/imp_docs

Folder containing config file and launcher scripts for IMP

Primary LanguageShellMIT LicenseMIT

IMP3_docs

  • Folder containing config file and launcher scripts for IMP

Setup

Conda

Conda user guide

# install miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod u+x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh # follow the instructions

Getting the repository including sub-modules

git clone git@github.com:susheelbhanu/imp_docs.git

Create the main snakemake environment

  • Note: This will create an environment called snakemake.
  • If you already have a snakemake conda env, this is not required.
# create venv
conda env create -f envs/requirements.yaml"

Description

  • Below is a list of the files
  • The changes that need to be made are indicated for each file
  • Edit or run each file in the order listed below, i.e. after #4-editing samples, run #5-launching jobs

  1. IMP_config.yaml: config file with necessary paths, databases, and parameters for snakemake

  2. launchIMP.sh: SLURM launcher script for runIMP.sh

  3. runIMP.sh: bash script to launch IMP using snakemake

  4. edit_samples.sh: bash script to make sample folder, add config.yaml, launchIMP and runIMP scripts and simultaneously edit them

  5. launch_jobs.sh: bash script to launch multiple samples

Changes to be made

  • Below files need to be edited or checked for file paths and database locations

-- IMP_config.yaml

  1. forward/reverse paths in line 14 for metaG/metaT
  2. outputdir: path in line 23
  3. summarydir: path n line 24
  4. filtering: select from hg38/PhiX,PhiX174
  5. db_path: ensure access to dbs in line 30 exist

-- launchIMP.sh

  1. Edit the time, N#, n#, and qos as needed
  2. For jobs estimated to be longer than 2 days use the -qos long option

-- runIMP.sh

  1. Check if access to the /work/projects/ecosystem_biology/local_tools is available

-- edit_samples.sh

  • Note: Run this script from the directory where the individual sample folders will exist

-- launch_jobs.sh

  • Prior to running do: chmod +x launch_jobs.sh