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

cuff configure
by Joshua Udall 03 Mar '13

03 Mar '13

I have a local install of Galaxy. Tophat2 and Cufflinks work. cuffcompare and cuffmerge do not. Errors are below. There isn't a .loc file for cufflinks (overall). It will run if I don't 'use sequence'. It appears that the name of the database (dbkey) is inherited from the Tophat2 output file, but it coming up empty for cuff compare and cuffmerge. Any thoughts how I can get this to work? An error occurred running this job: *cuffcompare v2.0.2 (3524M) No sequence data found for dbkey ?, so sequence data cannot be used. cp: /Users/galaxy/galaxy-dist/database/job_working_directory/001/1549/cc_output.input1.tmap: No such file or directory cp: /Users/galaxy/galaxy-dist/database/j* * * * *

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join tool of Operate on Genomic Intervals is queued and does not run
by Nir Kfir 03 Mar '13

03 Mar '13

Hello galaxy support I am trying to intersect two bed format files to see if they have any common genomic segments between them Using join tool of Operate on Genomic Intervals. Every job I enter either stayed queued or is killed due to error Please let me know if your site is acting up again or maybe I am doing something wrong Thank you Nir Kfir Prof. Gil Ast Lab Department of Human Molecular Genetics & Biochemistry Sackler Medical School Tel Aviv University, 69978 Tel Aviv, Israel Tel: 972-3-6406894 Fax: 972-3-6408581 Email: <mailto:gilast@post.tau.ac.il> NirKfir(a)post.tau.ac.il website: <http://www.tau.ac.il/~gilast/> http://www.tau.ac.il/~gilast/

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Public ToolShed Problem - Latest Version isn't the tip repo
by Fei-Yang Jen 01 Mar '13

01 Mar '13

Hi Galaxy_dev team, I have question with regards to public ToolShed. For some reason, the latest version of my tools didn't get picked as tip repo when I was trying to install it on my cloud instance. I have read about some unexpected behaviours of public ToolShed if I use it like a git repo. Without knowing that at the first place, I had been modifying my tools on public ToolShed and had multiple uploads of some files. Is it possible that this is the reason why the latest version of my upload doesn't get picked as a tip repo? If it is so, how can I go about to fix it ? (I was looking for a way to delete repositories, but there didn't seem to have one) Thanks, Fei-Yang (Arthur) Jen Student Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Toll-free: 1-866-678-6427 Twitter: @OICR_news www.oicr.on.ca<http://www.oicr.on.ca> This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

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Fwd: [Numpy-discussion] [ANN] SciPy2013: Call for abstracts
by Peter Cock 01 Mar '13

01 Mar '13

Dear all, Apologies if you've already seen the SciPy 2013 conference call. This year's SciPy should be of particular relevance to Python programmers working with Galaxy. There is a new bioinformatics mini-symposium this year (chaired by Brad Chapman who contributes to Galaxy, Biopython, etc), but also a special theme this year on reproducible science which is of course one of the goals of the Galaxy Project. I hope some Galaxy people submit abstracts - although the timing of SciPy 2013 (in Texas USA) just before the Galaxy Community Conference (in Norway) is unfortunate: http://wiki.galaxyproject.org/Events/GCC2013 Regards, Peter ---------- Forwarded message ---------- From: Jonathan Rocher <jrocher(a)enthought.com> Date: Wed, Feb 27, 2013 at 10:17 PM Subject: [Numpy-discussion] [ANN] SciPy2013: Call for abstracts To: SciPy Users List <scipy-user(a)scipy.org>, numfocus(a)googlegroups.com, Discussion of Numerical Python <numpy-discussion(a)scipy.org> [Apologies for cross-posts] Dear all, The annual SciPy Conference (Scientific Computing with Python) 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 deadline for abstract submissions is March 20th, 2013. Submissions are welcome that address general Scientific Computing with Python, one of the two special themes for this years conference (machine learning & reproducible science), or the domain-specific mini-symposia held during the conference (Meteorology, climatology, and atmospheric and oceanic science, Astronomy and astrophysics, Medical imaging, Bio-informatics). Please submit your abstract at the SciPy 2013 website abstract submission form. Abstracts will be accepted for posters or presentations. Optional papers to be published in the conference proceedings will be requested following abstract submission. This year the proceedings will be made available prior to the conference to help attendees navigate the conference. We look forward to an exciting and interesting set of talks, posters, and discussions and hope to see you at the conference. The SciPy 2013 Program Committee Chairs Matt McCormick, Kitware, Inc. Katy Huff, University of Wisconsin-Madison and Argonne National Laboratory _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion(a)scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

