docs/INSTALLATION.md
Installation {#installpage}
============
Dependencies
------------
* [htslib](https://github.com/samtools/htslib)
Note:
It is highly recommended that [samtools](https://github.com/samtools/samtools) also be installed alongside iVar. iVar uses the output of samtools mpileup to call variants and generate consensus sequences. In addition, samtools `sort` and `index` commands are very useful to setup a pipeline using iVar.
Installation
------------
To install ivar, run the following commands.
```
./autogen.sh
./configure
make
make install
```
If htslib has been installed in a non standard location, please run,
```
./autogen.sh
./configure --with-hts=/prefix/to/bin/folder/with/htslib
make
make install
```
Also, please add the following to your .bashrc so that iVar can find htslib dynamic libraries during runtime.
```
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/hts/lib/folder
```
Installing [GNU Autotools](https://www.gnu.org/software/automake/manual/html_node/Autotools-Introduction.html#Autotools-Introduction),
* OSX
Using [homebrew](https://brew.sh/),
```
brew install autoconf automake libtool
```
* Ubuntu
Using [APT](https://help.ubuntu.com/lts/serverguide/apt.html) on Ubuntu,
```
apt-get install autotools-dev
```
For bug reports please email gkarthik[at]scripps.edu or raise an issue on Github.