spack
#!/usr/bin/env bash
# require: spack
# author: Jianfeng
# email: lee_jianfeng@openbiox.org
# license: Apache-2.0
# version: v0.1.0
# Script to generate base env for bioinformatics analysis using spack
# Ensure source $SPACK_ROOT/share/spack/setup-env.sh
spack env create base
spack env activate base
# programming env
# spack install r miniconda3
# spack install julia lua
# spack install golang npm
# fetch data
spack install sra-toolkit
# QC
spack install fastqc rna-seqc
# alignment
spack install bwa bowtie2 star hisat2 gmap-gsnap tophat
# sequence and region manipulation
spack install htslib samtools bedtools2 bedops bamtools seqtk
# expression
spack install salmon
# variant Analysis
spack install freebayes vcftools varscan bcftools
# variant annotation
spack install snpeff
# Bigdata
# spack install spark hadhoop hdf5
conda
#!/usr/bin/env bash
# require: conda
# author: Jianfeng
# email: lee_jianfeng@openbiox.org
# license: Apache-2.0
# version: v0.1.0
# Script to generate base env for bioinformatics analysis using conda
conda create -n bioinfo
# Activate env
conda activate bioinfo || source activate bioinfo
# programming env
# conda install r
# conda install julia lua
# conda install go nodejs
# fetch data
conda install sra-tools
# QC
conda install fastqc qualimap multiqc rna-seqc
# aligment
conda install bwa bowtie2 star hisat2 gmap tophat
# sequence and region manipulation
conda install htslib samtools bedtools bedops bamtools seqtk
# expression
conda install salmon
# variant Analysis
conda install freebayes vcftools varscan bcftools
# variant annotation
conda install snpeff snpsift
# Bigdata
# conda install hdf5