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detailed-install-instructions.md

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Detailed install instructions

First, try:

python3 -m pip install -U cython wheel pip setuptools
python3 -m pip install pheweb
pheweb

(Note: In most cases this is equivalent to pip3 install pheweb, but if you have a bad version of pip3 on your $PATH, using python3 -m pip will avoid it.)

  • If you get the error Segmentation fault (core dumped), try running python3 -m pip install --no-binary=cffi,cryptography,pyopenssl pheweb instead. (more info)

  • If you get an error related to pysam, run python3 -m pip install -U cython; python3 -m pip install https://github.com/pysam-developers/pysam/archive/master.zip and try again.

  • If installation was successful but running pheweb results in "command not found", you need to add pheweb to your PATH. You should be able to just add the line PATH="$HOME/.local/bin:$PATH" to the end of ~/.bashrc, start a new terminal, and run pheweb again. If you're on macOS, you might need to add the line source "$HOME/.bashrc" to ~/.bash_profile.

  • If that command fails in a different way, then use one of the approaches below.

Installing on Linux with sudo:

(Note: If you're not sure whether you have permissions for sudo, just try it. If you don't have root access, it will say something like you are not in the sudoers file.)

Install prerequisites:

  • If you are running Ubuntu (or another apt-get-based distribution), run:

    sudo apt-get update
sudo apt-get install python3-pip python3-dev libz-dev libffi-dev

  • If you are running Fedora, RedHat, or CentOS (or another yum-based distribution), run:

    sudo yum install python3-devel gcc-c++ zlib-devel

Then run:

sudo python3 -m pip install wheel cython
sudo python3 -m pip install pheweb
sudo pheweb

If this doesn't work, try the miniconda3 approach instead.

Installing on Linux or Mac with Miniconda3:

If you are on macOS, install XCode Developer Tools with xcode-select --install.

To install miniconda3, follow the instructions here.

When you're installing miniconda3, you can close the terms & conditions with "q". You should install into the default directory of ~/miniconda3. You should let miniconda modify $PATH in your ~/.bash_profile or ~/.bashrc, so that you'll be able to run just pheweb instead of needing to type ~/miniconda3/bin/pheweb on the command line.

Next, close and re-open your terminal, to make the new $PATH take effect. You can check that you have the miniconda3 python set up by running which python3, which should reply something like /home/peter/miniconda3/bin/python3. Then run:

python3 -m pip install pheweb

If none of these work, open a Github issue.