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cancerit / telomerecat

Telomerecat: The telomere computational analysis tool
GNU General Public License v3.0
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setup.py asking for parabam release that doesn't exist #29

Closed chrispyatt closed 3 years ago

chrispyatt commented 3 years ago

Installing from tarball (pip install -e) gives the following error:

ERROR: Could not find a version that satisfies the requirement parabam>=3.0.0 (from telomerecat==4.0.0) (from versions: none) ERROR: No matching distribution found for parabam>=3.0.0 (from telomerecat==4.0.0)

presumably due to the following line in setup.py:

install_requires=["parabam>=3.0.0", "numpy", "pysam", "pandas", "click"],

The latest parabam release appears to 2.3.1

chrispyatt commented 3 years ago

Just to add: I realise that there is a 3.0.0 pre-release and have added that locally. I had previously acquired dependencies according to requirements.txt which specifies 2.3.1

keiranmraine commented 3 years ago

We need to update setup.py to specify the git repo (PEP-508) as we don't have control of the pypi repo (will contact original author to try and sort that out).

Untested:

install_requires = [
  'parabam @ https://github.com/cancerit/parabam/releases/download/3.0.0/parabam-3.0.0.tar.gz',
]
keiranmraine commented 3 years ago

@jhrf, Yaobo has left the group, could you drop me an email at Sanger to arrange the ability to publish updates to pypi? Thanks

byb121 commented 3 years ago

Sorry, the lagging mouse clicked on the wrong button...

keiranmraine commented 3 years ago

This has been fixed and the relevant versions exist on pypi, documentation update will arrive soon, but a simple install now works as you would expect:

pip3 install telomerecat