diff --git a/.travis.yml b/.travis.yml index e79981e..dd2c115 100644 --- a/.travis.yml +++ b/.travis.yml @@ -15,7 +15,8 @@ before_install: # scipy requirements - sudo apt-get install gcc gfortran python-dev libblas-dev liblapack-dev cython # matplotlib additional requirements -- sudo apt-get install libpng-dev libfreetype6-dev +- sudo apt-get install pkg-config libfreetype6 libfreetype6-dev libpng-dev +- pip install --upgrade pip - pip install 'setuptools >=14.0' install: pip install . diff --git a/doc/source/install.rst b/doc/source/install.rst index 6fedbf2..c506e72 100644 --- a/doc/source/install.rst +++ b/doc/source/install.rst @@ -8,16 +8,27 @@ micca requires `Python `_ >=2.7, `NumPy `_ (>= 1.8.0) and the software required in order to install `SciPy `_ (>= 0.13.0) through pip. -On Ubuntu Linux >=12.04 -^^^^^^^^^^^^^^^^^^^^^^^ +On Ubuntu Linux >= 12.04 +^^^^^^^^^^^^^^^^^^^^^^^^ -In Linux, we suggest install NumPy and requirements for SciPy through -the package manager. In Ubuntu Linux you can use `apt-get install`: +In Ubuntu Linux >= 12.04, we suggest install NumPy and the requirements for +SciPy and matplotlib through the package manager: .. code-block:: sh + sudo apt-get -qq update + sudo apt-get install build-essential sudo apt-get install python-numpy - sudo apt-get install gcc gfortran python-dev libblas-dev liblapack-dev cython + sudo apt-get install gcc gfortran python-dev libblas-dev liblapack-dev cython + sudo apt-get install pkg-config libfreetype6 libfreetype6-dev libpng-dev + +Then, upgrade pip and install setuptools: + +.. code-block:: sh + + pip install --upgrade pip + pip install 'setuptools >=14.0' + On OS X ^^^^^^^ @@ -26,18 +37,24 @@ In OS X, we recommend to install Python from `Homebrew `_: #. Install `Xcode `_; #. Install `Homebrew `_; + #. Make sure the environment variable ``PATH`` is properly setted in your + ``~/.bash_profile`` or ``~/.bashrc``:: + + .. code-block:: sh + export PATH=/usr/local/bin:$PATH + #. Install Python and gfortran: - + .. code-block:: sh - + brew update brew install python brew install gfortran Install NumPy: - + .. code-block:: sh - + pip install numpy @@ -49,7 +66,7 @@ The easiest way to install micca is to using pip, from PYPI: .. code-block:: sh sudo pip install micca - + or from the tarball (https://github.com/compmetagen/micca/releases): .. code-block:: sh @@ -65,7 +82,7 @@ In order to install micca from sources (with the standard procedure (>= 1.8.0) and SciPy (>= 0.13.0), the following Python packages must be installed: - * Pandas >=0.17.0, <0.18.0 + * Pandas >=0.17.0 * matplotlib >=1.3.0 * Biopython >=1.50 * cutadapt >=1.9 @@ -74,17 +91,16 @@ installed: The easiest way to install these packages is to is using pip: .. code-block:: sh - - sudo pip install 'pandas >=0.17.0, <0.18.0' 'matplotlib >=1.3.0' 'biopython >= 1.50' 'cutadapt >=1.9' 'biom-format >=1.3.1' + + sudo pip install 'pandas >=0.17.0' 'matplotlib >=1.3.0' 'biopython >= 1.50' 'cutadapt >=1.9' 'biom-format >=1.3.1' Download the latest version from https://github.com/compmetagen/micca/releases and complete the installation: .. code-block:: sh - + tar -zxvf micca-X.Y.Z.tar.gz - python setup.py build sudo python setup.py install If you don’t have root access, install micca in a local directory by @@ -96,10 +112,10 @@ specifying the ``--prefix`` argument. Then you need to set python setup.py install --prefix=/path/to/modules export PYTHONPATH=$PYTHONPATH:/path/to/modules/lib/python{version}/site-packages -.. note:: +.. note:: In order to export the variable permanently add the command - at the bottom of your ``.bashrc`` file. + at the bottom of your ``~/.bash_profile`` or ``~/.bashrc`` file. Testing the installation @@ -108,7 +124,7 @@ Testing the installation .. code-block:: sh micca -h - + Install RDP classifier (optional) --------------------------------- @@ -126,19 +142,19 @@ can be used in the :doc:`/commands/classify` command (option Download and unzip the file (RDP cladssifier v2.11 2015-09-14): .. code-block:: sh - + wget https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.11.zip unzip rdp_classifier_2.11.zip Now you must set the environment variable ``RDPPATH`` by typing: .. code-block:: sh - + $ export RDPPATH=/path-to-rdp-classifier/rdp_classifier_2.11/ -e.g. ``export RDPPATH=/Users/David/rdp_classifier_2.11``. +e.g. ``export RDPPATH=/Users/David/rdp_classifier_2.11``. .. note:: - + In order to export the variable permanently add the latest command at the bottom of your ``.bashrc`` file. diff --git a/setup.py b/setup.py index 1fc390f..695b0f5 100644 --- a/setup.py +++ b/setup.py @@ -122,8 +122,6 @@ def run(self): author_email='davide.albanese@fmach.it', maintainer='Davide Albanese', maintainer_email='davide.albanese@fmach.it', - # setup_requires must be repeated in install_requires - setup_requires=['numpy >= 1.8.0'], install_requires=[ 'numpy >= 1.8.0', 'scipy >=0.14.0',