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Re: [galaxy-dev] Problem with Upload File tool via url
by Dannon Baker 01 Mar '13

01 Mar '13

Glad it worked! Looping this back to the -dev list so that the solution is available for others in the future. -Dannon On Fri, Mar 1, 2013 at 9:00 AM, Zinonas Antoniou <z.antoniou(a)gmail.com>wrote: > Dannon, thank you that was the solution!! > > We copied the path environment variables from our local to our public > server and there was an interference. > > God bless you! I really appreciate your help!! > > > Kind regards, > Zinon > > > On 1/3/2013 3:37 μμ, Dannon Baker wrote: > > Oh, *your* public server! I misread that completely in your first email, > sorry. Are you using a proxy on your main server that might be interfering > here? > > > > On Fri, Mar 1, 2013 at 8:34 AM, Zinonas Antoniou <z.antoniou(a)gmail.com>wrote: > >> Weird indeed! >> >> Yes, I use the full url. >> >> It also works fine in our local development server, but in our public >> server no. Actually the problem is not only with our url source but with >> any url source. It seems that when we use the Upload File from url we have >> the same problem. >> >> >> >> On 1/3/2013 3:31 μμ, Dannon Baker wrote: >> >> Weird, this file works fine for me on main.g2.bx.psu.edu using the >> normal url upload. Are you pasting in the full url including http:// ? >> >>

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macs error for chipseq data
by Jennifer Jackson 01 Mar '13

01 Mar '13

Hi Kathryn, I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility. Thanks! Jen Galaxy team On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote: > > Hi Jen, > > Sorry that I missed some part of your email. It is not for local > galaxy install. I am using the cloudman from aws and it seemed to have > everything for having the input files and reference genome chose. The > job was shown on the right panel and then the error message coming out. > > It seems to me that MACS was installed.... What is the issue? > > Thank you very much, > > Kathryn > On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: > > Hi Jennifer, > > Thanks for the information on MACS tools. > > Yes, I forgot to mention that I used bowtie mapped files as the input. > > Thank you very much, > > Kathryn > > ** > > *From:*Jennifer Jackson [mailto:jen@bx.psu.edu] > *Sent:* Friday, January 11, 2013 3:48 AM > *To:* Sun, Wenping [USA] > *Cc:* galaxy-user(a)bx.psu.edu > *Subject:* [External] Re: [galaxy-user] macs error for chipseq data > > Hello Kathryn, > > This is occurring on your local Galaxy install? Have you installed the > actual MACS tool and set up the proper configuration paths? Details > for how to do this are in these wikis: > http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies > http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies > > Apart from that, I should let you know that prior to running MACS, > groomed fastq datasets first need to be mapped. An example can be > found in our Using Galaxy paper, protocol #3. Links to the paper and > supplemental materials (including a screencast walk-through) are > available here: > https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 > > If you need more help with your local install, directing questions to > the galaxy-dev(a)bx.psu.edu <mailto:galaxy-dev@bx.psu.edu> mailing list > would be best, > > Thanks! > > Jen > Galaxy team > > On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: > > Dear galaxy users, > > I've encountered the error while running macs on galaxy for > chipseq data. I used fastq groomed files as input and had the > following error > > An error occurred running this job: //bin/sh: macs: not found/ > > // > > Anybody can kindly provide some hints? > > Thanks, > > Kathryn > > > > > ___________________________________________________________ > > The Galaxy User list should be used for the discussion of > > Galaxy analysis and other features on the public server > > at usegalaxy.org. Please keep all replies on the list by > > using "reply all" in your mail client. For discussion of > > local Galaxy instances and the Galaxy source code, please > > use the Galaxy Development list: > > > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > To manage your subscriptions to this and other Galaxy lists, > > please use the interface at: > > > > http://lists.bx.psu.edu/ > > > > -- > Jennifer Hillman-Jackson > Galaxy Support and Training > http://galaxyproject.org -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Problem with Upload File tool via url
by Zinonas Antoniou 01 Mar '13

