August 2012 - galaxy-dev - lists.galaxyproject.org

Refreshing side bar
by Edward Hills 12 Aug '12

12 Aug '12

Hi Guys, So i'm looking at having the dataset history item that is currently running to load in text from a txt file, re-reading the txt file every few seconds or so. I have found where it gets displayed in the /templates/root/history_common.mako and have added <%include file="test.txt"/> so that it will read my text file but that obviously just reads it the once and then moves on. So what I need help with is being able to read it from the file multiple times while the tool is executing. Any help would be greatly appreciated. Cheers, Ed Department of Biochemistry, University of Otago, Dunedin, New Zealand.

1 0

E. grandis reference genome
by Saravanan Thavamanikumar 10 Aug '12

10 Aug '12

Dear Galaxy team, I am currently running a RNA-seq experiment and wishing to use Galaxy to do all analyses on a public server. My genome (Eucalyptus grandis: http://www.phytozome.net/eucalyptus.php) is not on the genome list. Could you please make it available? Many thanks Saro

2 1

Re: [galaxy-dev] [galaxy-user] Install Galaxy on Mac
by Hotz, Hans-Rudolf 10 Aug '12

10 Aug '12

Hi Edward I am moving your e-mail to 'galaxy-dev' since it's about a local Galaxy instance. I don't think there are any differences between installing Galaxy on Linux and Mac OS X. Hence you can follow the step-by-step instructions on the wiki (well, there are actually only two steps anyway...): http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy WRT checking the python version: just type 'python -V' on the command line, eg on my old MacBook: bash-3.2$ python -V Python 2.5.1 bash-3.2$ Hope this helps Regards, Hans On 08/10/2012 02:37 PM, Edward Turk wrote: > Hello, > Could someone provide instructions for installing galaxy on a Mac OS 10.7? The instructions provided by galaxy start off by asking me to check my python version, but I don't know how to do that. I figure someone has step-by-step instructions or a screen cast? > Thank you, > Edward > ___________________________________________________________ > 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/ >

6 12

Upload a file from a 'select' field
by Kohler Manuel 10 Aug '12

10 Aug '12

Hi, I have added one option on the 'Upload File (version 1.1.3)' page. The idea is to upload a file which is selected in this select field. I have added this to upload.xml: <param name="openBISDataSet" type="select" label="Files" help="select Files" dynamic_options="getURL()" > This works fine and I get the select field dynamically filled by an extra python script with the correct files. This script has a method called 'getURL()'. This returns a python list and I see the values are all correct in there when doing a print of this list with the use_printdebug = True: Log messages [[u'original/Seq_dir/some_file.txt', u'https://bs-openbis11.ethz.ch:8444/datastore_server/stream-content?streamI D=120810112558484-F1D4A3429AECDE24F8C8A6EABDD1E7DD', False], [u'original/Seq_dir/my_file.fastq.gz', u'https://bs-openbis11.ethz.ch:8444/datastore_server/stream-content?streamI D=120810112600832-126422C985537A9969C466878D453546', False]] One strange thing is that it is printed twice, which means it is called twice. I have no clue why. But how do I make the upload finally working? I always get an error message when hitting the Execute button (cf. screen shot). Any hints would be helpful. Just for completeness the "getURL()" function: <snip> def getURL(): sessionToken = login() fList = [] filePathList = [] files = dssServer.listFilesForDataSet(sessionToken, '20120807164613048-4184', '/', True) for file in files: if not file['isDirectory']: filePathList.append(file['pathInDataSet']) for file in filePathList: streamURL = dssServer.getDownloadUrlForFileForDataSet(sessionToken, '20120807164613048-4184', file) fList.append([file,streamURL, False]) print fList return fList </snip> Cheers Manuel -- Manuel Kohler Center for Information Sciences and Databases (C-ISD) Department of Biosystems Science & Engineering (D-BSSE) ETH Zurich, Maulbeerstrasse (1078, 1.02), CH-4058 Basel, +41 61 387 3132

1 0

GATK Unified Genotyper Error
by Sarah Diehl 10 Aug '12

10 Aug '12

Hello all, one of my users encounters a strange error with the GATK tool "Unified Genotyper". At the end of the message you see the original error report. The problem there was that the reference genome is missing. The tool was run as a part of a bigger workflow, but I double checked the workflow and the correct genome is specified there. All other GATK tools work, so there should be no error with the setup of the locally cached references. When I use the rerun button in Galaxy to repeat this step (without changing anything), everything works fine. Best regards, Sarah ----- Forwarded Message ----- From: diehl(a)immunbio.mpg.de To: diehl(a)immunbio.mpg.de, barenboim(a)immunbio.mpg.de Sent: Friday, August 10, 2012 10:08:12 AM Subject: Galaxy tool error report from barenboim(a)immunbio.mpg.de GALAXY TOOL ERROR REPORT ------------------------ ----------------------------------------------------------------------------- job id: 20471 tool id: gatk_unified_genotyper ----------------------------------------------------------------------------- job command line: python /galaxy/galaxy_server/tools/gatk/gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "/galaxy/galaxy_server/database/files/023/dataset_23795.dat" -d "-I" "/galaxy/galaxy_server/database/files/023/dataset_23792.dat" "bam" "gatk_input_0" -d "" "/galaxy/galaxy_server/database/files/_metadata_files/001/metadata_1060.dat" "bam_index" "gatk_input_0" -p 'java -jar "/galaxy/galaxy_server/tool-data/shared/jars/gatk/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" --num_threads 4 --out "/galaxy/galaxy_server/database/files/023/dataset_23793.dat" --metrics_file "/galaxy/galaxy_server/database/files/023/dataset_23794.dat" -R "" --genotype_likelihoods_model "BOTH" --standard_min_confidence_threshold_for_calling "30.0" --standard_min_confidence_threshold_for_emitting "30.0" ' -d "--dbsnp:dbsnp,%(file_type)s" "/galaxy/galaxy_data/gatk/b37/dbsnp_135.b37.vcf" "vcf" "input_dbsnp_0" ----------------------------------------------------------------------------- job stderr: ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 1.6-13-g91f02df): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-eEVeYq) does not exist. ##### ERROR ------------------------------------------------------------------------------------------ ----------------------------------------------------------------------------- job stdout: ----------------------------------------------------------------------------- job info: None ----------------------------------------------------------------------------- job traceback: None ----------------------------------------------------------------------------- (This is an automated message).

