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jeromekelleher committed Sep 13, 2014
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Expand Up @@ -3,31 +3,31 @@ Wormtable
===============================================

Wormtable is a write-once read-many table for large scale datasets.
It provides Python programmers with a simple and efficient method of
It provides Python programmers with a simple and efficient method of
storing, processing and searching datasets of essentially unlimited
size. A wormtable consists of a set of rows, each of which contains
values belonging to a fixed number of columns. Rows are encoded
in a custom binary format, designed to be flexible, compact and
size. A wormtable consists of a set of rows, each of which contains
values belonging to a fixed number of columns. Rows are encoded
in a custom binary format, designed to be flexible, compact and
portable. Rows are stored in a data file, and the offsets and lengths
of these rows are stored in a Berkeley DB database
to support efficient random access. Wormtable also
of these rows are stored in a Berkeley DB database
to support efficient random access. Wormtable also
supports efficient searching and retrieval of rows with particular
values through the use of indexes, also based on Berkeley DB.

The Variant Call Format (VCF) is supported directly by wormtable
through a command line conversion program, vcf2wt. There is also a
command line utility wtadmin to manage wormtables, including the ability to
command line utility wtadmin to manage wormtables, including the ability to
dump values and add, remove and view indexes.

If you use wormtable in your work, please cite the BMC Bioinformatics
`article <http://www.biomedcentral.com/1471-2105/14/356>`_. See
`article <http://www.biomedcentral.com/1471-2105/14/356>`_. See
the ``CITATION.txt`` file for details.

-------------
Documentation
-------------

Full documentation for ``wormtable`` is available at
Full documentation for ``wormtable`` is available at
`<http://pythonhosted.org/wormtable>`_.

------------
Expand All @@ -49,33 +49,33 @@ For Python 3, use ``python3-dev`` and ``pip3``.
General instructions
********************

Once Berkeley DB has been installed (see below) we can build the ``wormtable`` module using the
standard Python `methods <http://docs.python.org/install/index.html>`_. For
Once Berkeley DB has been installed (see below) we can build the ``wormtable`` module using the
standard Python `methods <http://docs.python.org/install/index.html>`_. For
example, using pip we have ::

$ sudo pip install wormtable

Or, we can manually download the package, unpack it and then run::

$ python setup.py build
$ sudo python setup.py install

Most of the time this will compile and install the module without difficulty.

It is also possible to download the latest development version of
``wormtable`` from `github <https://github.com/wormtable/wormtable>`_.
It is also possible to download the latest development version of
``wormtable`` from `github <https://github.com/wormtable/wormtable>`_.


**************
Python 2.6/3.1
**************

Wormtable requires the ``argparse`` package, which was introduced to the
standard library for version 3.2 (it is also included in 2.7). For users
of older Python versions, the ``argparse`` module must be installed for
Wormtable requires the ``argparse`` package, which was introduced to the
standard library for version 3.2 (it is also included in 2.7). For users
of older Python versions, the ``argparse`` module must be installed for
the command line utilities to work::

$ sudo pip install argparse
$ sudo pip install argparse

This is not necessary for recent versions of Python.

Expand All @@ -84,21 +84,21 @@ Installing Berkeley DB
----------------------

Wormtable requires Berkeley DB (version 4.8 or later),
which is available for all major platforms.
which is available for all major platforms.

*****
Linux
*****

Installing Berkeley DB is very easy on Linux distributions.
Installing Berkeley DB is very easy on Linux distributions.

On Debian/Ubuntu use::

$ sudo apt-get install libdb-dev
$ sudo apt-get install libdb-dev

and on Red Hat/Fedora use::

# yum install libdb-devel
# yum install libdb-devel

Other distributions and package managers should provide a similarly easy
option to install the DB development files.
Expand All @@ -107,20 +107,20 @@ option to install the DB development files.
Mac OS X
********

Berkeley DB can be installed from source on a mac, via
`macports <https://www.macports.org/>`_ or
Berkeley DB can be installed from source on a mac, via
`macports <https://www.macports.org/>`_ or
`homebrew <http://mxcl.github.io/homebrew/>`_.

For MacPorts, to install e.g. v5.3 ::

$ sudo port install db53
Then, to build/install wormtable, we need to set the CFLAGS and LDFLAGS environment

Then, to build/install wormtable, we need to set the CFLAGS and LDFLAGS environment
variables to use the headers and libraries in /opt::

$ CFLAGS=-I/opt/local/include/db53 LDFLAGS=-L/opt/local/lib/db53/ python setup.py build
$ sudo python setup.py install
$ sudo python setup.py install

For Homebrew, get the current Berkeley DB version and again build wormtable
after setting CFLAGS and LDFLAGS appropriately::

Expand All @@ -135,12 +135,12 @@ For more details of Berkely DB versions, see here: https://www.macports.org/port
Other Platforms
***************

On platforms that Berkeley DB is not available as part of the native packaging
On platforms that Berkeley DB is not available as part of the native packaging
system (or DB was installed locally because of non-root access)
there can be issues with finding the correct headers and libraries
when compiling ``wormtable``. For example,
if we add the DB 4.8 package on FreeBSD using::
when compiling ``wormtable``. For example,
if we add the DB 4.8 package on FreeBSD using::

# pkg_add -r db48

we get the following errors when we try to install wormtable::
Expand All @@ -154,27 +154,27 @@ we get the following errors when we try to install wormtable::
_wormtablemodule.c:3740: error: 'DistinctValueIterator' has no member named 'cursor'
error: command 'cc' failed with exit status 1

