--- tags: GeneLab title: Using `genelab-utils` to download GeneLab workflows --- # Using genelab-utils to download GeneLab workflows > This page demonstrates using a program in the [genelab-utils](https://github.com/AstrobioMike/genelab-utils#genelab-utils) package to programmatically download packaged workflows from our > [Data Processing github repository](https://github.com/nasa/GeneLab_Data_Processing). > > Contact Mike.Lee@nasa.gov if having trouble. --- [toc] --- ## tl;dr example usage ```bash conda activate genelab-utils GL-get-workflow MG-Illumina # The MG-Illumina workflow was downloaded to 'SW_MGIllumina_2.0.3/' # It was pulled from this release page: # https://api.github.com/repos/nasa/GeneLab_Data_Processing/releases ls SW_MGIllumina_2.0.3/ # Snakefile config config.yaml envs scripts ``` --- ## Installing `genelab-utils` if needed The genelab-utils package should be installed with conda/mamba. If you are not familiar with conda, you can find an introduction [here](https://astrobiomike.github.io/unix/conda-intro) if wanted, and if you are not familiar with mamba, there is a super-short introduction on that same page [here](https://astrobiomike.github.io/unix/conda-intro#bonus-mamba-no-5) – it's definitely worth using mamba if you use conda at all :+1: ```bash # if needing mamba conda install -c conda-forge -n base mamba mamba create -n genelab-utils -c conda-forge -c bioconda -c defaults \ -c astrobiomike 'genelab-utils>=1.3' ``` --- ## Downloading a workflow ```bash conda activate genelab-utils ``` ### Seeing workflows available Can see those available by just running the command by itself, or giving `-h/--help` for help: ```bash GL-get-workflow -h # usage: GL-get-workflow [-h] [--wanted-version WANTED_VERSION] # {MG-Illumina,MG-remove-human-reads,MG-estimate-host-reads,Amplicon-Illumina,Amplicon-454-IonTorrent,RNAseq,MethylSeq} # # This is a helper program for downloading GeneLab workflows. For verison info # run `GL-version`. # # options: # -h, --help show this help message and exit # --wanted-version WANTED_VERSION # Specify the version you'd like to download (leaving # out this argument will pull the latest by default) # # required arguments: # {MG-Illumina,MG-remove-human-reads,MG-estimate-host-reads,Amplicon-Illumina,Amplicon-454-IonTorrent,RNAseq,MethylSeq} # The first positional argument should be which one of # these workflows you'd like to download # # Ex. usage: GL-get-workflow MG-Illumina ``` ### Downloading latest version ```bash GL-get-workflow MG-Illumina ``` ### Downloading a specific version When we specify a specific version, it will check that a zip exists for it on the [releases page](https://github.com/nasa/GeneLab_Data_Processing/releases), and then download it if yes: ```bash GL-get-workflow MG-Illumina --wanted-version 2.0.2 ``` --- ---