - - [05/Apr/2013:15:08:26 -0400] "GET /root/tool_menu HTTP/1.1" 200 - "http://localhost:8000/" "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.11) Gecko/20121116 Firefox/10.0.11" 127.0.0.1 - - [05/Apr/2013:15:08:26 -0400] "GET /history HTTP/1.1" 200 - "http://localhost:8000/" "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.11) Gecko/20121116 Firefox/10.0.11" 127.0.0.1 - - [05/Apr/2013:15:08:27 -0400] "GET /history/get_display_application_links HTTP/1.1" 200 - "http://localhost:8000/history" "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.11) Gecko/20121116 Firefox/10.0.11" 127.0.0.1 - - [05/Apr/2013:15:08:30 -0400] "GET /datasets/1e8ab44153008be8/display/?preview=True HTTP/1.1" 200 - "http://localhost:8000/history" "Mozilla/5.0 (X11; Linux x86_64; rv:10.0.11) Gecko/20121116 Firefox/10.0.11" run.sh: line 78: 30831 Segmentation fault (core dumped) python ./scripts/paster.py serve universe_wsgi.ini $@ [jje16@rgs06 galaxy-dist]$ I am running Galaxy on Red Hat Linux under the most recent stable build. If it matters, it submits jobs to a cluster using the drmaa job runner. [jje16@rgs06 galaxy-dist]$ hg summary parent: 9232:9264cf7148c0 Added tag release_2013.04.01 for changeset 75f09617abaa branch: stable commit: 85 unknown (clean) update: (current) [jje16@rgs06 galaxy-dist]$ any ideas on where to look? thanks much, Jason Jason Evans jason.j.evans(a)gmail.com

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Running two Galaxy instances on the same Torque cluster
by Josh Nielsen 05 Apr '13

05 Apr '13

Hello, I have a question about running two Galaxy instances on separate hosts on the same Torque cluster. For various reasons, including some recent changes and/or removal of certain features (I am told BLAST was affected) in the newer versions of Galaxy, I would like to keep our current older version of Galaxy running while creating a separate Torque submit host to run the latest version of Galaxy on it. I do not think that will pose any issues for Torque since it will just see the new host as another submit host for jobs, but I would like to know if this would cause any unforeseen issues for either of the Galaxy instances. They will both mount and store their data on the same network filesystem but I will naturally have to create two separate directory trees for their /<basedir>/database/<files, pbs, job_working_directory, etc>/ paths. I am planning on making the local user the same on both submit nodes ('galaxy' - we are not using LDAP on that cluster although we may in the future). Will that cause any strange issues such as jobs being reported back to the wrong galaxy instance? Will IP address or DNS name be a factor? Additionally I hope there will not be an issue with the two instances both pointing to the same FTP upload directory. The idea seems sound in my head but I want to make sure I'm not excluding any critical considerations. Any suggestions or insights would be appreciated. Thanks, Josh Nielsen HudsonAlpha Institute for Biotechnology

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Call for papers for a special GCC2013 and Galaxy series in GigaScience
by Dave Clements 04 Apr '13

04 Apr '13

Hello all, I am pleased to inform you that talks presented at the 2013 Galaxy Community conference will be eligible for consideration to be published in the journal *GigaScience* and that BGI will generously cover the article processing fees for these articles. See the announcement below for details. thanks, Dave C -------------------------------- The 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> and BioMed Central <http://www.biomedcentral.com/> are announcing a special thematic series in *GigaScience <http://www.gigasciencejournal.com/> *, a new journal co-published in collaboration between BGI Shenzhen<http://www.genomics.cn/en/index> and BioMed Central <http://www.biomedcentral.com/> focused on studies utilizing large-scale datasets and workflows. Galaxy<http://galaxyproject.org/> is an open, web-based platform for data intensive biomedical research allowing their growing community of users to reproduce and share analyses. All accepted oral presentations from the meeting will be eligible for consideration in the series, and working with the scientific committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers#Scientific_Committee>, peer review will be coordinated, thorough and timely. BGI has been generously covering the open-access article-processing charges<http://www.gigasciencejournal.com/about/apcfaq> for the journal’s launch, and this offer will be extended to all submissions from the 2013 conference. Covering the themes of the conference, discussion and research is considered highlighting best practice for local Galaxy installation, management and use, as well as interesting tools, data sources, or novel uses of Galaxy. Addressing many of the goals of Galaxy to enable more accessible, reproducible, and transparent genomic science, submissions can utilize a novel format, where all of the workflows, tools and supporting data can be hosted and integrated into accepted papers using independently citable digital object identifiers<http://en.wikipedia.org/wiki/Digital_object_identifier> from the journal's Giga-Galaxy server <http://galaxy.cbiit.cuhk.edu.hk/> and GigaDB database <http://gigadb.org/>. Please contact the conference organizers <gcc2013-sci(a)galaxyproject.org> or GigaScience editors <editorial(a)gigasciencejournal.com> for further information, or submit a manuscript<http://www.gigasciencejournal.com/authors/instructions/research> or conference abstract<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts>, mentioning you would like to be considered in the series. The deadline for consideration for oral presentations to the meeting is 12th April, but later submissions for exceptional poster presentations (deadline 3rd May) and related work utilizing Galaxy may also be considered for the open series<http://www.gigasciencejournal.com/series> . Scott Edmunds Executive Editor *GigaScience <http://www.gigasciencejournal.com/>* -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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What is up with the multiple dataset selection for workflows
by Anthonius deBoer 04 Apr '13

04 Apr '13

Hi, There seem to be some undocumented changes to the way multiple datasets are provided to workflows. There seems to be some loss of functionality, since I cannot figure out how to select ALL files in the window... I can select individual files, but not all files that I can see.. It used to be possible to simply use the SHIFT click manner to select the whole list, but even the <PRESS ENTER> to select all does not seem to work...I also don't seem to get the search function to work... There is also a mysterious link icon that appears that looks like a chain of some sort, but is too small and does not have any mouse over help or antything... I suspect this is there for supporting paired end sequencing (WAY overdue) so you can match _R1 with _R2, but there is nothing in the news brief about this, but this option seems broken to me... Thanks Thon

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galaxy-dev April 2013