The second error may stem from running the tool directly from the command line (not via Galaxy)? If so, it can be run with: % PYTHONPATH=/path/to/galaxy_dist/lib python ... --nate Kelly Vincent wrote:
Hi Juan,
I believe that the problem is actually not the error that is printing below. Do you have the Samtools indices in place (specifically for hg18) and the loc file sam_fa_indices.loc created in the tool-data directory? Specifically, from my experience, it appears that you have to have both the index (hg18.fa.fai) and the original fasta file (hg18.fa) in the directory you specify in the loc file.
Let us know if that doesn't help, or if you need more information about setting up the loc file and indices.
Regards, Kelly
On Nov 9, 2009, at 10:59 AM, juan perin wrote:
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
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