s2s-profiles

Easy snakemake profile installation for either local computers or slurm clusters.

Installation

Installation has been made extremely easy and is done by cookiecutter!

Start with cloning the repo locally and moving into the directory:

git clone [email protected]:vanheeringen-lab/seq2science-profiles.git
cd seq2science-profiles

local machine installation

cookiecutter -f local

or with one of the provided configfiles (mb07 or threadripper):

cookiecutter -f --config-file=local/[[configfile]] local

slurm installation

cookiecutter -f slurm

or with one of the provided configfiles (moldev):

cookiecutter -f --config-file=slurm/[[configfile]] slurm

input

During the installation process users are prompted for input, these are the inputs we feel might need explanation:

• resources, config, additional: comma separated string of key-value pairs; e.g. "key1: val1, key2: val2"
• optional_rules: comma separated string of rule(key-value) pairs; e.g. "rule1(key1: val1, key2: val2), rule2(key3: val3)"

If added, the keys must be recognized by the snakemake API

These inputs only allow dictionaries (lists or nested dicts can be added afterward).

output

A profile that can be passer to seq2science using seq2science ... --profile profile_name.

The file can be found in ~/.config/snakemake/profile_name/config.yaml.