(This question is for Centos 6.5 server, python 2.7, November 2014 version of Galaxy)
I've been trying to fetch mouse mm9 genome from UCSC through data manager without success. I'd followed Daniel's video demo "Managing Galaxy's built-in data" (Thank you Dan :)). So I installed data manager accordingly. In the reference genome data manager form, I selected mouse mm9 and UCSC's dbkey = mm9, and click "execute".
But I didn't see the job in history as mentioned in the video. Then I went to Admin/Data/Manage local data/view data manager jobs/reference genome fetching. I saw the job with status 'running'
The command line box showed this:
python /mnt/drive2/home/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_fetch_genome_all_fasta/079f737d675f/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py "/mnt/drive2/home/galaxy/galaxy-dist/database/files/000/dataset_33.dat" --dbkey_description 'Mouse July 2007 (NCBI37/mm9) (mm9)
I did 'ps -ef | grep galaxy", I saw these two jobs:
galaxy 20191 20128 0 13:40 ? 00:00:00 /bin/sh /mnt/drive2/home/galaxy/galaxy-dist/database/job_working_directory/000/25/galaxy_25.sh
galaxy 20192 20191 0 13:40 ? 00:00:01 python /mnt/drive2/home/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_fetch_genome_all_fasta/079f737d675f/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py /mnt/drive2/home/galaxy/galaxy-dist/database/files/000/dataset_33.dat --dbkey_description Mouse July 2007 (NCBI37/mm9) (mm9)
I ran forever without producing anything as I checked database/files/000/dataset_33_files, only a zero-byte mm9.fa was created.
I also checked the i icon for the job detail. Both stdout and stderr showed 'none'.
Since the job is basically a python program, then I killed the above two tasks and ran data_manager_fetch_genome_all_fasta.py directly at terminal as below:
$ cd galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_fetch_genome_all_fasta/079f737d675f/data_manager_fetch_genome_all_fasta/data_manager
$ python data_manager_fetch_genome_all_fasta.py /mnt/drive2/home/galaxy/galaxy-dist/database/files/000/dataset_33.dat --dbkey_description 'Mouse July 2007 (NCBI37/mm9) (mm9)'
But I encountered import error
Traceback (most recent call last):
File "data_manager_fetch_genome_all_fasta.py", line 17, in <module>
from galaxy.util.json import from_json_string, to_json_string
ImportError: No module named galaxy.util.json
I checked json.py is in /mnt/drive2/home/galaxy/galaxy-dist/lib/galaxy/util/json.py
So, would it be due to path problem?
Any idea? Appreciated.