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iqbal-lab-org / gramtools

Genome inference from a population reference graph
MIT License
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Install issue into a python venv #135

Closed nzmacalasdair closed 5 years ago

nzmacalasdair commented 5 years ago

Trying to install the latest commit here into a python3 venv seems to have resulted in a dependency error with py-cortex-api. I was able to install commit 442ddfe7d68fca86ad97a123792673edff815b04 in June without any issues.

Terminal output:

Collecting git+https://github.com/iqbal-lab-org/gramtools@ebefb345735fe018aed76f9fd365bbbef65af8e2
Cloning https://github.com/iqbal-lab-org/gramtools (to revision ebefb345735fe018aed76f9fd365bbbef65af8e2) to /tmp/pip-req-build-cupl7svf
Requirement already satisfied: scipy>=1.0.1 in ./gramtools_venv/lib/python3.6/site-packages (from gramtools==2.0) (1.1.0)
Collecting pyvcf>=0.6.8 (from gramtools==2.0)
Using cached https://files.pythonhosted.org/packages/20/b6/36bfb1760f6983788d916096193fc14c83cce512c7787c93380e09458c09/PyVCF-0.6.8.tar.gz
Collecting py-cortex-api>=1.0 (from gramtools==2.0)
Could not find a version that satisfies the requirement py-cortex-api>=1.0 (from gramtools==2.0) (from versions: )
No matching distribution found for py-cortex-api>=1.0 (from gramtools==2.0)
ffranr commented 5 years ago

Thank you for your query.

The following pip3 flag is very important for installing gramtools: --process-dependency-links. Please ensure that this flag is included in your install command as shown in the README.

Further, please let us know the precise commands that you used to generate the above result.

nzmacalasdair commented 5 years ago

The command I used at first was pip3 install git+https://github.com/iqbal-lab-org/gramtools@ebefb345735fe018aed76f9fd365bbbef65af8e2

Adding --process-dependency-links fixed the install issue. Thanks!