March 2013 - galaxy-user - lists.galaxyproject.org

User dropdown menu as galaxy input file
by Alex Upton 12 Mar '13

12 Mar '13

Good afternoon, I have a query that I hope you can help me with. I am using RGalaxy, and have successfully built a number of useful tools for my instance of Galaxy, using this in R. At the moment, all these tools are using the default galaxy input file, following the example tools. Is there a way I can create an additional input for the tool, that the end user selects, and make this in the form of a drop-down list? So to illustrate with code, I have: inputfile = GalaxyInputFile() #this is the default input file option I would then like an additional input file option, ideally in the form of a drop-down box, that would then be used as an input for a function. What is the best way to do this? Kind regards, Alex -------------------------------------------------------------------------------------------- Alex Upton, BEng, MRes, PG Cert Business Administration PhD Researcher Biomedical Informatics, Signals and Systems School of Electronic, Electrical and Computer Engineering, College of Engineering and Physical Sciences, University of Birmingham Edgbaston, Birmingham, B15 2TT, United Kingdom Fax: +44 121 4144291 (school general office) Email: a.upton(a)pgr.bham.ac.uk Personal Web: http://postgrad.eee.bham.ac.uk/uptona/ --------------------------------------------------------------------------------------------

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Knowing who is currently logged into your system
by Akshay Vivek Choche 12 Mar '13

12 Mar '13

Hello All, I was wondering if there is a way to know all the users logged into your local galaxy server? Thanks, -Akshay Choche

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ftp upload problem
by Raaben, Matthijs 12 Mar '13

12 Mar '13

I have a problem uploading files to the ftp server. I recently tried to upload some files, but the connection crashed. Now I am no longer able to log onto the server. I get the following error: “530 Sorry, the maximum number of clients (3) for this user are > already connected. Could you help me out? Thanks! Matthijs

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Web Galaxy server and load
by Ann Holtz-Morris, M.S. 11 Mar '13

11 Mar '13

HI, Does anyone know how to check whether the Galaxy server(s) load is really high? My alignments, only 200,000 paired end reads seemed to be taking a long time. I read through the archives, and the answers were that 1) alignments take a while and that the server load really affects the turnaround time, and 2) But then again, it could also be your data & settings. I could not find how users could check whether the server load is really heavy, especially for alignments. I also suspect it could have been be my query being incorrectly set up because when the alignment finally did come back, the ~1% control DNA did not align correctly. Thanks aholtzmorris CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

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Amazon EC2: An error occurred running this job: Job output not returned from cluster
by Brian Lin 11 Mar '13

11 Mar '13

Hi guys, I'm running a galaxy cloudman instance and running the usual tophat->cufflinks->cuffdiff workflow from RNAseq data. I am using a m2.4xlarge as a master node, and autoscaling from 0-4 workers of the m2.xlarge type. I have gotten the error: An error occurred running this job: *Job output not returned from cluster* when running fasta groomer, tophat, and now cufflinks. Following up troubleshooting from other people in the mailing list, I have set a new line in universe_wsgi.ini of retry_job_output_collection=30 Unfortunately, this does not seem to have fixed the problem. The stdout is blank, and stderr gives Job output not returned from cluster Under manage jobs in the admin panel, it lists 4 out of the 6 jobs as currently running. What is confusing is that of the 4 "running," one has already returned the error in the user dataset panel and yet is still listed as running. >From the SGE log, I see these errors: 03/11/2013 14:32:52|worker|ip-10-159-47-223|W|job 42.1 failed on host ip-10-30-130-84.ec2.internal before writing exit_status because: shepherd exited with exit status 19: before writing exit_status 03/11/2013 14:32:52|worker|ip-10-159-47-223|W|job 43.1 failed on host ip-10-30-130-84.ec2.internal before writing exit_status because: shepherd exited with exit status 19: before writing exit_status 03/11/2013 14:39:41|worker|ip-10-159-47-223|E|adminhost "ip-10-30-130-84.ec2.internal" already exists 03/11/2013 14:40:07|worker|ip-10-159-47-223|E|exechost "ip-10-30-130-84.ec2.internal" already exists 03/11/2013 14:50:54|worker|ip-10-159-47-223|E|adminhost "ip-10-30-130-84.ec2.internal" already exists 03/11/2013 14:50:55|worker|ip-10-159-47-223|E|exechost "ip-10-30-130-84.ec2.internal" already exists Does anyone have any idea how to solve this error? It has removed my ability to use workflows completely and I still have not been able to run a single analysis to completion due to it. Thanks for any insight anyone provide! Brian -- Brian Lin contact(a)brian-lin.com brian.lin(a)tufts.edu

