Hi again,
I'm now stuck trying to get the samtools app's to work. I've finally gotten
the bwa and bowtie tools to run an alignment, but my attempts to convert the
resulting sam file to bam, using sam_to_bam fails. The error I get in the
browser is:
An error occurred running this job: *No sequences are available for 'hg18',
request them by reporting this error.*
The error, (after searching through the output for the command), seemed to
suggest that I was missing an 'egg': This was the output:
python /home/perin/galaxy-dist/tools/samtools/sam_to_bam.py
--input1=/home/perin/galaxy-dist/database/files/000/dataset_70.dat
--dbkey=hg18 --ref_file="None"
--output1=/home/perin/galaxy-dist/database/files/000/dataset_72.dat
--index_dir=/home/perin/galaxy-dist/tool-data
Traceback (most recent call last):
File "/home/perin/galaxy-dist/tools/samtools/sam_to_bam.py", line 17, in ?
from galaxy import eggs
ImportError: No module named galaxy
I'm guessing I'm either missing a config parameter that tells samtools how
to work, or that I need to scramble another egg. Not sure, however, and was
hoping for some help. I can't seem to find anything on the web. Thanks in
advance.
Juan Perin