01 Mar '13

Dear all, My problem is when I use the /Upload File /tool via URL, I get the message "The uploaded file contains inappropriate HTML content". I tried a lot of file formats. In our development server this tool works fine but in our public server we have this problem. Do you have any solution? Kind regards, Zinon

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Problem installing Deseq from toolshed
by Mahtab Mirmomeni 01 Mar '13

01 Mar '13

Hi all, I have installed Deseq (by vipints) from the main galaxy toolshed and have followed the make instructions but I'm still not unable to run it inside Galaxy and I get the following error. (Path is the path to our local galaxy instance) error: get_read_counts: Path/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/2b3bb3348076…: failed to load: /mnt/all/cloudman/galaxy/clare/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/2b3bb3348076/deseq_hts/deseq-hts_1.0/mex/get_reads.mex: undefined symbol: bam_index_destroy error: called from: error: Path/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/2b3bb3348076… at line 97, column 34 starting Octave failed I should add that I can run octave from command line and it seems to be working. Any suggestions is much appreciated. Thanks Mahtab

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Re: [galaxy-dev] all the data files in .loc files needed to download ?
by Carl Eberhard 01 Mar '13

01 Mar '13

Hello shenwiyn, You may want to have a look at http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more information specific to the indeces/data you'll need and how to install. Along with data management, that page has instructions on how to download (via rsync) the same data we use on our main server. It may be a good starting point. Thanks, Carl On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn <shenwiyn(a)foxmail.com> wrote: > ** > Hi Carl Eberhard, > Thank you very much for you help.I have another some questions : > First, > we need to install the needed data,for example sam_fa_indices.loc file of > SAM Tools : > index AaegL1 /afs/bx.psu.edu/depot/data/genome/AaegL1/sam_index/AaegL1. > fa > index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/AgamP3. > fa > index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/ > ailMel1.fa > index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/ > anoCar2.fa > index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/ > apiMel2.fa > index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/ > apiMel3.fa > index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/ > aplCal1.fa > .... > so we need to download AaegL1.fa,AgamP3.fa,ailMel1.fa,anoCar2.fa,apiMel2. > fa,apiMel3.fa,and so on ,then install all of this needed datas to /afs/bx. > psu.edu/depot/data/genome/aplCal1/sam_index/,is it right? > Second, > from the needed datas mentioned in the .loc files in > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup ,we need to > download too much data,can we get all these data from some website instead > of searching them on Iternet one by one? > > > Thanks, > shenwiyn > > > > ------------------------------ > > *From:* Carl Eberhard <carlfeberhard(a)gmail.com> > *Date:* 2013-02-22 01:20 > *To:* shenwiyn <shenwiyn(a)gmail.com> > *Subject:* Re: [galaxy-dev] all the data files in .loc files needed to > download ? > Hello, > Yes a local galaxy requires a few steps in order to install the needed > data. > > The following wiki page should help get you started: > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup > > Let me know if you need more information, > Carl > > > > On Tue, Feb 19, 2013 at 3:59 AM, shenwiyn <shenwiyn(a)gmail.com> wrote: > >> ** >> Hi all, >> Are all the data files in .loc files needed to download and put to the right directory when >> we install our local galaxy? >> >> thaks >> shenwiyn >> >> ------------------------------ >> shenwiyn >> >> ___________________________________________________________ >> 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/ >> > >

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first install, MySQL date
by Arnau Bria 01 Mar '13

01 Mar '13

Hi all, my name is Arnau Bria and I work at CRG, in BCN. I'm a sysadmin and I'm helping one user to install/configure galaxy and to run jobs in our SGE cluster. I think this is the correct list for asking SGE/MySQL questions, if not, let me apology in advance. I have a question about MySQL dates. system date is correct and uses CET (I'm in Spain), MySQL i sconfigured to use system's timezone: date Thu Feb 28 13:38:10 CET 2013 SELECT @@global.time_zone, @@session.time_zone; +--------------------+---------------------+ | @@global.time_zone | @@session.time_zone | +--------------------+---------------------+ | SYSTEM | SYSTEM | +--------------------+---------------------+ 1 row in set (0.02 sec) but SGE job dates are wrong: create_time 2013-02-28 12:37:48 notice it shows 12:37 and it should be 13:37. is this importatn? may I change glaxy's timezone in some way? TIA, Arnau

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