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Set metadata from within the tool
by roberto.dilauro＠uniparthenope.it 14 Aug '12

14 Aug '12

Hi everyone, How can I set dataset's metadata from within the tool? For example: From the command tag (in the xml tool specification) i call myscript.sh: <command> myscript.sh -input=$input -output=$output </command> My script.sh produce a value that i want to store as metadata of $input. I've checked the tool config syntax http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax and seems that i can read metadata (${input.metadata.somemetadata}) but not write. Maybe <code> tag can help me but it is deprecated. Thanks for the help, Roberto

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Old tool not showing up properly in Tool Shed
by Peter Cock 13 Aug '12

13 Aug '12

Hi all, I've just uploaded an update to my (previously protein only) sequence analysis bundle on the ToolShed, which is stuck with the original name: tmhmm_and_signalp This now offers Galaxy wrappers for several standalone command line sequence analysis tools: * SignalP 3.0 predicts signal peptides, see: http://www.cbs.dtu.dk/services/SignalP/ * TMHMM 2.0 predicts transmembrane helices, see: http://www.cbs.dtu.dk/services/TMHMM/ * Promoter 2.0 predicts eukaryotic PolII promoters [NEW WRAPPER], see: http://www.cbs.dtu.dk/services/Promoter/ * WoLF PSORT predicts Eukaryote protein sub-cellular localization, see: http://wolfpsort.org/ * Oomycete RXLR motif prediction - a Python script implementing three published methods, which calls SignalP 3.0 and HMMER 2.3.2 internally. In this update I added the new Promoter 2.0 wrapper, and made some small changes to the SignalP and TMHMM wrappers. The other tools are unchanged. Looking at the tool bundle via the Tool Shed, for revision 7:9b45a8743100 it only shows four "valid" tools: * Promoter 2.0 - Find eukaryotic PolII promoters in DNA sequences * RXLR Motifs - Find RXLR Effectors of Plant Pathogenic Oomycetes * SignalP 3.0 - Find signal peptides in protein sequences * TMHMM 2.0 - Find transmembrane domains in protein sequences Why is this missing?: * WoLF PSORT - Eukaryote protein subcellular localization prediction The missing tool is NOT showing up under "Browse my invalid tools", and the wrapper XML seems to still be there if I browse the tip files. Thanks, Peter

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Re: [galaxy-dev] FastQC Tool Errors
by Robert Chase 13 Aug '12

