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Trouble viewing interval files in UCSC with Apache+XSendFile
by Assaf Gordon 07 Apr '11

07 Apr '11

Hello, I've encountered a strange combination of factors that results in file access problems. Perhaps I'm doing something wrong - any advice will be appreciated. I'm using Apache + XSendFile. when viewing a strict BED file, everything works, because the actual dataset filename is passed on to Apache/XSendFile. When viewing any other kind of interval file, Galaxy first creates a temporary file in strict BED format ( in "Interval::as_ucsc_display_file()" ). This method uses "tempfile.mkstemp()", which is documented to create a temporary file with user-only read/write access (no group or world access). So when the file name is passed on to apache/XsendFile - apache can't read the file and returns 404. I'm wondering if anyone else encountered such problem, or is my configuration is somehow wrong. Thanks, -gordon

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samtools sam-to-bam problem
by Ryan Golhar 07 Apr '11

07 Apr '11

I've performed an alignment using BWA on a file of paired-end illumina reads. The SAM file looks fine, and contains header information. I'm converting it to BAM using the sam to bam converter, however it consistently errors out after running for a while. The error is: "Error extracting alignments from (/home/galaxy/galaxy-dist/database/files/000/dataset_785.dat), " but no error is provided. Looking at the sam_to_bam.py on line 156 is where the error is thrown. Nothing is in e (I think). BTW - If I run the samtools command from the shell by hand, the BAM file is created properly. I do see information on stderr: $ samtools view -bt /data/genomes/H_sapiens/hg19/hg19.fa.fai -o /tmp/killme.bam /home/galaxy/galaxy-dist/database/files/000/dataset_785.dat [samopen] SAM header is present: 25 sequences. I'm using samtools version 0.1.14 (r933:170) on Linux, 64-bit. What do I do? Ryan

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Enacting Taverna2 workflows through Galaxy
by Kostas Karasavvas 07 Apr '11

07 Apr '11

Hi all! I would like to bring to your attention a project that aims to make Taverna and Galaxy work better together. This new application is a first step towards making Galaxy and Taverna2 (http://www.taverna.org.uk) more interoperable. It allows for the automatic generation of a Galaxy tool from a Taverna2 workflow. That tool can then be installed as usual in a Galaxy server. It will allow the Taverna workflow to become part of a Galaxy pipeline. Users do not need to install the generator application themselves. It is available as part of the myExperiment (http://www.myexperiment.org) website. While browsing Taverna2 workflows the user will see an additional link "Download as Galaxy Tool" in the download section of the workflow. The next page provides instructions (and references) as well as an option to download the current workflow as a Galaxy tool. For more information and contact details: https://trac.nbic.nl/elabfactory/wiki/eGalaxy Cheers, Kostas

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Use of galaxy with Illumina Pipeline RTA / OLB/ CASAVA / GERALD etc
by WATSON Mick 06 Apr '11

06 Apr '11

Hi I'd be interested to hear from anyone who has tried, or even thought about, using galaxy to manage the Illumina pipeline (RTA, OLB, CASAVA, GERALD and all those familiar names). Thanks Mick The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Relative file path in Galaxy
by Zhe Chen 06 Apr '11

06 Apr '11

Hi, My tool has a script reads a file in the same directory as the script. When I try to use relative path to read the file, it works by directly run it, but does not work when calling from Galaxy. Absolute path will work, but I want to know is there a way to do it using relative path. Can you give me some suggestion? myTool.pl use the following code the read the file in the same directory my $genusfiles = "genus.txt"; open (GENUSGP, "$genusfiles") or die "$genusfiles: $! \n"; close(GENUSGP); Thanks

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SGE and Galaxy (a different approach)
by andrew stewart 06 Apr '11

06 Apr '11

I'm aware of how to configure Galaxy to use SGE in universe_wsgi.ini, however what I want to do is a little different. Because I only want certain processes to be submitted to the queue, I'd rather control this at the tool configuration level (the xml wrapper). For example: <command interpreter="bash"> qsub myscript.sh </command> This will work, except that the status of the job (in Galaxy) shows as completed even though the job has simply been submitted to SGE. Basically Galaxy 'loses track' of the process because the submission process (myscript.sh) has completed even if the actual job hasn't. Has anyone else tried anything like this before, or have anything helpful to suggest? One thought is to somehow cause the myscript.sh process to pause until the SGE job has completed... somehow. Any advice appreciated. Thanks, Andrew

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Freebayes
by Juan Carlos Perin 05 Apr '11

05 Apr '11

I'm trying to run Freebayes SNP calling on a bam file from a BWA alignment of solid data. I keep getting the following error: [bam_sort_core] merging from 40 files... freebayes: invalid option -- Y did you mean --bam ? I'm not sure where this is set in the code to try to debug things. I'm wondering if anyones had this error, and how to fix it? Just to note, I'm running Brad Chapmans branch of galaxy for the LIMS functionality. But it appears to be an issue with either galaxy-dist or this one. Thanks in advance for any advice. Juan Perin

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Optimizing Disk space using by combining mapping with SAM-to-BAM
by Ryan Golhar 05 Apr '11

05 Apr '11

Hi all - I find it redundant to hold on to SAM output from NGS Mapping tools such when I end up converting the SAM files to BAM files anyway. The cleanup scripts require the history items to be deleted, but I don't want to delete them yet as I want the entire workflow to be kept until we are done analyzing our data. So, I was thinking of a way to remove the intermediate SAM files and thought how I would do this on the command line...simply pipe the output of BWA to samtools to create a BAM file and never have a SAM file to deal with. The BWA tool runner can be modified to pipe BWA output directly to samtools so a SAM file is never physical stored on disk. Has anyone done this? Does this seem like a good idea? Ryan -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

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Missing Page Editor Components
by Charlis Hsia 05 Apr '11

05 Apr '11

Hi all, Wonder if I can get some help from here for the following questions: I just pulled the galaxy-central and installed it. It runs fine. However, when I tried to use the Edit Pages function, there is no "Embed Galaxy Object" and "Insert Link to Galaxy Object" in the "Page Editor". I have set the "enable_pages = True" in "universe_wsgi.ini". Wonder what else can cause the problem? Also, is there any documentations for the control syntax used in datatypes and tools configure xmls? Thanks! Charlie

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Updating BLAST+ wrapper
by Peter Cock 05 Apr '11

05 Apr '11

Hi all, The NCBI have just released BLAST 2.2.25+ which includes some interesting new stuff of interest to the tabular output, i.e. "Added support for query and subject length to tabular output" I would therefore like to update my BLAST+ wrappers in Galaxy to add these two columns to the 'extended tabular' output option. They are going to be very helpful as you can now calculate things like the percentage identity (or similarity) compared to the query or sequence. If there are no objections I propose to add these as columns 23 and 24 (i.e. at the end), so minimise disruption to anyone already using the tabular output. I would hope to have a branch ready for merging next week... Peter

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