- galaxy-dev - lists.galaxyproject.org

Galaxy multiple input files in a specific directory structure
by Henk van den Toorn 28 Sep '11

28 Sep '11

Dear all, I'm new here, although I was at a galaxy hack-a-thon before (Belgium this year). I've tried searching the history of the mailing list, but couldn't find something useful quickly, so I hope you can help! I have a rather specific problem with an application I am trying to incorporate into galaxy. This application does statistical analysis on any number of input files. The structure of the files in a (nested) directory structure determines which ones are conditions, and which ones are replicas etcetera. I'd like to be able to generate the input files in Galaxy, tell the application which file is what in terms of condition/replica, run the application and retrieve the output files (multiple again!). My question is, does anybody have experience in solving these kind of problems? If you have an answer, I'd be much grateful. If not, we'll try to find a solution ourselves. Of course we'll give it to the community if we do. Regards, Henk -- ------------------------------------------------------------------------------------------------------- *Henk van den Toorn, bioinformatician* Biomolecular Mass Spectrometry and Proteomics Group Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan, 8 3584 CH Utrecht The Netherlands E-mail: h.w.p.vandentoorn(a)uu.nl Tel: +31 30 253 6758 Fax: +31 30 253 6919 --------------------------------------------------------------------------------------------------

1 0

Data transfer between two galaxy instances
by lentaing＠jimmy.harvard.edu 28 Sep '11

28 Sep '11

Hi, We are running two instances of galaxy on our site--one internal, the other external. Some of our internal users have data on the external instance. What might be the easiest way to transfer the data of our internal users from the external to the internal instance? OR Is there a way to transfer data between galaxy instances? I thought that I'd give this mailing list a shot before telling our internal users that they would have to re-load the data on the internal instance. Thanks, Len Taing

3 3

Fetch failed in run.sh - Ubuntu 11.04 zlib not available
by Joe Harrison 28 Sep '11

28 Sep '11

Hello - I am a microbiologist and I am attempting to set up a a local instance of Galaxy. I'm very green with the Linux environment! So you will have to pardon a very naive question from a biologist... I have installed VirtualBox on my PC and I am currently running Ubuntu Linux 11.04 (64 bit). I have downloaded the galaxy distribution from the mercurial repository and have executed the run.sh script. However, Galaxy fails to launch, and I get the following error message: zipimport.ZipImportError: can't decompress data; zlib not available Fetch failed. Would anyone have a fix for this problem? I have tried installing zlibc using the following command: sudo apt-get install zlibc But this does not seem to resolve the issue... Is this something to do with Ubuntu (should I try a different Linux environment)? Any recommendations would be deeply appreciated. Joe --- Joe J. Harrison Senior Fellow Department of Microbiology University of Washington 1705 NE Pacific Street, HSB J181 Seattle WA USA (206) 543-3147

2 1

HOW TO RETRIEVE DATA FROM HISTORY??!!
by colin molter 28 Sep '11

28 Sep '11

Hi all, i am still stuck with the same problem. Is there a way to directly move/copy data from your galaxy history to a given location in the filesystem of the same galaxy server? Said differently, there is a nice way to import data from the server to galaxy, is it possible to do the reverse? So far, I am obliged to download the file from galaxy to my client machine and then back to the server!!!! with huge bam files of 3Gb it is not so convenient!! thank you all colin

5 6

conversion of fastq files
by mallika V 28 Sep '11

28 Sep '11

hi I am very new to the galaxy software. I have to convert one fastq file of nearly 5 gb size and unable to do that. i tried to install galaxy in locally but it tells some eggs are out of date. Can anyone plz help me in this regard -- "The best and most beautiful things in the world cannot be seen or even touched. They must be felt within the heart" (Helen Keller)

2 1

Error in displaying data in galaxy browser with less than 1MB size.
by Jerico Nico De Leon Revote 28 Sep '11

28 Sep '11

Hi, I've a setup a local instance of galaxy in our server using PostgreSQL/nginx. I've followed the instructions from the production server configuration as stated from here: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server. Galaxy is running and tried the "Galaxy 101" tutorial but I get http 404 error when trying to view any dataset with less than 1MB in size in the galaxy browser: Not Found The resource could not be found. No route for /_x_accel_redirect/home/galaxy/galaxy-dist/database/files/000/dataset_4.dat The dataset files are definitely present on the server and resides on galaxy's database files directory (e.g. /database/files/000). I can load and view in the browser any dataset that has >1MB in size, at least those ones produced from the "Galaxy 101" tutorial. Any suggestion is appreciated. Regards, Jerico

