example_watch_folder.py problem importing file

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example_watch_folder.py problem importing file

Liisa Koski-2
I am testing the example_watch_folder.py script on my local instance of Galaxy (Feb.10 distribution). I have set up a simple workflow with the Fasta-to-Tabular tool. It takes a single input fasta file. Works in Galaxy UI.

I have created input and output folders and followed the steps here http://gmod.827538.n3.nabble.com/Trouble-Shooting-example-watch-folder-py-td4030355.html

But when I run the script and put a simple fasta file in the input folder I get the following error in the logs:

galaxy.jobs.runners.drmaa DEBUG 2014-04-10 11:11:03,127 (1899) command is: python galaxy_dist_dev/tools/data_source/upload.py galaxy_dist_dev galaxy_dist_dev/database/tmp/tmpK40iV3galaxy_dist_dev/database/tmp/tmpx_5QyU         3802:galaxy_dist_dev/database/job_working_directory/001/1899/dataset_3802_files:galaxy_dist_dev/database/files/003/dataset_3802.dat; return_code=$?; cd galaxy_dist_dev; galaxy_dist_dev/set_metadata.sh ./database/files galaxy_dist_dev/database/job_working_directory/001/1899 . galaxy_dist_dev/universe_wsgi.ini galaxy_dist_dev/database/tmp/tmpK40iV3 galaxy_dist_dev/database/job_working_directory/001/1899/galaxy.json; sh -c "exit $return_code"
galaxy.jobs.runners.drmaa DEBUG 2014-04-10 11:11:03,127 (1899) native specification is: -V -q all.q -l hostname="hostname.ca"
galaxy.jobs.runners.drmaa INFO 2014-04-10 11:11:03,133 (1899) queued as 678390
galaxy.jobs DEBUG 2014-04-10 11:11:03,180 (1899) Persisting job destination (destination id: name_hwew)
galaxy.jobs.runners.drmaa DEBUG 2014-04-10 11:11:03,579 (1899/678390) state change: job is running - - [10/Apr/2014:11:11:07 -0400] "POST /api/workflows?key=dd3916dfb37dffc08f070f1e3503015a HTTP/1.1" 200 - "-" "Python-urllib/2.6"
galaxy.jobs.runners.drmaa DEBUG 2014-04-10 11:11:07,778 (1899/678390) state change: job finished normally
galaxy.jobs DEBUG 2014-04-10 11:11:08,082 setting dataset state to ERROR
galaxy.jobs DEBUG 2014-04-10 11:11:08,227 job 1899 ended
galaxy.datatypes.metadata DEBUG 2014-04-10 11:11:08,227 Cleaning up external metadata files
galaxy.jobs DEBUG 2014-04-10 11:11:08,652 (1900) Working directory for job is: galaxy_dist_dev/database/job_working_directory/001/1900
galaxy.datatypes.metadata DEBUG 2014-04-10 11:11:08,770 Cleaning up external metadata files
galaxy.jobs.handler INFO 2014-04-10 11:11:08,795 (1900) Job unable to run: one or more inputs in error state - - [10/Apr/2014:11:11:31 -0400] "GET /history/list HTTP/1.1" 200 - "http://galaxy.server.ca:8080/root" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:11.0) Gecko/20100101 Firefox/11.0"

And in the dataset itself in the resulting Galaxy history UI

WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with extension 'asn1', using datatype from galaxy_dist_dev/database/tmp/tmpK40iV3.

Yesterday, before I did the upgrade to Feb.10. The input files would import (as a green dataset in the History UI) put be empty and say 'no peak'

Thanks in advance for any help,

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