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hringbauer / hapROH

Software to call ROHs
GNU General Public License v3.0
15 stars 3 forks source link

Conda environment #6

Closed eshab5 closed 2 years ago

eshab5 commented 2 years ago

Hi Harald,

I am trying to install hapROH on gardner (CRI), but running into a problem with algopy while pip tries to install the package. Is there a conda environment that can help me?

Right now without activating conda environment, I tried installing the package with python/3.7.6 as well as python/3.8. Both time showing error with algopy. Thank you so much in advance.

Best, Esha

hringbauer commented 2 years ago

Hi Esha! Generally, hapROH does not require specific versions of its Python package dependencies so it should be installable with pip in pretty much any not completely outdated python3 setting.

The newer hapROH versions have a dependency on the package numdifftools that in turn needs algopy, the latter seems to cause your trouble. However, numdifftools is only used for estimating contamination (hapCon) - so if want to run ROH detection you don't need it.

To check whether the normal installation goes through, could you install hapROH via pip using the no-dependency switch?

python3 -m pip install --user --no-deps hapROH

eshab5 commented 2 years ago

Hi Harald,

So I tried the --no-deps thing as you suggested. Still shows me that algopy error. Should I try pip install --root <path to scratch-space>? Incase it is trying to install in my home directory and I am running out of space?

Best, Esha

eshab5 commented 2 years ago

Okay, I tried with the --root thing. I think it was a success!

hringbauer commented 2 years ago

Okay, I will close this issue for now!

For anyone interested, we are working on a biocondarelease of hapROH.