Skip to content

Latest commit

 

History

History
87 lines (55 loc) · 2.86 KB

detailed-install-instructions.md

File metadata and controls

87 lines (55 loc) · 2.86 KB

Detailed install instructions

First, try:

python3 -m pip install pheweb
pheweb --help

(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 the command pheweb --help is not found, run echo 'PATH="$HOME/.local/bin:$PATH"' >> ~/.bashrc, start a new terminal, and try pheweb --help again. If you're on macOS, you might need echo 'source "$HOME/.bashrc" >> ~/.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 pheweb

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

Installing on Linux or Mac with Miniconda3:

To install miniconda3,

  • if you're on macOS, run:

    curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh > install-miniconda3.sh
bash install-miniconda3.sh

  • if you're on Linux, run:

    curl https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh > install-miniconda3.sh
bash install-miniconda3.sh

Type <enter> to view the terms & conditions. When you're done with them, type "q" to close them, and then "yes" <enter> to accept them.

Type <enter> to agree to use the directory ~/miniconda3.

Type "yes" and <enter> to let miniconda modify $PATH in your ~/.bash_profile or ~/.bashrc. (This allows you to type just pheweb instead of ~/miniconda/bin/pheweb on the command line.)

Miniconda3 makes python an alias for python3 and pip an alias for pip3. That's likely to cause problems, so I recommend running:

rm ~/miniconda3/bin/python
rm ~/miniconda3/bin/pip

Next, close and re-open your terminal (to make the new $PATH take effect) and then run:

python3 -m pip install pheweb