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convert to BigWig
by Kristin Denise Kernohan 09 Mar '13

09 Mar '13

Hello I have been trying to convert a number of BedGraph files to BigWig for several weeks now. This converter tool seems to take weeks before it will run, but in the past has only taken overnight. Last week one of my files ran overnight, while the remainder stayed in the que, though they were set up at the same time. Is something wrong, or has this que just gotten that long that it takes ~2weeks? Thank you very much Kristin

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SciPy 2013 Conference Announcement
by Matthew McCormick 08 Mar '13

08 Mar '13

SciPy 2013, the twelfth annual Scientific Computing with Python conference, will be held this June 24th-29th in Austin, Texas. SciPy is a community dedicated to the advancement of scientific computing through open source Python software for mathematics, science, and engineering. The annual SciPy Conference allows participants from academic, commercial, and governmental organizations to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. The conference consists of two days of tutorials by followed by two days of presentations, and concludes with two days of developer sprints on projects of interest to attendees. Specialized Tracks ------------------ This year we are happy to announce two specialized tracks that run in parallel to the general conference: *Machine Learning* In recent years, Python's machine learning libraries rapidly matured with a flurry of new libraries and cutting-edge algorithm implement and development occurring within Python. As Python makes these algorithms more accessible, machine learning algorithm application has spread across disciplines. Showcase your favorite machine learning library or how it has been used as an effective tool in your work! *Reproducible Science* Over recent years, the Open Science movement has stoked a renewed acknowledgement of the importance of reproducible research. The goals of this movement include improving the dissemination of progress, prevent fraud through transparency, and enable deeper/wider development and collaboration. This track is to discuss the tools and methods used to achieve reproducible scientific computing. Domain-specific Mini-symposia ----------------------------- Introduced in 2012, mini-symposia are held to discuss scientific computing applied to a specific scientific domain/industry during a half afternoon after the general conference. Their goal is to promote industry specific libraries and tools, and gather people with similar interests for discussions. Mini-symposia on the following topics will take place this year: - Astronomy and astrophysics - Bioinformatics - Medical imaging - Meteorology, climatology, and atmospheric and oceanic science Tutorials --------- Multiple interactive half-day tutorials will be taught by community experts. The tutorials provide conceptual and practical coverage of tools that have broad interest at both an introductory or advanced level. This year, a third track will be added, which target specifically programmers with no prior knowledge of scientific python. Developer Sprints ----------------- A hackathon environment is setup for attendees to work on the core SciPy packages or their own personal projects. The conference is an opportunity for developers that are usually physically separated to come together and engage in highly productive sessions. It is also an occasion for new community members to introduce themselves and recieve tips from community experts. This year, some of the sprints will be scheduled and announced ahead of the conference. Birds-of-a-Feather (BOF) Sessions --------------------------------- Birds-of-a-Feather sessions are self-organized discussions that run parallel to the main conference. The BOFs sessions cover primary, tangential, or unrelated topics in an interactive, discussion setting. This year, some of the BOF sessions will be scheduled and announced ahead of the conference. Important Dates --------------- - March 20th: Presentation abstracts, poster, tutorial submission deadline. Application for sponsorship deadline. - April 15th: Speakers selected - April 22nd: Sponsorship acceptance deadline - May 1st: Speaker schedule announced - May 6th: Early-bird registration ends - June 24th-29th: 2 days of tutorials, 2 days of conference, 2 days of sprints We look forward to a very exciting conference and hope to see you all at the conference. The SciPy2013 organization team: * Andy Terrel, Co-chair * Jonathan Rocher, Co-chair * Katy Huff, Program Committee co-chair * Matt McCormick, Program Committee co-chair * Dharhas Pothina, Tutorial co-chair * Francesc Alted, Tutorial co-chair * Corran Webster, Sprint co-chair * Peter Wang, Sprint co-chair * Matthew Turk, BoF co-chair * Jarrod Millman, Proceeding co-chair * Stéfan van der Walt, Proceeding co-chair * Anthony Scopatz, Communications co-chair * Majken Tranby, Communications co-chair * Jeff Daily, Financial Aid co-chair * John Wiggins, Financial Aid co-chair * Leah Jones, Operations chair * Brett Murphy, Sponsor chair * Bill Cowan, Financial chair