2 1

EST download from any source?
by Timothy Wu 28 Sep '11

28 Sep '11

Hi, I'm trying to wrap up my own tool in Galaxy. The input to my tool include the set of EST (such as the entire human collection). I tried using UCSC genome browser but it doesn't seem to let me download the whole human collection due to the size of the data. I tried to implement my own FTP client and try to wrap that up in galaxy. I intend to have the FTP client download data from NCBI's FTP server directly, and have the downloaded files as output files to feed back into galaxy. I intend to make the FTP client somewhat generic, so as not to enforce the type of files. Though in my case, I would be download gzipped genbank files. But galaxy support for multiple output files kind of tripped me over. I do not know exactly what to do, since it looks as if galaxy requires a strict naming convention for the outputs, according to http://gmod.827538.n3.nabble.com/Multiple-output-not-known-until-tool-run-t… case I have is obviously that the number of files would not be known until run time). I guess it doesn't really, really matter, if I send those files, whatever the naming convention are, and fed it to a gzip decompressor (which I am planning to do a simple wrap up, just to be able to handle my stuff). Then it should all work out fine. Alternatively, I can just ask user to download from NCBI ftp themselves, decompress them, and upload it to galaxy. What's the best approach here? And I noticed that file types does not include genbank types nor gzip types. Is there some generic type I could use? Just Data class? Timothy

4 7

Passing the number of mpi processors to SGE from xml file
by Chorny, Ilya 28 Sep '11

28 Sep '11

Any thoughts on how to pass the number of processor I want to use from my xml wrapper to the job template. I am trying to wrap pBWA and use mpi. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

3 6

Re: [galaxy-dev] picard error.
by Ross 27 Sep '11

27 Sep '11

A fix for these warnings is in revision 6048 of galaxy-central - again, thanks for pointing them out Michael. For the record, the warnings were from the HSmetrics and GCbias tools and arose because there is a user configurable maxheap parameter that is not available by default - it is commented out in the tool form - but it had not been commented out from the test - since it is not enabled by default that generated a warning. The test parameter is now also commented out by default and must be uncommented for sites running into ram limits with very large datasets. On Tue, Sep 27, 2011 at 8:04 AM, Ross <ross.lazarus(a)gmail.com> wrote: > Michael, > > Thanks for pointing these warning errors out. I think they're harmless > and can be ignored but I'll definitely take a look later today and > check in a fix. > As I recall, we had some discussion some months ago about whether to > allow the user to set the size of the java heap and decided that it > was not necessary - these messages suggest the parameter is still > somewhere in the tool tests - oddly enough I can't see it but I'm > seeing the same messages! > I'll let you know what I find once I've had a chance to take a look. > > > On Mon, Sep 26, 2011 at 11:06 PM, michael burrell (TOC) > <michael.burrell(a)nbi.ac.uk> wrote: >> Good afternoon, >> >> >> >> When starting galaxy I find the following errors logged in the paster.log >> >> >> >> galaxy.tools DEBUG 2011-09-26 13:58:21,577 Loaded tool: PicardASMetrics 0.03 >> >> galaxy.tools.test DEBUG 2011-09-26 13:58:21,625 Error in add_param for >> maxheap: Unable to determine parameter type of test input 'maxheap'. Ensure >> that the parameter exists and that any container groups are defined first. >> >> >> >> galaxy.tools DEBUG 2011-09-26 13:58:21,703 Loaded tool: PicardInsertSize >> 0.3.0 >> >> galaxy.tools.test DEBUG 2011-09-26 13:58:21,737 Error in add_param for >> maxheap: Unable to determine parameter type of test input 'maxheap'. Ensure >> that the parameter exists and that any container groups are defined first. >> >> >> >> Our galaxy version is. >> >> >> >> galaxy@jic55666:~/software/galaxy-central$ hg tip >> >> changeset: 6042:2469c53051ea >> >> tag: tip >> >> user: Daniel Blankenberg <dan(a)bx.psu.edu> >> >> date: Sun Sep 25 13:27:14 2011 -0400 >> >> summary: Some random lines tool tweaks. >> >> >> >> Thank you for your assistance. >> >> >> >> Michael. >> >> >> >> ________________________________ >> Please note, that my email address is no longer >> givenname.surname(a)bbsrc.ac.uk. Please update your records to reflect my new >> email address of givenname.surname(a)nbi.ac.uk as shown on this email. >> ___________________________________________________________ >> 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/ >> > > > > -- > Ross Lazarus MBBS MPH; > Associate Professor, Harvard Medical School; > Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; > Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; > -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

1 0

Proxy login issues
by Alex R Bigelow 27 Sep '11

27 Sep '11

Hi, I've set up an apache proxy server to allow external access to my galaxy instance, following the directions at http://wiki.g2.bx.psu.edu/Admin/Config/Apache Proxy<http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy>. When I access galaxy directly (locally), everything works fine. When I try to access it through the proxy server, I get a login screen that works like it should - it gives me errors if I enter non-existent usernames or wrong passwords - but when I enter the correct information, it shows this screen for half a second, and then immediately redirects back to the login page: [cid:d04125f7-b29c-4492-b075-4073921c3fc3@umail.utah.edu] I prefer Galaxy handling usernames and passwords on its own, so I didn't add the "External user authentication" bits - are these required for a proxy server? I've attached the relevant parts of my httpd.conf, as well as my universe_wsgi.ini file if they help at all. Thanks again for the excellent support, Alex Bigelow

1 0