From f0aa940e94f2813265a940784925a5f68513d57e Mon Sep 17 00:00:00 2001 From: Bohdan Kovalenko Date: Sun, 17 Jul 2022 04:42:30 +0300 Subject: [PATCH] Add docker-compose config --- .gitignore | 4 ++++ Dockerfile | 9 +++++++++ README.md | 5 +++++ docker-compose.yml | 7 +++++++ 4 files changed, 25 insertions(+) create mode 100644 .gitignore create mode 100644 Dockerfile create mode 100644 docker-compose.yml diff --git a/.gitignore b/.gitignore new file mode 100644 index 000000000..53dccac30 --- /dev/null +++ b/.gitignore @@ -0,0 +1,4 @@ +.snakemake/ +example_data/output/ +example_data/reference/STARIndex/ +example_data/reference/SalmonIndex/ \ No newline at end of file diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 000000000..d54f1452f --- /dev/null +++ b/Dockerfile @@ -0,0 +1,9 @@ +FROM continuumio/miniconda3 + +WORKDIR /app + +# Prepare environment +RUN conda config --add channels bioconda +RUN conda config --add channels conda-forge +RUN conda install -y -c conda-forge mamba=0.23.3 +RUN mamba install -y -c bioconda snakemake=6.10.0 diff --git a/README.md b/README.md index 75e1f6775..8269fc009 100755 --- a/README.md +++ b/README.md @@ -19,6 +19,11 @@ git clone https://github.com/csoneson/ARMOR.git cd ARMOR && snakemake --use-conda ``` +Or using docker: +``` +docker-compose up +``` + To use the ARMOR workflow on your own data, follow the steps outlined in the [wiki](https://github.com/csoneson/ARMOR/wiki). ## Workflow graph diff --git a/docker-compose.yml b/docker-compose.yml new file mode 100644 index 000000000..ce515c7ef --- /dev/null +++ b/docker-compose.yml @@ -0,0 +1,7 @@ +version: "3.9" +services: + armor: + build: . + volumes: + - ./:/app + command: snakemake --use-conda --cores all \ No newline at end of file