Tools

Tools

Organization

• One subdirectory per tool containing a script and a README
• A subdirectory for images (absent by default)
• A script "images.sh" generating all the images in image's folder
• A README file

Images Resume

Useful links

Tools

• FASTQ Dump
• STAR
• FASTQC
• Subread
• DESeq2
• Samtools

Articles

• Recurrent mutations at codon 625 of the splicing factor SF3B1 in uveal melanoma
• SF3B1 mutations are associated with alternative splicing in uveal melanoma

Useful commands

Install Singularity

For Ubuntu (from the Repo directory) :

sudo apt-get update

sudo apt-get install -y build-essential libssl-dev uuid-dev libgpgme11-dev \
    squashfs-tools libseccomp-dev wget pkg-config git cryptsetup 

wget https://dl.google.com/go/go1.13.linux-amd64.tar.gz

sudo tar --directory=/usr/local -xzvf go1.13.linux-amd64.tar.gz

export PATH=/usr/local/go/bin:$PATH

wget https://github.com/singularityware/singularity/releases/download/v3.5.3/singularity-3.5.3.tar.gz

tar -xzvf singularity-3.5.3.tar.gz

cd singularity

./mconfig

cd builddir

make

sudo make install

Generate images

For Ubuntu (from the Tools directory) :

./images.sh

Please do not commit images on the git repository.

Final result

The following text will appear once all the containers are successfully compiled.