On Sun Jan 04 2015 at 7:53:51 PM Waldron, Michael H <mwaldron@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.gruening@gmail.com]
Sent: Sunday, January 04, 2015 12:46 PM
To: Waldron, Michael H; Björn Grüning; galaxy-dev@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.gruening@gmail.com]
> Sent: Saturday, January 03, 2015 6:42 AM
> To: Waldron, Michael H; galaxy-dev@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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