Hello, I am working on a local install of Galaxy and when running a test data set I get this error when invoking the Fastqc commans: /home/mnkyboy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 20 class FastQC(): ^ SyntaxError: invalid syntax This is Illumina data from a single tile of qseq.txt data converted to FASTQ and run through the FASTQ groomer. Fastqc is working properly outside of Galaxy so any advice would be appreciated. Thanks, Matt T.
Hi Mathew, The tool xml has a clunky way of finding the fastqc perl script - which has to be in the same directory as the jars it requires: <command interpreter="python"> rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix" -f $input_file.ext -e ${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc #if $contaminants.dataset and str($contaminants) > '' -c "$contaminants" #end if </command> so it's looking for the fastQC install under [galaxyroot]/tool-data/shared/jars/FastQC If you want, you could change the -e parameter (in tools/rgenetics/rgFastQC,xml) to reflect your local installation choice but it might be easier to symlink the fastQC install directory to tool_data/shared/jars I hope this helps... On Fri, Sep 2, 2011 at 8:57 AM, Matthew J. Thomas <mnkyboy@u.washington.edu> wrote:
Hello,
I am working on a local install of Galaxy and when running a test data set I get this error when invoking the Fastqc commans:
/home/mnkyboy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 20
class FastQC():
^
SyntaxError: invalid syntax
This is Illumina data from a single tile of qseq.txt data converted to FASTQ and run through the FASTQ groomer. Fastqc is working properly outside of Galaxy so any advice would be appreciated.
Thanks,
Matt T.
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Matthew J. Thomas <mnkyboy <at> u.washington.edu> writes:
Hello, I am working on a local install of Galaxy and when running a test data set I
get this error when invoking the Fastqc commans:
/home/mnkyboy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 20 class FastQC(): ^ SyntaxError: invalid syntax This is Illumina data from a single tile of qseq.txt data converted to FASTQ and run through the FASTQ groomer. Fastqc is working properly outside of Galaxy so any advice would be appreciated. Thanks, Matt T.
*************************************************************** Hi Ross and Matthew, I'm a newbie to Galaxy and got the same error while trying to process some Illumina data... Thanks for your posting and tips! So, just to confirm the understanding: when installing a local instance of Galaxy you'd still need to install the FASTQC package independently and, subsequently, provide the "linkage" of GALAXY and FASTQC by, for instance, using the symlink approach suggested by Ross, right? This means that FASTQC is not "bundled" in the Galaxy local instance package, right? Thanks again for your attention and regards, Antonio ***************************************************************
Hi, Antonio - yes, that's right - FastQC is not 'bundled' and has to be obtained from the tool authors - we just provide a wrapper to make it work inside Galaxy. The Galaxy distribution includes code for some of the inbuilt tools like the fastq groomer, but most of the distribution tool wrappers rely on popular third party packages such as cufflinks, bwa, FastQC, R/BioC packages and so on. There's a list of third party dependencies at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies - they have to be available on the computational nodes for Galaxy jobs requiring them to run. On Sun, Sep 25, 2011 at 9:33 PM, Antonio Ribeiro <acbellorib@gmail.com> wrote:
Hi Ross and Matthew, I'm a newbie to Galaxy and got the same error while trying to process some Illumina data... Thanks for your posting and tips!
So, just to confirm the understanding: when installing a local instance of Galaxy you'd still need to install the FASTQC package independently and, subsequently, provide the "linkage" of GALAXY and FASTQC by, for instance, using the symlink approach suggested by Ross, right? This means that FASTQC is not "bundled" in the Galaxy local instance package, right?
Thanks again for your attention and regards, Antonio
***************************************************************
___________________________________________________________ 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:
-- 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;
Thanks very much, Ross, for your reply and tips! I've made FastQC to work and will check for the other dependencies. Best regards, Antonio -----Mensagem original----- De: Ross [mailto:ross.lazarus@gmail.com] Enviada em: domingo, 25 de setembro de 2011 09:32 Para: Antonio Ribeiro Cc: galaxy-dev@lists.bx.psu.edu Assunto: Re: [galaxy-dev] Error in FastQC Hi, Antonio - yes, that's right - FastQC is not 'bundled' and has to be obtained from the tool authors - we just provide a wrapper to make it work inside Galaxy. The Galaxy distribution includes code for some of the inbuilt tools like the fastq groomer, but most of the distribution tool wrappers rely on popular third party packages such as cufflinks, bwa, FastQC, R/BioC packages and so on. There's a list of third party dependencies at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies - they have to be available on the computational nodes for Galaxy jobs requiring them to run. On Sun, Sep 25, 2011 at 9:33 PM, Antonio Ribeiro <acbellorib@gmail.com> wrote:
Hi Ross and Matthew, I'm a newbie to Galaxy and got the same error while trying to process some Illumina data... Thanks for your posting and tips!
So, just to confirm the understanding: when installing a local instance of Galaxy you'd still need to install the FASTQC package independently and, subsequently, provide the "linkage" of GALAXY and FASTQC by, for instance, using the symlink approach suggested by Ross, right? This means that FASTQC is not "bundled" in the Galaxy local instance package, right?
Thanks again for your attention and regards, Antonio
***************************************************************
___________________________________________________________ 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:
-- 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;
participants (4)
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Antonio Cláudio Bello Ribeiro -
Antonio Ribeiro
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Matthew J. Thomas -
Ross