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64 README
@@ -1,4 +1,5 @@
-**Biopython README file**
+Biopython README file
+=====================
The Biopython Project is an international association of developers of freely
available Python tools for computational molecular biology.
@@ -20,45 +21,49 @@ molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3
http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878
-**For the impatient**
+For the impatient
+=================
To build and install Biopython, download and unzip the source code, go to this
directory at the command line, and type:
-python setup.py build
-python setup.py test
-sudo python setup.py install
+ python setup.py build
+ python setup.py test
+ sudo python setup.py install
-**System Requirements**
-o Python 2.4, 2.5, 2.6 or 2.7, see http://www.python.org
+System Requirements
+===================
+
+- Python 2.4, 2.5, 2.6 or 2.7, see http://www.python.org
We are phasing out support for Python 2.4.
See below for notes about testing with Python 3.
-
-o NumPy, see http://numpy.scipy.org (optional, but strongly recommended)
+
+- NumPy, see http://numpy.scipy.org (optional, but strongly recommended)
This package is only used in the computationally-oriented modules.
It is required for Bio.Cluster, Bio.PDB and a few other modules. If you
think you might need these modules, then please install NumPy first BEFORE
installing Biopython. The older Numeric library is no longer supported in
Biopython.
-o ReportLab, see http://www.reportlab.org/downloads.html (optional)
+- ReportLab, see http://www.reportlab.org/downloads.html (optional)
This package is only used in Bio.Graphics, so if you do not need this
functionality, you will not need to install this package. You can install
it later if needed.
-o psycopg2, see http://initd.org/software/psycopg/ (optional) or
+- psycopg2, see http://initd.org/software/psycopg/ (optional) or
PyGreSQL (pgdb), see http://www.pygresql.org/ (optional)
These packages are used by BioSQL to access a PostgreSQL database.
-o MySQLdb, see http://sourceforge.net/projects/mysql-python (optional)
+- MySQLdb, see http://sourceforge.net/projects/mysql-python (optional)
This package is used by BioSQL or Bio.GFF to access a MySQL database.
In addition there are a number of useful third party tools you may wish to
install such as standalone NCBI BLAST, EMBOSS or ClustalW.
-**Python 3.x**
+Python 3.x
+==========
Note we do not intend to support Python 3.0, please use Python 3.1 or later.
Python 3 support is still incomplete (and we do not yet officially support
@@ -68,31 +73,34 @@ converted using the 2to3 script. This is done automatically by the setup.py
script. Use "python3 setup.py build" etc (see installation notes below).
-**Installation**
+Installation
+============
-*** Make sure that Python is installed correctly ***
+**Make sure that Python is installed correctly**
Installation should be as simple as going to the biopython source code
directory, and typing:
- 'python setup.py build'
- 'python setup.py test'
- 'sudo python setup.py install'
+ python setup.py build
+ python setup.py test
+ sudo python setup.py install
If you need to do additional configuration, e.g. changing the base
-directory, please type 'python setup.py', or see the documentation for
+directory, please type `python setup.py`, or see the documentation for
Distutils.
-**Testing**
+Testing
+=======
Biopython includes a suite of regression tests to check if everything is
running correctly. To do the tests, go to the biopython source code directory
and type:
- 'python setup.py test'
+ python setup.py test
Do not panic if you see messages warning of skipped tests:
+
test_DocSQL ... skipping. Install MySQLdb if you want to use Bio.DocSQL.
This most likely means that a package is not installed. You can
@@ -101,7 +109,8 @@ planning on using. If you did want to use that module, please install
the required dependency and re-run the tests.
-**Source Code Repository**
+Source Code Repository
+======================
Like most of the Open Bioinformatics Foundation (OBF) projects, Biopython
currently uses git for distributed source code control, hosted by github
@@ -112,7 +121,8 @@ on the OBF servers. These will remain online for a while as "read only"
static backups of everything up to and including Biopython 1.52.
-**Bugs**
+Bugs
+====
While we try to ship a robust package, bugs inevitably pop up. If you are
having problems that might be caused by a bug in Biopython, it is possible
@@ -139,18 +149,20 @@ Biopython version (or git version/date), (4) traceback that occurs, and also
ideally (5) the code that breaks, and (6) a data file that causes the problem.
-**Contributing, Bug Reports**
+Contributing, Bug Reports
+=========================
Biopython is run by volunteers from all over the world, with many types of
backgrounds. We are always looking for people interested in helping with code
development, web-site management, documentation writing, technical
administration, and whatever else comes up.
If you wish to contribute, please visit the web site http://www.biopython.org
-and join our "mailing list":http://biopython.org/wiki/Mailing_lists
+and join our mailing list: http://biopython.org/wiki/Mailing_lists
-**Distribution Structure**
+Distribution Structure
+======================
README -- This file.

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