JBrowse-cv11

This package contains the material to setup a JBrowser instance for the Chlamydomonas genome.

Pre-requisite: install JBrowse

Docker

Using the docker image consist in two main steps, namely

• building the docker image
• running the a docker container of the image

Here is the full procedure:

$ cd docker
$ docker build -t jbrowse:1.12.0 .
$ docker run --rm --name jb -p 8080:80 -v `pwd`/../data/cv11:/data jbrowse:1.12.0

Alternatively, one can use the Makefile present in the docker directory:

$ cd docker
$ make build
$ make run

System

The installation instructions to install the JBrowse instance on a system in based on the docker image construction instruction (see docker/Dockerfile).

1. Install system dependancies:

   $ sudo apt-get update && sudo apt-get install -yqq build-essential\
       apache2\
       git\
       libexpat-dev\
       libpq-dev\
       libpng12-dev\
       libxml2-dev\
       postgresql-client\
       unzip\
       wget\
       zlib1g-dev

2. Download and install JBrowse:

   $ # Clone JBrowse repository and update to tag 1.12.0-release
   $ git clone --recursive --branch 1.12.0-release https://github.com/gmod/jbrowse jbrowse-1.12.0
   $ # Install dependencies
   $ cd jbrowse-1.12.0
   $ sudo ./bin/cpanm --force\
       Devel::Size\
       DBD::SQLite\
       Digest::Crc32\
       Exception::Class\
       File::Next\
       File::Copy::Recursive\
       Hash::Merge\
       Heap::Simple\
       Heap::Simple::XS\
       JSON\
       JSON::XS\
       List::MoreUtils\
       local::lib\
       Parse::RecDescent\
       PerlIO::gzip\
       Test::Warn\
       Bio::Perl\
       Bio::FeatureIO\
       Bio::GFF3::LowLevel::Parser\
       Bio::SeqFeature::Annotated\
       Bio::DB::SeqFeature::Store\
       Bio::DB::Das::Chado && \
       ./setup.sh
   $ # Build and install JBrowse itself
   $ perl Makefile.PL && make && sudo make install
   $ sudo rm -r /var/www/html && sudo ln -s $HOME/jbrowse-1.12.0 /var/www/html

Install Chlamydomonas data and setup JBrowse

Installing and setting-up cv11 data consist in two steps:

1. Setup environment variables:

   $ echo "export JBROWSE=$HOME/jbrowse-1.12.0" > $HOME/.jbrowserc
   $ echo "export JBROWSE_DATA=\$JBROWSE/data"  >> $HOME/.jbrowserc
   $ echo "export CV11_REPO=$HOME/jbrowse-cv11" >> $HOME/.jbrowserc
   $ echo "export CV11_DATA_DIR=\$CV11_REPO/data" >> $HOME/.jbrowserc
   $ # Add this line to $HOME/.profile so that jbrowserc is sourced at each login.
   $ echo '[ -f "$HOME/.jbrowserc" ] && . $HOME/.jbrowserc' >> $HOME/.profile
   $ . $HOME/.jbrowserc

2. Download the cv11 data repository:

   $ git clone https://github.com/benoistlaurent/jbrowse-cv11.git $CV11_REPO

• Setup JBrowse instance (copy files at appropriate places and run JBrowse setup scripts):

  $ cd $CV11_REPO
  $ bash install.bash

Update data

To update data from an existing JBrowse instance, the procedure is the same as for installation:

$ cd $CV11_REPO
$ bash install.bash