0.11.5

Installation

These are the steps to install FastQC:

  1. Download the latest version of the software (Binaries - zip) (http://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc):
cd /home/$USER/apps/fastqc/src
wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip
unzip fastqc_v0.11.5.zip
  1. For installation, the following steps must be done:
cd FastQC
sudo mkdir -p /share/apps/fastqc/0.11.5/bin
sudo mkdir -p /share/apps/fastqc/0.11.5/lib
sudo cp *.jar /share/apps/fastqc/0.11.5/lib/
sudo cp -r uk/ org/ net/ fastqc /share/apps/fastqc/0.11.5/bin/

Module

#%Module1.0#####################################################################
##
## module fastqc/0.11.5
##
## /share/apps/modules/fastqc/0.11.5     Written by Mateo Gomez-Zuluaga
##

proc ModulesHelp { } {
    puts stderr "\tfastqc/0.11.5 - sets the Environment for FastQC in \
    \n\tthe share directory /share/apps/fastqc/0.11.5\n"
}

module-whatis "\n\n\tSets the environment for using FastQC 0.11.5 \
               \n\tprecompiled\n"

# for Tcl script use only
set       topdir     /share/apps/fastqc/0.11.5
set       version    0.11.5
set       sys        x86_64-redhat-linux

conflict fastqc

module load java/jdk-1.8.0_112

prepend-path PATH                   $topdir/bin

prepend-path CLASSPATH                      $topdir/lib/cisd-jhdf5.jar
prepend-path CLASSPATH                      $topdir/lib/jbzip2-0.9.jar
prepend-path CLASSPATH                      $topdir/lib/sam-1.103.jar

Mode of use

Load the necessary environment through the module:

module load fastqc/0.11.5

TO-DO

References

  • INSTALL.txt (file inside .zip)

Author

  • Mateo Gómez Zuluaga