This is because the compiler does not know where to find the headers and library
files for Berkeley DB.
To remedy this we must set the
``LDFLAGS`` and ``CFLAGS`` environment variables to
their correct values. Unfortunately there is no simple method to do this
and some knowledge of where your system keeps headers and libraries
is needed. To complete the installation for the FreeBSD example above,
This is because the compiler does not know where to find the headers and library
files for Berkeley DB.
To remedy this we must set the
``LDFLAGS`` and ``CFLAGS`` environment variables to
their correct values. Unfortunately there is no simple method to do this
and some knowledge of where your system keeps headers and libraries
is needed. To complete the installation for the FreeBSD example above,
we can do the following::

$ CFLAGS=-I/usr/local/include/db48 LDFLAGS=-L/usr/local/lib/db48 python setup.py build
$ sudo python setup.py install

--------------------------------
Installation without root access
--------------------------------

If you need to install wormtable on a system where Berkeley DB is not
installed (and your system administrator refuses to install it, for
If you need to install wormtable on a system where Berkeley DB is not
installed (and your system administrator refuses to install it, for
some reason), we can still compile and install it locally.
Here is a recipe that worked on a Debian squeeze machine; however, this is not guaranteed
to work on any given system and you may need to tweak things a little to suit
Here is a recipe that worked on a Debian squeeze machine; however, this is not guaranteed
to work on any given system and you may need to tweak things a little to suit
your environment::

$ mkdir -p $HOME/.local
Expand All @@ -184,16 +184,16 @@ your environment::
$ ../dist/configure --prefix=$HOME/.local
$ make install

This downloads a version of Berkeley DB from Oracle, compiles and
then installs it to the directory $HOME/.local. (The version of Berkeley DB
This downloads a version of Berkeley DB from Oracle, compiles and
then installs it to the directory $HOME/.local. (The version of Berkeley DB
you use doesn't really matter once it's at least 4.8.)
Now, download
Now, download
the latest version of wormtable, untar it and `cd` to the new directory.
We can then install it locally::

$ CFLAGS=-I$HOME/.local/include LDFLAGS=$HOME/.local/lib/ python setup.py install --user

Now we need to set up some paths so that we can use this at run time. Put the following
Now we need to set up some paths so that we can use this at run time. Put the following
lines into your $HOME/.bashrc (or equivalent if you use another shell)::

export LD_LIBRARY_PATH=$HOME/.local/lib:$LD_LIBRARY_PATH
Expand All @@ -217,31 +217,31 @@ It is a good idea to run these immediately after installation::
Tested platforms
****************

Wormtable is highly portable, and
has been successfully built and tested
Wormtable is highly portable, and
has been successfully built and tested
on the following platforms:

==================== ======== ====== ===========
Operating system Platform Python Compiler
==================== ======== ====== ===========
Ubuntu 13.04 x86-64 2.7.4 gcc 4.7.3
Ubuntu 13.04 x86-64 3.3.1 gcc 4.7.3
Ubuntu 13.04 x86-64 2.7.4 clang 3.2.1
Debian squeeze x86-64 2.6.6 gcc 4.4.5
Debian squeeze x86-64 3.1.3 gcc 4.4.5
Debian squeeze x86-64 3.1.3 clang 1.1
Debian squeeze ppc64 2.6.6 gcc 4.4.5
Debian squeeze ppc64 3.1.3 gcc 4.4.5
==================== ======== ====== ===========
Operating system Platform Python Compiler
==================== ======== ====== ===========
Ubuntu 13.04 x86-64 2.7.4 gcc 4.7.3
Ubuntu 13.04 x86-64 3.3.1 gcc 4.7.3
Ubuntu 13.04 x86-64 2.7.4 clang 3.2.1
Debian squeeze x86-64 2.6.6 gcc 4.4.5
Debian squeeze x86-64 3.1.3 gcc 4.4.5
Debian squeeze x86-64 3.1.3 clang 1.1
Debian squeeze ppc64 2.6.6 gcc 4.4.5
Debian squeeze ppc64 3.1.3 gcc 4.4.5
Debian wheezy armv6l 2.7.3 gcc 4.6.3
Fedora 17 i386 2.7.3 gcc 4.7.2
Fedora 17 i386 3.2.3 gcc 4.7.2
FreeBSD 9.0 i386 3.2.2 gcc 4.2.2
FreeBSD 9.0 i386 2.7.2 gcc 4.2.2
FreeBSD 9.0 i386 3.1.4 clang 3.0
FreeBSD 9.0 i386 3.2.2 gcc 4.2.2
FreeBSD 9.0 i386 2.7.2 gcc 4.2.2
FreeBSD 9.0 i386 3.1.4 clang 3.0
OS X 10.8.4 x86-64 2.7.2 clang 4.2
Solaris 10 SPARC 3.3.2 gcc 4.8.0
Solaris 11.1 SPARC 2.6.8 gcc 4.5.2
Solaris 11.1 SPARC 2.6.8 Sun C 5.12
Solaris 10 SPARC 3.3.2 gcc 4.8.0
Solaris 11.1 SPARC 2.6.8 gcc 4.5.2
Solaris 11.1 SPARC 2.6.8 Sun C 5.12
Scientific Linux 6.2 x86-64 2.6.6 icc 12.0.0
==================== ======== ====== ===========
==================== ======== ====== ===========

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