Commit 1eab3d83 authored by Paul Igor Costea's avatar Paul Igor Costea
Browse files

Update README.md

parent cf8e47e5
......@@ -22,15 +22,7 @@ Dependencies
* Python-2.7 or above
Setup & Compilation
===================
MetaSNP is mainly implemented in C/C++ and needs to be compiled.
I. Setup
--------
#### Dependencies on Ubuntu/debian
#### Installing dependencies on Ubuntu/debian
On an Ubuntu/debian system, the following sequence of commands will install all
required packages (the first two are only necessary if you have not enabled the
......@@ -42,7 +34,7 @@ universe repository before):
sudo apt-get install libhts-dev libboost-dev
### Dependencies using anaconda
### Installing dependencies using anaconda
If you use [anaconda](https://www.continuum.io/downloads), you can create an
environment with all necessary dependencies using the following commands:
......@@ -52,11 +44,6 @@ environment with all necessary dependencies using the following commands:
export CFLAGS=-I$CONDA_ENV_PATH/include
export LD_LIBRARY_PATH=$CONDA_ENV_PATH/lib:$LD_LIBRARY_PATH
Setting the `CFLAGS` environmental variable is necessary so that the boost
includes are found. The `LD_LIBRARY_PATH` variable is not necessary to build
the software, but is necessary to later run it. Thus, it is necessary to reset
it whenever you activate the environment.
If you do not have a C++ compiler, anaconda can also install G++:
conda create --name metaSNV boost htslib pkg-config
......@@ -68,6 +55,12 @@ If you do not have a C++ compiler, anaconda can also install G++:
export CFLAGS=-I$CONDA_ENV_PATH/include
export LD_LIBRARY_PATH=$CONDA_ENV_PATH/lib:$LD_LIBRARY_PATH
Setup & Compilation
===================
I. Setup
--------
### Download reference database
In order to download a reference database, run:
......@@ -82,8 +75,6 @@ II. Compilation:
make
Workflow:
=========
## Required Files:
......
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