pip3 install pheweb fails in official Python 3.8 docker image

[huy-nguyen]

Steps to reproduce:

• Run the official python 3.8 container by issuing the command docker run --rm -ti python:3.8.0 /bin/bash
• Inside the Docker container, run pip3 install pheweb. It fails with the attached log file. log.txt. Essentially the failure happens here

  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pysam

  I've tried the more detailed installation instructions but got the same errors. Here's the info on the Docker image's Linux distribution:

  PRETTY_NAME="Debian GNU/Linux 10 (buster)"
  NAME="Debian GNU/Linux"
  VERSION_ID="10"
  VERSION="10 (buster)"
  VERSION_CODENAME=buster
  ID=debian
  HOME_URL="https://www.debian.org/"
  SUPPORT_URL="https://www.debian.org/support"
  BUG_REPORT_URL="https://bugs.debian.org/"

[huy-nguyen]

This seems related to https://github.com/pysam-developers/pysam/issues/860 because installing pheweb works fine on python 3.7.

[pjvandehaar]

The same error happened when python 3.7 was released. The pysam devs need a couple weeks to update. I'll see about a workaround.

[pjvandehaar]

For now, run

pip3 install -U cython
pip3 install https://github.com/pysam-developers/pysam/archive/master.zip
pip3 install pheweb

And let me know whether that works.

[huy-nguyen]

Thanks. Your quick fix works. I think it's worth adding these notes to the documentation so that newcomers are not stumped every time a new Python version is released.

[pjvandehaar]

That's a good suggestion. Instructions are in the "detailed install instructions" linked from https://github.com/statgen/pheweb#1-install-pheweb .