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