Install pvac-seq on Ubuntu

pvac-seq.md

Install dependecies

$ sudo apt-get install mysql-server mysql-client mysql-common libmysqlclient-dev
$ sudo apt-get install build-essential git-core cmake zlib1g-dev libncurses-dev patch
$ sudo apt-get install samtools

Create a new enviromnent to pvac-sec

Once you have conda installed, create a new env to pvac-seq.

$ conda create --name pvac-seq pip python=3
$ source activate pvac-seq
$ pip install pvacseq

Create a folder to handle pvac-seq files.

$ mkdir $HOME/pvacseq
$ cd $HOME/pvacseq

Install VEP

Install VEP to create VCF annotated. Reference: VEP Before VEP installation, install CPAN and some packages

# if you are on the env pvac-seq, exit it.
$ source deactivate
$ cpan App::cpanminus
# accept all questions from command above
$ source ~/.bash_rc
$ cpanm DBI
$ cpanm DBD::mysql

Now, install VEP.

$ source activate pvac-seeq
$ wget https://github.com/Ensembl/ensembl-tools/archive/release/85.zip -O ensembl-tools.zip
$ unzip ensembl-tools.zip
$ cd ensembl-tools-{release}
$ cd scripts/variant_effect_predictor/
$ perl INSTALL.pl
# if it fails, try with --NO_HTSLIB
# check if all tests pass
$ All tests successful.
# Accept to install cache files. You will ask to create the directory.
$ Do you want to install any cache files (y/n)? y
# Select the desired cache file or use all to download all files. You can download it later by using --cache on the run.

Donwload and install VEP plugins

$ cd $HOME/pvac-seq
$ wget https://github.com/Ensembl/VEP_plugins/archive/release/85.zip -O vep_plugins.zip
$ unzip vep_plugins.zip
$ pvacseq install_vep_plugin VEP_plugins-{release}

Install bam-readcount

Bam-readcount uses a bam file as input, and the bam may either contain snvs or indels. Indel bams must be run in a special insertion-centric mode. Any mixed input bams must be split into snvs and indels, and bam-reacount must then be run on each file individually.

$ cd HOME/pvacseq
$ git clone https://github.com/genome/bam-readcount.git
$ cd bam-readcount
$ mkdir build
$ cd build
$ cmake ..
$ make

Exemple of execution

bam-readcount -f <reference fasta> -l <site list> <bam_file>

Install Cufflinks

$ cd $HOME/pvacseq
$ wget http://bitbucket.org/eigen/eigen/get/3.2.9.tar.gz
$ tar -zxvf 3.2.9.tar.gz
$ cd eigen-{version}
$ sudo cp -r Eigen/ /usr/local/include

Donwload and copy to install dir

$ wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
$ tar -zxvf cufflinks-2.2.1.Linux_x86_64.tar.gz
$ sudo cp cuff* /usr/local/bin
$ sudo cp g* /usr/local/bin