You are probably missing the samtools and bowtie2 dependencies. Make sure Galaxy can find the binaries.

-Raj

On Fri Mar 7 00:16:07 2014, Langhorst, Brad wrote:

I’m slowly wrapping my head around the new data manager stuff… but I don’t think I quite have it yet.

I was able to download hg19 using the reference genome tool

I see where it puts downloaded files now - took me a while to figure that out.

When I run the sam fa build tool it fails like this: Traceback (most recent call last): File "/mnt/ngswork/galaxy/galaxy-toolshed-tools.0214/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_sam_fa_index_builder/926e50397b83/data_manager_sam_fa_index_builder/data_manager/data_manager_sam_fa_index_builder.py http://bx.psu.edu/repos/blankenberg/data_manager_sam_fa_index_builder/926e50397b83/data_manager_sam_fa_index_builder/data_manager/data_manager_sam_fa_index_builder.py", line 71, in <module> if __name__ == "__main__": main() File "/mnt/ngswork/galaxy/galaxy-toolshed-tools.0214/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_sam_fa_index_builder/926e50397b83/data_manager_sam_fa_index_builder/data_manager/data_manager_sam_fa_index_builder.py http://bx.psu.edu/repos/blankenberg/data_manager_sam_fa_index_builder/926e50397b83/data_manager_sam_fa_index_builder/data_manager/data_manager_sam_fa_index_builder.py", line 66, in main build_sam_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME ) File "/mnt/ngswork/galaxy/galaxy-toolshed-tools.0214/testtoolshed.g2.bx.psu.edu/repos/blankenberg/data_manager_sam_fa_index_builder/926e50397b83/data_manager_sam_fa_index_builder/data_manager/data_manager_sam_fa_index_builder.py http://bx.psu.edu/repos/blankenberg/data_manager_sam_fa_index_builder/926e50397b83/data_manager_sam_fa_index_builder/data_manager/data_manager_sam_fa_index_builder.py", line 25, in build_sam_index proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) File "/usr/lib64/python2.6/subprocess.py", line 639, in __init__ errread, errwrite) File "/usr/lib64/python2.6/subprocess.py", line 1228, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

What am I missing here?

I can’t tell what file it’s referring to.

The bowtie2 index builder also fails.

————

The old interface that allowed download, then building of chosen indices was more convenient. It’s not fun to download, wait, then click each builder to schedule a build.

Is a replacement for the more unified interface planned? Am I supposed to just build a workflow that builds all the stuff i want?

————

I can’t tell what I’m supposed to feed as “dbkey” to the ncbi downloader… It’s also not easy for me to find the list of dbkeys available at ucsc. (eschColi_K12 does not seem to work - don’t know why, but i guess it doesn’t know to try to microbes)

it would be very nice to allow users to select which genome they want by choosing from a list.

I’m headed back for manual loc file territory for now - but I’d love some enlightenment about how this is supposed to work and or information about how others are using it.

Brad

-- Brad Langhorst, Ph.D. Applications and Product Development Scientist

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