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:jls2...@columbia.edu

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