forked from carlferr/HOME-BIO
/
Dockerfile
29 lines (23 loc) · 855 Bytes
/
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
FROM biohaz/basic_ubuntu:latest
# Locale
ENV LC_ALL C.UTF-8
ENV LANG C.UTF-8
# Anaconda
RUN wget -q https://repo.anaconda.com/archive/Anaconda3-2020.02-Linux-x86_64.sh -O /tmp/Anaconda3-2020.02-Linux-x86_64.sh
RUN /bin/bash /tmp/Anaconda3-2020.02-Linux-x86_64.sh -bp /opt/Anaconda3
RUN rm /tmp/Anaconda3-2020.02-Linux-x86_64.sh
# Anaconda environment setting
RUN echo "export PATH=/opt/Anaconda3/bin:$PATH" > /etc/profile
ENV PATH /opt/Anaconda3/bin:$PATH
# Software
RUN apt-get update
RUN pip3 install multiqc
RUN pip install configparser
RUN source activate
RUN conda update -n base -c defaults conda
RUN conda install -c bioconda -c conda-forge fastqc cutadapt bowtie bowtie2 star kraken2 bracken spades kaiju krona
#Creating user
RUN useradd -ms /bin/bash homebio
USER homebio
ENTRYPOINT ["python", "./Script.py", "-c", "config_file.txt"]
#END