Installation¶
Installation should take less than 10 minutes
System Requirements¶
CentOS Linux 7 or above
Clone repository¶
git clone https://github.com/shendurelab/MPRAflow.git
Set up conda environment¶
This pipeline uses python2.7 and python3.6 with additional R scripts. Three .yml files are provided to create the appropriate environments and is completely handled by nextflow. The whole pipeline is set up to run on a Linux system. The general environment with nextflow located in the home directory called environment.yml.
Install the the conda environment. The general conda environment is called MPRAflow.
cd MPRAflow
conda env create -n MPRAflow -f environment.yml
If you do not have access to the internet, you have to run the previous command on a node with internet. Afterwards you need to start nextflow too (see Steps to run the pipeline). After creation of the second conda environment by nextflow you can cancel it and start it on your internal node. Be aware that folders must have access on all nodes.
Nextflow has problems using conda 4.7 and highet, because the source activate command is replaced by conda activate. If you get error messages after running you can make a symbolik link of the activate command from you bin folder of the conda or miniconda folder to your MPRAflow environment bin folder. E.g. like:
ln -s ~/miniconda3/bin/activate ~/miniconda3/envs/MPRAflow/bin/activate
Quick test¶
conda activate MPRAflow
nextflow run count.nf --help
nextflow run association.nf --help
nextflow run saturationMutagenesis.nf --help