This guide will go through the steps required to install a bleeding-edge version of PaPy on a UNIX machine using the bash shell. The user is left with two options to install PaPy globally or into a sandbox and to use a stable version or possibly unstable sources.
An easy_install assumes that your default interpreter is Python 2.6, you have setuptools installed and you want to install PaPy into system-wide site-packages (the location where Python looks for installed libraries). If the default Python interpreter for your operating system is different from Python 2.6 or you do not want to put PaPy or its dependencies in the system directories or finally you’d like the latest source-code revision of PaPy read further choose the fancy way of installing PaPy.
PaPy is indexed on the PyPI (Python Package Index). And can be installed simply via:
$ su -c "easy_install papy"
This will install the papy, numap, nubio, nubox and rpyc packages. If this did not work please try to use the manual source code distributions.
download PaPy, NuMap, NuBio, NuBox, RPyC snapshots from http://muralab.org/papy
install it via easy_install:
$ su -c "easy_install rpyc_YYY.tar.gz" $ su -c "easy_install numap_YYY.tar.gz" $ su -c "easy_install nubox_YY.tar.gz" $ su -c "easy_install nubio_YYY.tar.gz" $ su -c "easy_install papy_YYY.tar.gz"replacing XXX with the version numbers of the downloaded files.
Optional dependencies to install/build/deploy PaPy are:
- easy_install (setuptools)
- Sphinx (sphinx)
PaPy and Python development is much easier using the following tools:
- virtualenv
- virtualevnwrapper
The fancy (and cleaner) way of using PaPy is to create a virtual environment to use PaPy. The general stream of action is to install Python 2.6 (if required) install setuptools for Python 2.6 (if required). Later we create sandbox environment by using virtualenv and virtualenvwrapper that is finally populated with PaPy and dependencies checked-out from a source repository. This guide assumes you are using bash and a recent version of something UNIX-like.
Most Linux distributions and Mac OSX ship a recent version of Python. You can (and should) skip this step if you have Python 2.6 and it is the default Python interpreter. To check this open a shell and type:
$ python
This should return something similar to this:
Python 2.6.2 (r262:71600, Jun 12 2009, 10:38:05)
[GCC 4.1.2 (Gentoo 4.1.2 p1.1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Notice the version in the first line. If it is is not 2.6.x or higher, but not 3.X skip this section as you already have a supported Python version. Otherwise it might be that your operating system still provides you a Python 2.6, but the name of the executable is different try:
$ python2.6
If, and only if, this fails with python2.6: command not found or something similar proceed with the manual system-wide installation of Python 2.6 below.
This installation will not change the default Python interpreter for your distribution. A compiled version of Python 2.6 for your distribution might be available from official distribution or third-party repositories, please check them before instead of proceeding with the following os-independent method.
Download Python 2.6 from http://www.python.org/download/ you want a source tarball and the highest 2.6.x version available. You do not want to install Python 3.0.x or 3.1.x
Unpack the compressed tarball intp any directory e.g.:
tar xfv Python-2.6.2.tgzgo to the root of the unpacked directory and compile Python2.6:
cd ./configure –prefix=/usr make su -c “make altinstall”
this will install an executable python2.6 into /usr/bin
try if it worked:
$ python2.6
Be careful! Some of the following steps are different depending on whether you built your own Python 2.6 distribution or your system is using Python 2.6 by default. Make shure yout always type python2.6 not python to be on the safe side.
We will use setuptools to install PaPy, the tools to necessary create a sandbox environment and PaPy‘s dependencies. This is a very common package and is most likely already installed. But we need it for explicitly for Python 2.6. To test if it is there it try:
$ easy_install2.6
If you encounter an error, and you did not build Python 2.6 manually you should try to install it from your distribution’s repository. On Gentoo the package is called “dev-python/setuptools” on Fedora it is “python-setuptools” and “python-setuptools-devel” for Ubuntu the package is called “python-setuptools” You can install them by e.g.:
# Gentoo
$ su -c "emerge setuptools"
# Ubuntu
$ sudo apt-get install python-setuptools
# Fedora
$ su -c "yum install python-setuptools"
If you had to manually compile Python 2.6 the standard distribution setuptools package are most likely installed but only for the default system-wide Python e.g. Python 2.5. You will have to install setuptools manually for the just built and installed Python 2.6 interpreter.
