Hi Mike,

give it a shot for sure. If you want some details have a look at
https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial

M.

On Sun Jan 04 2015 at 7:53:51 PM Waldron, Michael H <mwald...@email.unc.edu>
wrote:

> It's mostly due to my lack of thorough knowledge about Galaxy. So should I
> just try to do the tool shed install by going to Admin->Tool Sheds and
> selecting fastqc from there?
>
> Mike Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
>
> ________________________________________
> From: Björn Grüning [bjoern.gruen...@gmail.com]
> Sent: Sunday, January 04, 2015 12:46 PM
> To: Waldron, Michael H; Björn Grüning; galaxy-...@bx.psu.edu
> Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
>
> Hi Mike,
>
> it can happen that wrappers versions do not work well with older/newer
> FASTQC versions. This is the reason we try to couple "binary" versions
> of tools to wrappers versions.
>
> Any reason you don't use the toolshed installation with dependencies?
>
> Cheers,
> Bjoern
>
> Am 03.01.2015 um 17:44 schrieb Waldron, Michael H:
> > It is FastQC-0.11.2. It's a separate install from Galaxy, and a symlink
> points to it under tool-data/shared/jars:
> >
> > $ pwd
> > /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars
> >
> > FastQC -> /nas02/apps/galaxy-prod/fastqc-0.11.2/FastQC
> >
> >
> > Mike Waldron
> > Systems Specialist
> > ITS - Research Computing Center
> > University of North Carolina at Chapel Hill
> >
> >
> > ________________________________________
> > From: Björn Grüning [bjoern.gruen...@gmail.com]
> > Sent: Saturday, January 03, 2015 6:42 AM
> > To: Waldron, Michael H; galaxy-...@bx.psu.edu
> > Subject: Re: [galaxy-dev] Problem using FastQC in Galaxy
> >
> > Hi Michael,
> >
> > which version of the FASTQC wrapper are you running? Can you point us to
> > the exact build and toolshed version?
> >
> > Thanks,
> > Bjoern
> >
> > Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:
> >> Having a problem with directing FastQC output in Galaxy. User is
> running a job whose command line looks like this:
> >>
> >> # FastQC cl = 
> >> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
> --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files
> /proj/galaxy/job_working_directory/010/10467/dataset_
> 13836_files/SRR016862.fastq
> >>
> >> Job output looks like this:
> >>
> >> ## odpath=None: No output found in None. Output for the run was:
> >> # FastQC cl = 
> >> /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc
> --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files
> /proj/galaxy/job_working_directory/010/10467/dataset_
> 13827_files/SRR016862.fastq
> >> Started analysis of SRR016862.fastq
> >> Approx 5% complete for SRR016862.fastq
> >> Approx 10% complete for SRR016862.fastq
> >> Approx 15% complete for SRR016862.fastq
> >> Approx 20% complete for SRR016862.fastq
> >> Approx 25% complete for SRR016862.fastq
> >> Approx 30% complete for SRR016862.fastq
> >> Approx 35% complete for SRR016862.fastq
> >> Approx 40% complete for SRR016862.fastq
> >> Approx 45% complete for SRR016862.fastq
> >> Approx 50% complete for SRR016862.fastq
> >> Approx 55% complete for SRR016862.fastq
> >> Approx 60% complete for SRR016862.fastq
> >> Approx 65% complete for SRR016862.fastq
> >> Approx 70% complete for SRR016862.fastq
> >> Approx 75% complete for SRR016862.fastq
> >> Approx 80% complete for SRR016862.fastq
> >> Approx 85% complete for SRR016862.fastq
> >> Approx 90% complete for SRR016862.fastq
> >> Approx 95% complete for SRR016862.fastq
> >> Analysis complete for SRR016862.fastq
> >>
> >> The job_working_directory/010/10467 directory is created, however it
> is empty. It appears this "odpath" needs to be set somehow?
> >>
> >> Does anyone know a solution for this?
> >>
> >> Mike Waldron
> >> Systems Specialist
> >> ITS - Research Computing Center
> >> University of North Carolina at Chapel Hill
> >>
> >>
> >>
> >>
> >> ___________________________________________________________
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> >>
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> >>
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