viromeqc does not work with current versions of python and samtools #9
Description
Dear SegataLab,
I'm trying to run viromeQC, but there are a series of errors that seem to relate to dependency versions.
E.g. cmseq does not install by default. Upon getting the newest version of cmseq and inserting it into the viromeQC folder, LSU and SSU reads are undetected with a cmseq python error
Upon installing an old version of cmseq matching the date of the viromeQC release, the following error is produced upon running:
[main_samview] fail to read the header from "-".
This seems to be related to the way newer versions of samtools process stdin and stdout.
Trying to installing an older version of samtools fails through conda because it requires an outdated version of Python (3.1) which is older than the 3.6 you tested with viromeqc
Is it possible for you to update the viromeQC repo so that it can run with current versions of dependencies?