Install¶

To use savnet, htslib and bedtools need to be installed and added to the PATH.

% wget https://github.com/samtools/htslib/releases/download/1.7/htslib-1.7.tar.bz2
% tar jxvf htslib-1.7.tar.bz2
% cd htslib-1.7 && make && export PATH=$PATH:$PWD && cd ..

% wget https://github.com/arq5x/bedtools2/releases/download/v2.27.0/bedtools-2.27.0.tar.gz
% tar zxvf bedtools-2.27.0.tar.gz
% cd bedtools2 && make && export PATH=$PATH:$PWD/bin && cd ..

You may want to check whether they are installed correctly through typing following commands:

% tabix

# Following messages will appear
Version: 1.7
Usage:   tabix [OPTIONS] [FILE] [REGION [...]]

Indexing Options:

% bedtools

# Following messages will appear
bedtools is a powerful toolset for genome arithmetic.

Version:   v2.27.0
About:     developed in the quinlanlab.org and by many contributors worldwide.

If help messages appear, then installation seems to be successful.

Next, install the savnet package using pip

% pip install savnet

Then, other dependent python packages (pysam, annot_utils, junc_utils, intron_retention_utils, chimera_utils) will also be installed. If you are using shared computational environment where you do not have root account, you may want to add the option --user.

To confirm successful installation, please type:

% savnet --version

# Following messages will appear
savnet 0.4.0

Alternatively, if docker is installed in your environment, you can directly use the savnet through docker.

% docker run friend1ws/savnet:0.3.2 savnet --version