samtools check updated to work in Batch mode #121
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"samtools view" will fail in non interactive shells.
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When running in a batch job (from a conda environment), i.e. ssh [server] bash -c "unset DISPLAY; unset TERM; $HOME/bin/samtools view > log 2>&1" this will return: [main_samview] fail to read the header from "-" May very well be an issue with the bioconda recipe, and suggests this is only compatible with samtools < 1.10 |
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"samtools view" will fail in non interactive shells.