susheelbhanu / imp_docs

Folder containing config file and launcher scripts for IMP

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 [e-mail]: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