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
Office: 212-305-6360
E-mail:jls2282@columbia.edu

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