Plastid requires Python 3.6 or 3.3 or greater.
Compiling plastid requires a standard C build system (e.g. GCC or clang,
plus the standard C library, and linking tools) as well as zlib,
libcrypto, and libssl. The good news is that these are already required
by plastid's dependencies, so you probably already have them.
`bowtie`_ (not `bowtie 2`_) is required to un :py:mod:`~plastid.bin.crossmap`
Bioconda is a channel for the conda package manager with a focus on
bioinformatics software. Once you have Bioconda installed, installing
plastid is as easy as running:
$ conda create -n plastid plastid
$ source activate plastidThis will install all of the necesary dependencies for plastid in an
isolated environment.
Releases of :data:`plastid` can be fetched from `PyPi`_ using `Pip`_. Simply type from the terminal:
$ pip install plastidTest your installation within Python:
>>> from plastid import *And then re-test the installation. If installation continues to fail, please see :ref:`faq-install-fails` 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
~/bin or ~/.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 .bashrc, .bash_profile, or .profile:
export PATH=~/bin:~/.local.bin:/usr/local/bin:$PATHAlso, 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 :data:`Plastid` inside a sandbox is to use `virtualenv`_:
# install virtualenv if you don't have it.
$ pip install 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 --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
# 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 .If you make alterations to any of the cython sources, or if install fails,
you can build extensions or install using the --recythonize option:
# inside plastid folder
$ python setup.py build_ext --recythonize --inplace
# or
$ pip install --user -e . --install-option='--recythonize'Building the documentation requires plastid to be installed. In addition,
sphinx and a few other dependencies are required. Install these:
$ pip install -r docs/requirements.txt
Then make the documentation and open it in a browser:
$ cd docs $ make html $ firefox build/html/index.html
:data:`plastid` installs fairly easily in most Linux and Macintosh setups. If you run into issues running or installing, please see our FAQ section on :ref:`installation <faq-run>` and then `our issue tracker`_ to see if anybody else has encountered your issue, and if instructions already exist.
Frequently, problems can be solved by installing :data:`plastid` in a clean environment. For instructions, see :ref:`install-inside-venv`, above.
For other troubleshooting, please see our FAQ section on :ref:`installation <faq-run>`.