From 157ebf16b6bcd488e48c055c920895992d0460a0 Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Tue, 23 Jun 2015 15:03:49 +0100 Subject: [PATCH] Updated docs. --- README.txt | 27 ++++++++++++++++++--------- 1 file changed, 18 insertions(+), 9 deletions(-) diff --git a/README.txt b/README.txt index df997107d..17f3359b0 100644 --- a/README.txt +++ b/README.txt @@ -8,6 +8,15 @@ and are not fully documented, but the command line interface ``mspms`` is reliable and ready for use. This program provides a fully ``ms`` compatible interface, and can be used as a drop-in replacement in existing workflows. +Msprime can simulate the coalescent with recombination much +faster than programs based on the Sequentially Markov Coalescent +for large sample sizes and has very reasonable memory requirements. Msprime +makes it possible to simulate chromosome sized regions with hundreds of +thousands of samples. + +Please see the `documentation `_ +for further details. + *********** Quick Start *********** @@ -64,16 +73,16 @@ TODO - Add instructions for HomeBrew/MacPorts. -************* +************ Installation -************* +************ The simplest method of installation is to use PyPI and pip:: + # pip install msprime -will install msprime your Python installation. This will -work in most cases (but see the `Requirements`_ section). See -below for platform specific build instructions when this +This will work in most cases, once the `Requirements`_ have been +satisfied. See below for platform specific build instructions when this fails. If you do not have root access to your machine, you can install @@ -81,8 +90,8 @@ If you do not have root access to your machine, you can install $ pip install msprime --user -To use the ``mspms`` you must ensure -that the ``~/.local/bin/`` directory is in your ``PATH``, or +To use the ``mspms`` program you must ensure +that the ``~/.local/bin`` directory is in your ``PATH``, or simply run it using:: $ ~/.local/bin/mspms @@ -95,7 +104,7 @@ To uninstall ``msprime``, simply run:: Platform specific installation ------------------------------ -This section contains instructions to build on specific platforms +This section contains instructions to build on platforms that require build time flags for GSL and HDF5. ++++++++++++ @@ -108,7 +117,7 @@ Install the prerequisitites, and build ``msprime`` as follows:: # CFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib pip install msprime This assumes that root is logged in using a bash shell. For other shells, -different methods are need to get the ``CFLAGS`` and ``LDFLAGS`` environment +different methods are need to set the ``CFLAGS`` and ``LDFLAGS`` environment variables. ---