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',