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