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Re: [galaxy-user] [galaxy-dev] not enough memory space on my galaxy session
by Jeremy Goecks 08 Mar '13

08 Mar '13

Hello, Apologies for the slow reply. I've moved this thread to the galaxy-user mailing list because it centers on using Galaxy rather than developing it. > 2. deleted the first files, like the first fastq files, but I'm affraid to have an error messages Deleting your fastq files after you have mapped your reads is fine and will not cause any errors. Make sure to both delete and purge your datasets to clear them from your account: http://wiki.galaxyproject.org/Learn/Managing%20Datasets#Delete_vs_Delete_Pe… > 3. to obtain more memory, just for the time of the study. Your best bet to obtain more memory quickly is to use a cloud instance: http://wiki.galaxyproject.org/CloudMan Good luck, J.

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Reminder: Galaxy Main & Test Server downtime for hardware relocation Thursday, March 14, 2013
by Jennifer Jackson 08 Mar '13

08 Mar '13

Original Notice Date: Thursday, March 7, 2013 Reminder NoticeDate: Friday, March 8, 2013 Greetings Galaxy *Main* & *Test* Users, The *Galaxy* *Public* *Main Galaxy Server* <http://wiki.galaxyproject.org/Main> at *http://main.g2.bx.psu.edu* (/usegalaxy.org/) and *Test Galaxy Server <http://wiki.galaxyproject.org/Test>* at *http://test.g2.bx.psu.edu* will be *down on Thursday, March 14, while the team _/relocates core hardware /to a new server room_*. Please note that_/jobs running at the time of the shutdown may be terminated/_. Once the move is complete, any terminated jobs can be easily restarted using the "re-run" function. dataset re-run The /yellow banner on //*Main*//and //*Test*//will provide updates/ (when the servers are up) as well our *@galaxyproject Twitter* posts. Don't use Twitter? See our *Twitter Wiki <http://wiki.galaxyproject.org/Galaxy%20on%20Twitter>*. *Galaxy's **Tool Shed <http://toolshed.g2.bx.psu.edu>**, **GalaxyProject.org <http://wiki.galaxyproject.org>**Wiki, and **Mailing list <http://wiki.galaxyproject.org/MailingLists>**services* will be /*unaffected*/ during this time. /Thanks for using Galaxy!!/ Galaxy team

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How should I include biological replicates in cufflink/cuffdiff?
by Qian Dong 08 Mar '13

08 Mar '13

Dear team, I have a few questions regarding RNA-seq data analysis. I want to compare transcriptome profile of a bacterium between 5 time points, and for each time point I have three biological replicates. Right now I have each of the replicates' sequences aligned with Bowtie and assembled transcripts generates using Cufflinks. I understand that if I am just comparing two time points (if each of time point has only one sample, no replicate) I just need to cuffmerge the two time points and cuffdiff the merged file. My question is, if I need to compare between 5 time points, should I do comparison pairwise? And also, how should I include three biological replicates for each time point? I can only find 'include replicates' in Cuffdiff. Could you check is the following methodology correct? let's say I have samples in time 0 , 1hour, 2hours, 3 hours and 4 hours. I will name each of the replicates as 0hour-1, 0hour-2, 0hour-3,etc. I will first compare expression between 0hour and 1hour. I will use cuffmerge to merge 0hour-1, 0hour-2, 0hour-3, 1hour-1,1hour-2.1hour-3 to generate one cuffmerge file. Then I will run cuffdiff using the merged file, include two groups, group 1 is 0 hour (add 0hour 1-3 in group 1) and group 2 is 1hour (add 1hour1-3 in group 2). Does this sound reasonable? Thank you very much, Qian -- Qian Dong Bauer Lab, MCBD Simon Hall: 313-317 212 S. Hawthorne Dr. Bloomington, IN 47405 Email:dong3@indiana.edu Lab Phone:812-855-8443

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