Hello,

It looks like galaxy can't find you're fastx installation. Was it installed
through the tool shed or separately?

Thanks,
Carl




On Wed, Jan 16, 2013 at 4:13 PM, Jorge Sepulveda <jls2...@columbia.edu>wrote:

> Hi,
>
> Fresh new installation of galaxy on a MacPro 12 core Mountain Lion
> Trying to run fastx_quality_stats:
>
> galaxy.jobs.manager DEBUG 2013-01-16 16:03:49,646 (7) Job assigned to
> handler 'main'
> galaxy.jobs DEBUG 2013-01-16 16:03:54,759 (7) Working directory for job
> is: /Users/JS/galaxy-dist/database/job_working_directory/000/7
> galaxy.jobs.handler DEBUG 2013-01-16 16:03:54,759 dispatching job 7 to
> local runner
> galaxy.jobs.handler INFO 2013-01-16 16:03:54,854 (7) Job dispatched
> galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:54,919 Local runner:
> starting job 7
> galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:55,198 executing: cat
> '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' |
> fastx_quality_stats -Q 33 -o
> '/Users/JS/galaxy-dist/database/files/000/dataset_7.dat'
> galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:55,396 execution
> finished: cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' |
> fastx_quality_stats -Q 33 -o
> '/Users/JS/galaxy-dist/database/files/000/dataset_7.dat'
> galaxy.jobs DEBUG 2013-01-16 16:03:55,440 Tool did not define exit code
> or stdio handling; checking stderr for success
> galaxy.jobs DEBUG 2013-01-16 16:03:55,496 setting dataset state to ERROR
> galaxy.tools DEBUG 2013-01-16 16:03:55,618 Error opening galaxy.json file:
> [Errno 2] No such file or directory:
> '/Users/JS/galaxy-dist/database/job_working_directory/000/7/galaxy.json'
> galaxy.jobs DEBUG 2013-01-16 16:03:55,679 job 7 ended
> 127.0.0.1 - - [16/Jan/2013:16:03:59 -0400] "GET /history HTTP/1.1" 200 - "
> http://127.0.0.1:8080/root"; "Mozilla/5.0 (Macintosh; Intel Mac OS X
> 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
> Safari/536.26.17"
>
> Galaxy reports the following error:
>      /bin/sh: fastx_quality_stats: command not found
>      cat: stdout: Broken pipe
>
> When run on the cmd line, it runs fine:
>
> $ cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' |
> fastx_quality_stats -Q 33 -o
> '/Users/JS/galaxy-dist/database/files/000/dataset_6.dat'
> $ more /Users/JS/galaxy-dist/database/files/000/dataset_6.dat
> column  count   min     max     sum     mean    Q1      med     Q3
>  IQR     lW      rW      A_Count C_Count G_Count T_Count N_Count Max_count
> 1       912999  7       46      31022469        33.98   32      35      37
>      5       25      44      153534  361457  322516  75492   0
> 912999
> 2       912999  3       46      29744797        32.58   31      34      36
>      5       24      43      316245  255564  197711  143479  0
> 912999
>
>
>
> Jorge Sepulveda, MD, PhD
> Associate Director for Laboratory Medicine,
> Medical Director of Laboratory Informatics,
> Columbia University Medical Center
> Associate Professor,
> Department of Pathology & Cell Biology
> Columbia University College of Physicians and Surgeons
> PH1590B
> 622 W 168 St
> New York, NY 10032
> Cell: (917) 862-6050 <347-891-1122>
> Office: 212-305-6360
> E-mail: <jls2...@columbia.edu>jls2...@columbia.edu
>
>
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