13 Aug '12

Hello, We are having trouble running FastQC on our production server. The original stacktrace looked like this; Fastq failed. Error executing FastQC. Unknown option: djava.awt.headless Exception in thread "main" java.lang.NoClassDefFoundError: uk/ac/bbsrc/babraham/FastQC/FastQCApplication Caused by: java.lang.ClassNotFoundException: uk.ac.bbsrc.babraham.FastQC.FastQCApplication at java.net.URLClassLoader$1.run(URLClassLoader.java:200) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:188) at java.lang.ClassLoader.loadClass(ClassLoader.java:307) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:252) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320) Could not find the main class: uk.ac.bbsrc.babraham.FastQC.FastQCApplication. Program will exit. Then I tried to update java to the most current version. The current version is java -version java version "1.7.0_05" Java(TM) SE Runtime Environment (build 1.7.0_05-b06) Java HotSpot(TM) 64-Bit Server VM (build 23.1-b03, mixed mode) This changed the error message we got when we ran FastQC. The new trace looks like this; Fastq failed. Error executing FastQC. Unknown option: djava.awt.headless Error: Could not find or load main class uk.ac.bbsrc.babraham.FastQC.FastQCApplication The strange thing is that the tools works on our test server, which is almost an exact copy of the production server. -Rob __________________________ Sure enough, this fixed the problem. I just installed the latest Sun JRE and it is working now. Thanks for the suggestion! I would have never guessed. -Josh On Mon, Jun 25, 2012 at 11:34 AM, simon andrews <[hidden email]<http://dev.list.galaxyproject.org/user/SendEmail.jtp?type=node&node=4655462…> > wrote: Yes, that's the broken version of gcj. I don't have a Centos machine here at the moment, but I think if you install OpenJDK and use the alternatives system to select that as the default JRE then that should fix things. Simon. On 25 Jun 2012, at 17:19, Josh Nielsen wrote: Hi Simon, I recently installed Java with the yum package manager on our compute nodes, and our cluster is a Centos 6 environment. Here is what the results of "java -version" returned on the compute nodes: "*bash# java -version* *java version "1.5.0"* *gij (GNU libgcj) version 4.4.4 20100726 (Red Hat 4.4.4-13)* * * *Copyright (C) 2007 Free Software Foundation, Inc.* *This is free software; see the source for copying conditions. There is NO* *warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE* ." Is this version of Java too old? Perhaps I need to install the JRE manually? Thanks! On *Sat Jun 23 04:20:53 EDT 2012*, Simon Andrews <[hidden email]<http://dev.list.galaxyproject.org/user/SendEmail.jtp?type=node&node=4655462…> wrote: > Are you by any chance running an older version of gcj as your java version? There is a known bug in some of these where they don't correctly configure the headless environment, even if the correct parameters are passed. This causes exactly the kind of errors you're seeing. > > If this is the case you'll need to install a more recent JRE (or update your path to point to one which is already present). > > Simon. > > > On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen <[hidden email]<http://dev.list.galaxyproject.org/user/SendEmail.jtp?type=node&node=4655462…>> > wrote: > > Hello, > > > > I am having an issue with getting the FastQC tool to work with Galaxy on > our > > server. I downloaded the FastQC files (version 0.8.0) and changed the > > directory that the wrapper script looks for the 'fastqc' executable in, > but > > when we run a job with it we have been getting the following output: > > > > "Started analysis of Clip > > > > Approx 5% complete for Clip > > Approx 10% complete for Clip > > ... > > ... > > Approx 95% complete for Clip > > Approx 100% complete for Clip > > > > Analysis complete for Clip > > > > (.:9754): Gtk-WARNING **: cannot open display: " > > > > And then the job shows as failed in Galaxy. The output .dat file just has > > that same output/error message in it (though it seems to indicate it got > to > > 100%). Also when I try to execute the fastqc file directly (albeit with > no > > arguments) I get this: > > > > "Exception in thread "main" java.awt.HeadlessException: > > No X11 DISPLAY variable was set, but this program performed an operation > > which requires it. > > at > > java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) > > at java.awt.Window.<init>(Window.java:437) > > at java.awt.Frame.<init>(Frame.java:419) > > at java.awt.Frame.<init>(Frame.java:384) > > at javax.swing.JFrame.<init>(JFrame.java:174) > > at > > > uk.ac.bbsrc.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:271) > > at > > > uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102)" > > > > Both errors seem to have something to do with the graphical GUI > component of > > FastQC (which I have seen some screenshots for on the FastQC webpage). If > > this application is GUI-driven how did the online PSU Galaxy get it to > work > > with their wrapper script when the tools are run in a command-line > > environment with no X11 or Gtk? Essentially I'm just wondering what steps > > I'm missing here to getting this to work with our Galaxy mirror, other > than > > just dropping the executable in place? Any suggestions? > > > > Thanks, > > Josh > > > > > > ___________________________________________________________ > > 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; > Head, Medical Bioinformatics, BakerIDI; Tel: <a > href="tel:%2B61%20385321444" value="+61385321444" target="_blank"> +61 > 385321444; > The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT *Registered Charity No. 1053902.* The information transmitted in this email is directed only to the addressee. If you received this in error, please contact the sender and delete this email from your system. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Babraham Institute. Full conditions at: www.babraham.ac.uk<http://www.babraham.ac.uk/email_disclaimer.html>

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Deploy a tool from the Galaxy toolshed to my local version of Galaxy
by Edward Turk 13 Aug '12

13 Aug '12

Hello, I have a local instance, I am the only user, and I would like to use a tool that is in the galaxy tool shed but not in my local instance. After reading the toolshed wiki (http://wiki.g2.bx.psu.edu/Tool%20Shed) I have a few questions. 1. Do I need a local tool shed? I need to use an available tool but do not need to develop tools 2. According to this part of the wiki (http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool…) I need to be logged in as "Admin". How do I make myself an Admin? Thank you, Edward

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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.

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E. grandis reference genome
by Saravanan Thavamanikumar 11 Aug '12

11 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

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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/ >

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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

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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).

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RabbitMQ work-around?
by Zerbe, Brandon 10 Aug '12

10 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

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