2 How to install and update iRAP

Main requirements

• Linux Operating system
• tested with Fedora, RedHat, Scientific Linux, Ubuntu
• Development tools and libraries installed: zlib-devel python-devel bzip2-devel python readline-devel libgfortran gcc-gfortran gcc-c++ libX11-devel libXt-devel numpy gd-devel libxml2-devel libxml2 libpng libcurl-devel expat-devel libpangocairo db-devel java python gcc g++ gfortran curl-config git which make bzip2 bison gettext-devel texlive unzip make wget sqlite sqlite-devel db4-devel libdb-devel graphviz tar java (1.6 or above) Please check the dockerfiles (in the docker folder) for an up-to-date list of required packages.
• Internet connection (during the installation)
• A terminal with a Bash shell

Install (option 1)

1. Get iRAP from the repository git clone https://github.com/nunofonseca/irap.git irap_clone

2. Install iRAP and all dependencies (3rd party software) to a directory (e.g. irap_install)

./irap_clone/scripts/irap_install.sh -a irap_install -s irap_clone

Note: the . in ./irap_clone/scripts is not a typo. To avoid to have the CPAN configuration cleared do export INIT_CPAN=no before running irap_install.sh.

Upon the successful installation you should see the following message

`[INFO] Installation complete`

The irap_install.sh script will try to install many software dependencies (e.g., R, make, ruby, mappers, quantification methods, etc) but it does not install system devel/header packages (e.g., the X11 devel packages) - the devel/header packages need to be installed in the computer to successfully compile the different tools/programs.

Some of the packages that need to be installed before installing iRAP and other 3rd party tools are: zlib-devel, python-devel, bzip2-devel, python, readline-devel, libgfortran, gcc-gfortran, libX11-devel, libXt-devel,numpy,gd-devel (see full list above).

Check the Finish the configuration topic below to conclude the installation.

Install failed? Please try the manual install described below.

Manual Install (option 2)

The following steps can be used to install iRAP and required tools "step by step". This procedure may be useful when the full automatic installation procedure described above fails.

Please run the following commands in the same bash shell.

1. export IRAP_DIR=path_to_directory_where_irap_will_be_installed
2. scripts/irap_install.sh -s . -x deps
3. scripts/irap_install.sh -s . -x core
4. source $IRAP_DIR/irap_setup.sh
5. scripts/irap_install.sh -s . -x R_packages
6. scripts/irap_install.sh -s . -x R3_packages
7. scripts/irap_install.sh -s . -x mappers
8. scripts/irap_install.sh -s . -x quant
9. scripts/irap_install.sh -s . -x fastq_qc
10. scripts/irap_install.sh -s . -x perl_packages
11. scripts/irap_install.sh -s . -x data
12. scripts/irap_install.sh -s . -v

Finish the configuration

In order to run iRAP several environment variables need to be defined in the shell. To setup the shell (Bash) environment using the irap_setup.sh file: e.g., assuming that you installed IRAP in irap_install you could setup the environment using

source irap_install/irap_setup.sh

or, assuming that you use Bash as your shell, add the contents of the irap_setup.sh file to your ~/.bash_profile file

Update

1. Go to the iRAP directory obtained from the repository (see point 1 above in Install)
2. Get the updates: git pull
3. Update iRAP's installed code (use only when the minor version changed): ./scripts/irap_install.sh -u -s .
4. Update iRAP's installed code and all dependencies: ./scripts/irap_install.sh -a -s .