-
Notifications
You must be signed in to change notification settings - Fork 0
/
Dockerfile
41 lines (34 loc) · 1.13 KB
/
Dockerfile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
# Docker inheritance
FROM rocker/r-base
RUN apt-get update && apt-get install -y \
libcurl4-gnutls-dev \
libssl-dev \
libopenblas-dev \
libz-dev
# Install required Bioconductor package
RUN R -e 'install.packages("BiocManager")'
RUN R -e 'BiocManager::install("DESeq2")'
# Required for GLM
RUN R -e 'BiocManager::install("apeglm")'
# Install python
RUN apt-get update && \
apt-get install -y --no-install-recommends \
python3-full \
python3-pip \
python3-venv
WORKDIR /opt
RUN python3 -m venv .venv
# Install pydeseq2
ARG PYDESEQ2_VERSION=0.4.4
RUN echo "Install pydeseq2 version=${PYDESEQ2_VERSION}"
RUN /opt/.venv/bin/python3 -m pip install pydeseq2==${PYDESEQ2_VERSION}
# Install dependencies for compare_r_py_deseq2
RUN /opt/.venv/bin/python3 -m pip install pandas
COPY compare_r_py_deseq2.py .
COPY deseq2.R .
COPY __init__.py .
RUN mkdir data
RUN mkdir output
# To just run R DESeq2 and get results from R
# ENTRYPOINT [ "Rscript", "deseq2.R ", "data", "output"]
ENTRYPOINT [ "/opt/.venv/bin/python3", "-m", "compare_r_py_deseq2", "--deseq2_rscript_path=deseq2.R", "--data_directory_path=data", "--output_directory_path=output"]