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alekseyzimin / masurca

GNU General Public License v3.0
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POLCA.sh fix for samtools current version #326

Open hyphaltip opened 1 year ago

hyphaltip commented 1 year ago

I noticed issues with the way polca is calling samtools which breaks with current versions of samtools. When masurca is installed in an env with other samtools dependencies it is not possible to install the old version of samtools.

I modified the script slightly to work for the latest version - wonder if this can be applied to future releases to ensure compatibility? The fixed version is available in stajichlab/AAFTF#25 as https://github.com/stajichlab/AAFTF/blob/main/patches/polca.sh and as this patch https://github.com/stajichlab/AAFTF/blob/main/patches/polca.patch

This might also be impacting #317 and #303

Ifigene commented 8 months ago

Thank you so much! I have had the same error as #317 and can confirm that this patch fixed the issue for masurca/4.1.0.

It would be nice if the developers address this in the next version of masurca! Let's see :)