This framework was developed to compare EPCY ouput with other main DEG tools.
- python 3.7.1
- R >= 4.2
and dependency (see lib_install.r)
cd [to_epcy_paper_folder]
# Install dependency
python3 -m venv venv
source venv/bin/activate
pip3 install pip setuptools --upgrade
pip3 install wheel
pip3 install epcy==0.1.3
pip3 install -r Requirement.txt
mkdir -p R_lib
echo "R_LIBS=$PWD/R_lib" > .RenvironThis analysis is limited to analyse the smallest design (28_inv16_vs_28), to be run on an single workstation. Full analysis follow bellow.
- 4 multicore and 2Go
- Take 8 hours on 2GHz intel Core i5 (MacBook Pro)
cd [your_epcy_paper_folder]
# Install dependency
python3 -m venv venv
source venv/bin/activate
pip3 install pip setuptools --upgrade
pip3 install wheel
pip3 install epcy==0.1.3
pip3 install -r Requirement.txt
# Step 1: Create some files used as input in next script
bash run_init.sh
# Step 2: Create all cross-validated datasets and run DEG and EPCY analysis
bash run_ismb_small.sh
#Note that run_ismb_small.sh have a smart restart mechanism.
#Rerun it, until all jobs finish their execution correctly
# Step 3: When all job are completed run
# Analyse DEG and EPCY outputs and create graphes
bash run_res_ismb_small.sh- python3 and dependency
- pip3 install -r Requirements.txt
- R and dependency (see lib_install.r)
- To run full analysis it's recomanded to use a cluster with a scheduler.
- 8 multicore and
- 80Go to run Deseq2 in parallel on 400 samples and more.
- 4Go is enough for Limma, EdgeR and EPCY.
- We have implemented:
- torque
Create an issue if you need slurm, or add it in DEG_analysis.sh (see exec_cmd function).
cd [your_epcy_paper_folder]
# Step 1: Create some files used as input in next script
bash run_init.sh
# Step 2: Create all cross-validated datasets and run DEG and EPCY analysis
bash run_ismb.sh
#Note that run_ismb.sh have a smart restart mechanism.
#Rerun it, until all jobs finish their execution correctly
# Step 3: When all job are completed run
# Analyse DEG and EPCY outputs and create graphes
bash run_res_ismb.sh