install unix binaries

[Douglas_Yu]

I am thinking about using posit cloud to teach some bioinformatic tutorials, but i would need to install some unix binaries. I was able to upload one binary and run it (seqkit). Is this your recommended way to install all unix binaries, or is there something i'm missing (e.g. a posit version of homebrew for instance)?

thanks

[technocrat]

For Debian derivatives, {r2u} is an interface to a repository of compiled CRAN packages (super-comprehensive).

[Douglas_Yu]

Thanks for the answer. i later realised that i could just download binaries and makefiles directly

installation code

cd /cloud/project
mkdir bin
cd bin

# samtools
# https://www.htslib.org/download/
# https://rnabio.org/module-00-setup/0000/10/01/Installation/
curl -L https://github.com/samtools/samtools/releases/download/1.18/samtools-1.18.tar.bz2 | tar -jxvf - 
cd samtools-1.18
make
cd ..
mv samtools-1.18/samtools ./

# minimap2
curl -L https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-linux.tar.bz2 | tar -jxvf -
mv minimap2-2.26_x64-linux/minimap2 ./

# seqkit
curl -L https://github.com/shenwei356/seqkit/releases/download/v2.5.1/seqkit_linux_amd64.tar.gz | tar -xzvf -

# ASCIIGenome
# https://asciigenome.readthedocs.io/en/latest/
wget https://github.com/dariober/ASCIIGenome/releases/download/v1.17.0/ASCIIGenome-1.17.0.zip
unzip ASCIIGenome-1.17.0.zip
ASCIIGenome-1.17.0/ASCIIGenome

# FastQC
curl -L https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip --output fastqc.zip
unzip fastqc.zip


# test if binaries run
cd /cloud/project/
bin/samtools
bin/minimap2
bin/seqkit
bin/ASCIIGenome-1.17.0/ASCIIGenome # q to quit. Needs to be in directory with its java file
bin/FastQC/fastqc --help # Needs to be in directory with its java file