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artic-network / civet

Cluster Investigation & Virus Epidemiology Tool
https://cov-lineages.org/resources/civet.html
GNU General Public License v3.0
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Install error #144

Open mabouelk opened 2 years ago

mabouelk commented 2 years ago

I am trying to install civet on macOS but I keep getting this error message:

Pip subprocess error: Running command git clone -q https://github.com/cov-ert/datafunk.git /private/var/folders/vy/29g9j_0j5zb1kb7bk66t6dz80000gn/T/pip-req-build-k1c5v6ad Running command git clone -q https://github.com/cov-ert/reportfunk.git /private/var/folders/vy/29g9j_0j5zb1kb7bk66t6dz80000gn/T/pip-req-build-98xm72dt Running command git clone -q https://github.com/cov-ert/clusterfunk.git /private/var/folders/vy/29g9j_0j5zb1kb7bk66t6dz80000gn/T/pip-req-build-oijwpoq1 ERROR: Package 'jsonschema' requires a different Python: 3.6.13 not in '>=3.7'

failed

CondaEnvException: Pip failed

ViralVerity commented 2 years ago

This sounds like an environment error - the Python specified in the environment provided for civet is 3.6, so that will cover that package's requirements. Make sure that you have built and activated the civet environment properly and then try installing in the environment again

mabouelk commented 2 years ago

python 3.6 is no longer available

ViralVerity commented 2 years ago

I took another look, and it's that one of the packages we use requires a different python version to the one that we specify in the environment. Jsonschema needs 3.7, and we specify 3.6.13.

This is a slightly tricky issue, and we're currently trying to move beyond this version of civet - I recommend you try and use the newer version of civet (civet3) which we will be releasing soon: https://github.com/cov-ert/civet3