1 0

RabbitMQ work-around?
by Zerbe, Brandon 09 Aug '12

09 Aug '12

Hello, I'm doing a local install of the bcbb/nextgen pipeline and galaxy on a SGE cluster. Our administrator has expressed a little concern over RabbitMQ, which I have interpreted as requiring both a RabbitMQ-server install and RabbitMQ-client installs on the individual nodes (feel free to correct me). Has anyone implemented any alternative middleware protocols, or is RabbitMQ a requirement to tie everything together? Thanks loads, Brandon

1 0

TopHat paired end
by suzan katie 09 Aug '12

09 Aug '12

Hello, I am trying to do RNAseq analysis on Paired end data Illumina. I have about 4 files for each sample (2 forward and 2 reverse). I want to analyze the data in Galaxy. Do I have to groom and run the QC for each file? Should I join the paired files and run both tools on each pair, or should I combine all of the data for each sample (which I don't know how to do) and then groom and run the QC for all of the reads for the sample. Ultimately, How do I run TopHat for paired-end data. When I select paired end data in Galaxy, it gives an option to upload both files should I upload both forward files once and reverse files once. Or should I combine both the files before running the TopHat. I am all confused. Any kind of help will be appreciated Thanks in advance

2 1

upgrading over several releases
by Robert M. Flight 09 Aug '12

09 Aug '12

Hi Everyone, Our current Galaxy instance is from August 30, 2011. This was our first deployment, and we have never upgraded. We are going to upgrade it, but I am trying to determine whether the best process would be to upgrade incrementally over the six dist releases since then, or to try and do it all in one shot, upgrading to the latest dist. Looking at the news briefs, I'm also considering upgrading in 3 steps, upgrade to before the major changes in the tool shed, then to the first release with major tool shed changes, and then finally to the latest release. I would appreciate any insights and advice on this process. Thank you, -Robert Robert M. Flight, Ph.D. University of Louisville Bioinformatics Laboratory University of Louisville Louisville, KY PH 502-852-1809 (HSC) PH 502-852-0467 (Belknap) EM robert.flight(a)louisville.edu EM rflight79(a)gmail.com robertmflight.blogspot.com bioinformatics.louisville.edu/lab github.com/rmflight/general/wiki The most exciting phrase to hear in science, the one that heralds new discoveries, is not "Eureka!" (I found it!) but "That's funny ..." - Isaac Asimov

3 2

Problem with get data/uploading file
by David Roquis 09 Aug '12

09 Aug '12

Dear Galaxy community, I have a problem with uploading data on Galaxy, using the get data/upload file tool, and I can't figure out where the trouble comes from. Basically, when I try to upload files (size ranging from less than 1 Mo up to 600 Mo), sometimes it works, sometimes it doesn't (keep uploading forever), and I don't get any error message when it doesn't work. I can't find a pattern on when it works or not, it seems pretty random. It don't think it is related to the files I use, because I tried with different files, of different types and format, and the exact same file can sometimes be uploaded, sometimes not. One thing I have noticed is that when the upload is successful, a file is created in /tmp/, and when the upload runs forever, no new file appears in /tmp/. I have tried a couple of basic things to solve the problem: emptying the /tmp/, restarting galaxy, deleting permanently my history, etc. Sometimes I can upload 4-5 files in a row, then it stops working, and some other time I can't even upload one. When one upload keep running forever, even if I cancel it, no further uploads will work. I have to stop the uploads and restart galaxy, but it doesn't work 100% of the time (sometimes I have to try 2-3 times before I can upload again). I am facing this problem on two different instances of galaxy. A development one that I simply installed on my /home/ using mercurial and didn't modified at all, and a production one that I just set up following the Galaxy Team recommendations (using PostgreSQL and nginx with the upload module, and working on a dedicated Galaxy user account). I am a beginner in informatics, and since I get no error message, I don't know where to look for a way to solve this annoying problem. Uploading files using data libraries under the admin menu seems to be working perfectly all the time. Thank you very much for your help and advice. Sincerely David Roquis Ph.D. student University of Perpignan additional info: - I am using the latest version of galaxy, and my OS is Fedora 16 - I tried working with and without virtualenv (made no difference). - I don't know if this is related or not, but it seems quite strange to me. Whenever I try to access "manage jobs" in the admin section (on both instances), I get the following error message: "This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs." How is that possible since I am not using multiple servers (especially for the development instance, which I haven't modified at all)? - debug = False is causing me a server error in the history frame (so I use True instead).

2 3

galaxy-central does not start
by Björn Grüning 09 Aug '12

09 Aug '12

Hi, galaxy-central does not start because of commit 9f790bc90769. The attached patch should fix it. Salve, Bjoern -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruening(a)pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/

2 1