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2 How to install and update iRAP

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Nuno Fonseca edited this page Oct 2, 2018 · 15 revisions

Main requirements

  • Linux Operating system
  • tested with Fedora, RedHat, Scientific Linux, Ubuntu, Amazon Linux
  • 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. The names of the packages may change between Linux distributions and versions.
  • Internet connection (during the installation)
  • A terminal with a Bash shell

Install (option 1)

This option will try to install iRAP and all dependencies by running a single command - this will often not work due to the Linux distribution used or version of some of the dependencies (e.g., bash, gcc compiler, etc). In this case you may have to: i) add some extra options to the install (run irap_install.sh with -h to get the full list of options) or go to the install option 2 below.

1.a Get the latest version of iRAP from https://github.com/nunofonseca/irap/releases/latest (replace 1.0.0a by the latest version)

wget https://github.com/nunofonseca/irap/archive/v1.0.0a.tar.gz -o irap.tar.gz && tar xzvf irap.tar.gz && mv irap-1.0.0a irap_clone

1.b Get iRAP using git clone

git clone https://github.com/nunofonseca/irap.git irap_clone

  1. 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. Since version 0.7.1 is possible to use -l option (instead of -a) to install a lightweight version of iRAP (tophat2, star, htseq, cufflinks, plus the supported differential expression methods).

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 and in the top-level iRAP source directory (e.g.,irap_clone folder if the above git clone command was used to download iRAP).

  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 mappers
  7. scripts/irap_install.sh -s . -x quant
  8. scripts/irap_install.sh -s . -x fastx
  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

Several environment (shell) variables need to be defined in order to run iRAP . 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 iRAP

  1. Go to the iRAP directory obtained using git clone or by downloading the lastest tarball (see point 1 above in Install). Ensure that iRAP's environment is set up - assuming that iRAP was installed in the irap_install folder do source irap_install/irap_setup.sh

  2. If the folder was cloned (obtained using git clone) then update the contents otherwise skip to next step

    git pull

  3. Update iRAP's installed code (recommended when only the patch number was incremented):

    ./scripts/irap_install.sh -u -s .

  4. Alternatively to step 3, to update iRAP's code and all 3rd party dependencies:

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

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