Download setuptools from http://pypi.python.org/pypi/setuptools you will want the latest source version at the time of writing it is setuptools-0.6c11.tar.gz.
Unpack the compressed tarball into any directory:
$ tar xvf setuptools-0.6c11.tar.gzGo to the root of the extracted directory:
$ cd setuptools-0.6c11Now we install setuptools using the python 2.6 executable, but first we have to make sure that we don’t override /usr/bin/easy_install. If setuptools is by default installed for a different Python interpreter. If there is no other Python interpreter or you do not care you can skip the following and just issue:
# python2.6 setup.py install
To prevent overriding /usr/bin/easy_install we edit the setupy.py file:
<snip> "console_scripts": [ "easy_install = setuptools.command.easy_install:main", "easy_install-%s = setuptools.command.easy_install:main" % sys.version[:3]], <snip>by commenting out the second line i.e.:
<snip> "console_scripts": [ # "easy_install = setuptools.command.easy_install:main", "easy_install-%s = setuptools.command.easy_install:main" % sys.version[:3]], <snip>now we can safely run the installation:
$ python2.6 setup.py installand verify that we have to type easy_install-2.6:
# CORRECT $ easy_install-2.6 error: No urls, filenames, or requirements specified (see --help) # NOT CORRECT -bash: easy_install-2.6: command not found
Generally we do not want to pollute the system-wide distribution with PaPy and its dependencies, but we can and this step is optional, although maintanence of PaPy might be easier in a virtual environment. We will create a virtual environment just for PaPy. We will install virtualenv and virtualenvwrapper into the newly created Python installation or standard Python2.6 using easy_install-2.6.:
$ su -c "easy_install-2.6 virtualenv"
$ su -c "easy_install-2.6 virtualenvwrapper"
Note that these packages are installed system-wide. Now we have to configure virtualenvwrapper on a per-user basis. We have to edit the .bashrc file.
determine where the wrapper got installed:
$ which virtualenvwrapper.shcreate a directory where you will hold the virtual enviroment(s):
$ mkdir $HOME/.virtualenvsadd the following two lines to ~/.bashrc replace __REPLACE_ME__ with whatever the output from the first command was.:
export WORKON_HOME=$HOME/.virtualenvs source __REPLACE_ME__
Now we have to source the edited .bashrc file:
$ source ~/.bashrc
This should not generate any errors. We are finally ready to create a virtual Python2.6 environment for PaPy.:
$ mkvirtualenv -p python2.6 --no-site-packages papy26
This will install a clean virtual environment called papy26 and activate it. Working with virtual environments is easy. To use it type workon papy26 to leave it type deactivate.
First we have to switch to the virtual environement to host all PaPy related code:
$ workon papy26
Next we install various librarires on which PaPy depends. The general install command is:
$ easy_install-2.6 PACKAGE_NAME
You do not have to be root to install the packages into the virtual environement:
installing RPyC to use PaPy on a grid:
$ easy_install-2.6 papyinstall Sphinx to build PaPy documentation:
$ easy_install-2.6 sphinxIf the above did not work because e.g. some of the tarfiles could not be downloaded we have to download snapshots manually from http://muralab.org/papy/downloads to install the libraries. The general installation command is:
$ easy_install-2.6 PACKAGE_NAME.tar.gzThe required packages are rpyc, nubox, numap and nubio.
To install PaPy from sources please follow the instructions for installing PaPy the fancy way and create a papy26_dev sandbox and install rpyc only (we will use papy, nubox, nubio and numap from the repository).
make sure you have subversion:
$ svn Type 'svn help' for usage.If this returns an error you have to install the subversion package:
# on Gentoo $ su -c "emerge subversion" # on Fedora $ su -c "yum install subversion" # On Ubuntu $ sudo apt-get install subversioncreate a workspace to hold the source code
$ mkdir ~/workspace
check-out all the necessary sources:
switch to the papy26_dev environment:
$ workon papy26_devadd all the required source code directories:
$ add2virtualenv ~/workspace/papy/src $ add2virtualenv ~/workspace/numap/src $ add2virtualenv ~/workspace/nubio/src $ add2virtualenv ~/workspace/nubox/srcVerify it worked.:
$ python2.6 >>> import papy >>> import nubio >>> import nubox >>> import NuMap