Newer
Older
Thamer Alsulaiman
committed
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
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
#FROM ubuntu:20.04
FROM continuumio/miniconda3:24.3.0-0
WORKDIR /motif-search/
ENV DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC
# Environment variables for the campus proxy.
ENV http_proxy="http://proxy.swmed.edu:3128" \
https_proxy="http://proxy.swmed.edu:3128"
COPY ./meme-5.5.4.tar.gz .
# RUN wget https://meme-suite.org/meme/meme-software/5.5.4/meme-5.5.4.tar.gz
RUN tar -zxf ./meme-5.5.4.tar.gz
RUN rm meme-5.5.4.tar.gz
COPY entrypoint.sh .
RUN apt update \
&& apt-get install -y --no-install-recommends \
wget \
build-essential \
ca-certificates \
curl \
imagemagick \
libexpat1-dev \
libxml2-dev \
libxslt1-dev \
libgs-dev \
libgd-dev \
#libexslt1-dev \
python3 \
zlib1g-dev \
perl \
libxml-simple-perl \
libxml-libxml-perl \
libxml-parser-perl \
libhtml-template-compiled-perl \
libxml-opml-simplegen-perl \
libxml-libxml-debugging-perl \
&& apt-get clean
# Install meme-chip
RUN cd meme-5.5.4 && \
./configure --prefix=/motif-search/meme --with-url="http://meme-suite.org" --enable-build-libxml2 --enable-build-libxslt && \
make && \
# make test && \
make install && \
export PATH=/motif-search/meme/bin/:/motif-search/meme/libexec/meme-5.5.4:$PATH && \
meme -version && \
meme-chip --version && \
spamo --version && \
centrimo --version && \
# apt-get remove -y build-essential libxml2 libxml2-dev libxslt1-dev && \
apt-get clean
# Enable the use of bash-specific conda commands in the layer.
RUN eval "$(conda shell.bash hook)" && \
chmod +x entrypoint.sh && \
#conda create -y -c bioconda -c conda-forge -c defaults -n motifSearch python=2.7.12 pip=9.0.1 && \
conda create -y -c bioconda -c conda-forge -c defaults -n motifSearch python=3.6.1 && \
conda activate motifSearch && \
python --version && \
# Install pandas and numpy.
pip install numpy==1.12.1 && \
pip install pandas==0.20.1 && \
# Install BEDTools 2.26 .0
conda install -y --solver=libmamba -c bioconda bedtools=2.26.0 && \
bedtools --version && \
conda clean -y --all && \
conda deactivate
ENTRYPOINT ["/motif-search/entrypoint.sh"]