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Trackster and bedtools error
by Perez, Ricardo 12 Jul '13

12 Jul '13

Dear all, As I was trying to do visualize my data set in trackster, I get the following error: /bin/sh: 1: bedtools: not found sort: fflush failed: standard output: Broken pipe sort: write error needLargeMem: trying to allocate 0 bytes (limit: 100000000000) When doing a sudo find / -name "bedtools" in my system, I get the following output: /usr/share/bedtools /usr/share/doc/bedtools Do I have bedtools installed in the wrong place? Thank you for your help, --Ricardo Perez

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Using Jar files in Galaxy
by sridhar srinivasan 12 Jul '13

12 Jul '13

Dear Developers, I am using java jar files for softwares like fastqc, GATK. For running these tools i install the softare and set path in bash_profile file. My doubt is i placed the jar files in galaxy dist folder ( galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc ) is this enough to call the jar files from galaxy?? After placing the jar file i tried running the tool using the interface it gives ERROR as # FastQC cl = /illumina/data/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/illumina/data/galaxy/galaxy-dist/database/job_working_directory/000/216/dataset_546_files --f=bam /illumina/data/galaxy/galaxy-dist/database/job_working_directory/000/216/dataset_546_files/Bowtie2_on_data_7_and_data_6__aligned_reads Exception in thread "main" java.lang.NoClassDefFoundError: uk/ac/babraham/FastQC/FastQCApplication Caused by: java.lang.ClassNotFoundException: uk.ac.babraham.FastQC.FastQCApplication at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) Could not find the main class: uk.ac.babraham.FastQC.FastQCApplication. Program will exit. I got same error for GATK also ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 2.5-2-gf57256b): ##### 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 website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-a3rr8t) does not exist. ##### ERROR ----------------------------------------------------------------------------------------- Could you please suggest on the same.. Thanks Sridhar

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Tool availability
by vijayalakshmi 11 Jul '13

11 Jul '13

Hi, Are any of the following tools available in galaxy? 1) IDR http://www.uwencode.org/software/hotspot 2) Hotspot https://sites.google.com/site/anshulkundaje/projects/idr 3) Wiggler https://code.google.com/p/align2rawsignal/ 4) PhantomPeakQualTools Regards, Vijayalakshmi.

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Short-term access to a galaxy server for teaching
by Max Heiman 11 Jul '13

11 Jul '13

Hi, We would like to use Galaxy to introduce genomic analysis in our introductory graduate genetics course. Would anyone be willing to let us "borrow" a server for two hours (9-11 am Boston time, Sept 25)? The students will be uploading ~1M 30-bp reads, running QC and trimming barcodes, using BOWTIE to align them to the yeast genome and then MACS to call peaks. There will be about 40 users total. Each task runs quickly on the public server, but we are concerned about the queue times when dealing with a 90-min class. Thank you for any help or advice, best Max

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Config specific tools that auto hide other panels to get more room
by Peng Li 11 Jul '13

11 Jul '13

Dear All I develop one data display tool for my local galaxy instance, I want to make the history panel and tools panel auto hidden while I load this tools since I need more room to show the data, does anyone has any clue for this? Like change the tools xml or add a JS function to operate father web-frame? Many thanks wbflame

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queue system
by Jasper Jan Koehorst 11 Jul '13

11 Jul '13

Is it possible to create a queue system for separate jobs. I have a module which roughly consumes all CPUs on our machine and if another user decides to run the same module with other data it should wait till all other runs are finished to prevent overloading. Is there a setting for this? Jasper Koehorst Wageningen UR

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virtualenv, jpype, and tool_dependencies.xml
by Michael E. Cotterell 11 Jul '13

