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tecangenomics / nudup

NuDup -- Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.
http://www.tecangenomics.com
GNU Lesser General Public License v3.0
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more descriptive error messages when samtools isn't in $PATH? #20

Open andrewejaffe opened 5 years ago

andrewejaffe commented 5 years ago

Hi, I tried running this tool, and got an empty error message, which made it hard to debug. I ended up getting it working by initiating samtools. It might therefore be helpful if the tool checks to see if samtools is installed:

[ajaffe@compute-094 preprocessed_data]$ python $NUDUP -f $ID1 -T ./ $BAM
2019-01-30 14:33:42,476 [     INFO] - Deduplicating NuGEN single end reads...
2019-01-30 14:33:43,278 [     INFO] - Using molecular tag sequence from Index FASTQ read
2019-01-30 14:33:43,279 [     INFO] - Appending molecular tag sequence to SAM/BAM read name
2019-01-30 14:33:43,295 [    ERROR] -