Simply type from the terminal:
$ sudo pip install numpy pysam cython $ sudo pip install plastid
or, for a single-user install:
$ pip install --user numpy pysam cython $ pip install --user plastid
Test your installation within Python:
>>> import plastid
To do so, first make sure all the dependencies are installed. Then type:
$ pip install --verbose --user --no-cache-dir --install-option="--recythonize" plastid
And then re-test the installation. If installation continues to fail, please see Installation fails in pip with no obvious error message for common errors or our issue tracker to report a new one.
Command-line scripts will be installed wherever system configuration dictates. On OSX and many varities of linux, the install path for a single-user install is
~/.local/bin. For system-wide installs, the path is typically
/usr/local/bin. Make sure the appropriate location is in your
PATH by adding to your
Also, type the line above in any open terminal (or login and out again) to apply the changes.
Often users or systems administrators need to install multiple versions of the same package for different scientific purposes. To do so they use sandboxes that insulate packages from each other.
The easiest way to install
Plastid inside a sandbox is to use
# install virtualenv if you don't have it. # use either "sudo" or "--user", not both. # Use this line for a system-wide install $ sudo pip install virtualenv # or, use this line for single user install $ pip install --user virtualenv # With virtualenv installed, create & activate vanilla environment # when prompted, do NOT give the virtualenv access to system packages # create $ virtualenv ~/some/path/to/venv # activate $ source ~/some/path/to/venv/bin/activate # Fresh install of plastid. # Note- no use of `sudo` here. It confuses the virtualenv (venv) $ pip install numpy pysam cython (venv) $ pip install --no-cache-dir plastid # test (venv) $ python -c "from plastid import *"
To fetch the latest development versions, clone it from our github repository. From the terminal:
# get the source $ git clone git://github.com/joshuagryphon/plastid.git # Do to a quirk in Python setup scripts (fixed in new versions of pip), # numpy, cython, and pysam must must be installed first: $ pip install --user --upgrade numpy pysam # Install in develop mode. Use `--recythonize` flag to regenerate # C files if necessary (e.g. after upgrading pysam) $ cd plastid $ pip install --install-option='--recythonize' --user -e .
Plastid has a number of non-Python dependencies:
The following are not required for full functionality, but are required for specific functions or just plain useful:
plastid installs fairly easily in most Linux and Macintosh setups. If
you run into issues running or installing, please see our
FAQ section on installation
and then our issue tracker to see if anybody else has encountered your issue,
and if instructions already exist.
Numerous users have reported unexpected behaviors when installing
plastid in conda/Anaconda environments. These can appear
plastid is not the only package to experience this
These issues can take a long time to resolve and frequently the solution is
installation inside a clean environment that does not use conda. We’re
looking into this issue to improve our compatibility, but at present, conda
is not supported. If you need to run
plastid inside a sandbox,
we strongly recommend using virtualenv. To do so, see Inside a virtualenv, above.
For other troubleshooting, please see our FAQ section on installation.