iVar

docs/INSTALLATION.md
1 Installation {#installpage}
2 ============
3
4 Dependencies
5 ------------
6
7 * [htslib](https://github.com/samtools/htslib)
8
9 Note:
10
11 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.
12
13 Installation
14 ------------
15
16 To install ivar, run the following commands.
17
18 ```
19 ./autogen.sh
20 ./configure
21 make
22 make install
23 ```
24
25 If htslib has been installed in a non standard location, please run,
26
27 ```
28 ./autogen.sh
29 ./configure --with-hts=/prefix/to/bin/folder/with/htslib
30 make
31 make install
32 ```
33
34 Also, please add the following to your .bashrc so that iVar can find htslib dynamic libraries during runtime.
35
36 ```
37 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/hts/lib/folder
38 ```
39
40 Installing [GNU Autotools](https://www.gnu.org/software/automake/manual/html_node/Autotools-Introduction.html#Autotools-Introduction),
41
42 * OSX
43
44 Using [homebrew](https://brew.sh/),
45
46 ```
47 brew install autoconf automake libtool
48 ```
49
50 * Ubuntu
51
52 Using [APT](https://help.ubuntu.com/lts/serverguide/apt.html) on Ubuntu,
53
54 ```
55 apt-get install autotools-dev
56 ```
57
58 For bug reports please email gkarthik[at]scripps.edu or raise an issue on Github.