11 Jul '13

I'm trying to setup a virtualenv with JPype via tool_dependencies.xml. I've verified that JPype is available from PyPI via pip, however, when Galaxy tries to install the dependency, it's not finding a distribution. JPype 0.5.4.2 https://pypi.python.org/pypi/JPype Here is the <package> snippet from my tool_dependies.xml file: <package name="jpype" version="0.5.4.2"> <install version="1.0"> <actions> <action type="setup_virtualenv">JPype==0.5.4.2</action> </actions> </install> <readme> In order to install JPype, you must agree to the Apache License, Version 2.0, January 2004 (http://www.apache.org/licenses/) </readme> </package> Here is the error that I get when trying to install the dependency: New python executable in /home/mepcotterell/galaxy-tool-shed/tool-deps/jpype/0.5.4.2/mepcotterell/web_service_tools/65a0d7bb35d6/venv/bin/python Installing setuptools............done. Installing pip...............done. Downloading/unpacking JPype==0.5.4.2 (from -r /home/mepcotterell/galaxy-tool-shed/tool-deps/jpype/0.5.4.2/mepcotterell/web_service_tools/65a0d7bb35d6/requirements.txt (line 1)) Could not find any downloads that satisfy the requirement JPype==0.5.4.2 (from -r /home/mepcotterell/galaxy-tool-shed/tool-deps/jpype/0.5.4.2/mepcotterell/web_service_tools/65a0d7bb35d6/requirements.txt (line 1)) No distributions at all found for JPype==0.5.4.2 (from -r /home/mepcotterell/galaxy-tool-shed/tool-deps/jpype/0.5.4.2/mepcotterell/web_service_tools/65a0d7bb35d6/requirements.txt (line 1)) Storing complete log in /home/mepcotterell/.pip/pip.log Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) mepcott(a)uga.edu (mailto:mepcott@uga.edu) mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/

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problem with python output
by vijayalakshmi 10 Jul '13

10 Jul '13

Hi, I am trying to integrate a tool into galaxy. The tool runs in two parts - 1) Computes correlation and provides an ouput 'txt' file (Java) 2) Takes the previously ouput txt file and outputs a 'pdf' file. (Python) I am having trouble with the second tool. If I provide a sample 'txt' file as input, it's working fine. But if I run it in galaxy, it is not working (for some reason it is not reading the 'txt' file from the previous output). Below is the code. #!/usr/bin/python import sys, os import numpy as np import matplotlib.pyplot as plt input_file = sys.argv[1] output_file = sys.argv[2] print 'Number of arguments:', len(sys.argv), 'arguments.' print 'Argument List:', str(sys.argv) txt_in = input_file + '.txt' mydata = np.loadtxt(txt_in) plt.figure(1) plt.plot(mydata[:,0],mydata[:,1],label = "Feature"); plt.plot(mydata[:,0],mydata[:,2], label = "Variance"); plt.xlabel('Distance from feature(bp)'); plt.ylabel('Score'); plt.title(sys.argv[1]); plt.legend(loc="best") pdf_out = output_file + '.pdf' plt.savefig(pdf_out) data = file(pdf_out, 'rb').read() fp = open(output_file, 'wb') fp.write(data) fp.close() os.remove(txt_in) os.remove(pdf_out) Below is the xml code. <tool id="archtex_massdata_extraction" name="Extract mass data"> <description> for the given BAM file </description> <command> java -jar Extraction.jar $input_bam_file $ref_filename $ref_filetype $output1 </command> <command interpreter="python"> plot.py $output1 $out_file1 </command> <inputs> <param name="input_bam_file" type="data" format="BAM" label="Input BAM file" help="Choose an input BAM file"/> <param name="ref_filename" type="data" format="gen,txt,gtf,bed" label="Reference/Coordination file" help="Choose a reference file"/> <param name="ref_filetype" type="select" label="Choose the reference file type"> <option value="custom">Custom</option> <option value="refgene">refGene</option> <option value="GFF">GFF</option> <option value="bed">BED</option> </param> </inputs> <outputs> <data name="output1" format="txt" /> <data name="out_file1" format="pdf" /> </outputs> </tool> I am forcing the input to be 'tx't and the output to be 'pdf' in the python script. When I run the code, it is not showing any errors but it's not showing any output either. I am able to download the first output 'txt' file but there is no download button option in the right pane of galaxy for the second part. Any help is appreciated! Thanks, VJ.

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GATK DepthofCoverage tool
by Jaworek, Thomas 10 Jul '13

10 Jul '13

Hi Galaxy, When I try to process my exome data bam files using DepthOfCoverage under GATK tools (on the main instance), the program seems to keep running forever without ever completing. There is no error message output but the program never ends after going for several days! Could it be something wrong with my files or has any one else reported having an issue with it? Regards, Tom --------------------------------------------- Thomas Jaworek Department of Ophthalmology Cincinnati Children's Hospital 3333 Burnet Avenue Research Building R2409 Cincinnati, OH 45229 thomas.jaworek(a)cchmc.org 513-803-2951

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tool availability
by vijayalakshmi 10 Jul '13

10 Jul '13

Hi, Are any of the following tools available in galaxy? 1) IDR http://www.uwencode.org/software/hotspot 2) Hotspot https://sites.google.com/site/anshulkundaje/projects/idr 3) Wiggler https://code.google.com/p/align2rawsignal/ 4) PhantomPeakQualTools Regards, Vijayalakshmi.

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