2.2 conda¶

Purpose¶

Install RiboParser and external bioinformatics dependencies in a reproducible environment.

Create environment¶

conda create -n ribo python=3.12
conda activate ribo

or:

micromamba create -n ribo python=3.12
micromamba activate ribo

Install external dependencies¶

conda install bowtie samtools cutadapt star bedtools subread rsem gffread sra-tools \
  ucsc-genepredtogtf ucsc-gtftogenepred ucsc-gff3togenepred ucsc-bedgraphtobigwig ucsc-bedsort \
  -c bioconda

conda install pigz -c conda-forge

Install RiboParser¶

conda install riboparser -c rensc

or:

micromamba install riboparser -c rensc

Main external tools¶

Tool	Use
Bowtie	classification against rRNA/tRNA/ncRNA/mRNA/genome indexes
SAMtools	BAM sorting, indexing, and filtering
Cutadapt	adapter trimming and read filtering
STAR	splice-aware genome alignment
RSEM	transcript/gene expression quantification
gffread	cDNA extraction from genome and annotation
SRA Toolkit	public dataset download
UCSC utilities	bedGraph/bigWig and annotation conversion