-
Notifications
You must be signed in to change notification settings - Fork 8
/
Copy pathDockerfile
executable file
·88 lines (69 loc) · 3.22 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
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
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
FROM rocker/tidyverse:3.5.1
MAINTAINER ccdl@alexslemonade.org
WORKDIR /rocker-build/
RUN apt-get update && apt-get install -y --no-install-recommends apt-utils
RUN apt-get install dialog apt-utils -y
RUN apt-get update -qq && apt-get -y --no-install-recommends install \
build-essential \
libxml2-dev \
libsqlite-dev \
libmariadbd-dev \
libmariadbclient-dev \
libmariadb-client-lgpl-dev \
libpq-dev \
libssh2-1-dev \
pandoc \
libmagick++-dev \
time
# scater and scran need updated rlang
RUN R -e "devtools::install_url('https://cran.r-project.org/src/contrib/Archive/rlang/rlang_0.3.1.tar.gz')"
RUN apt update && apt install -y dirmngr curl bash
RUN apt-get update -qq && apt-get -y --no-install-recommends install \
&& install2.r --error \
--deps TRUE \
rjson \
ggpubr \
Rtsne \
png
RUN R -e "BiocManager::install(c('ensembldb', 'DESeq2', 'qvalue', 'org.Hs.eg.db', 'org.Dr.eg.db', 'org.Mm.eg.db', 'org.Cf.eg.db', 'ComplexHeatmap', 'ConsensusClusterPlus', 'scran', 'scater'), update = FALSE)"
# Install R packages from github and urls
# Need most updated version of tximport so AlevinQC will install later
RUN R -e "devtools::install_github('mikelove/tximport', ref = 'b5b5fe11b0093b4b2784f982277b2aa66d2607f7')"
RUN R -e "devtools::install_github('wgmao/PLIER', ref = 'a2d4a2aa343f9ed4b9b945c04326bebd31533d4d', dependencies = TRUE)"
RUN R -e "devtools::install_github('const-ae/ggsignif', ref = 'aadd9d44a360fc35fc3aef4b0fcdfdb7e1768d27')"
RUN R -e "devtools::install_github('csoneson/alevinQC', ref = '6ca73b1744cbd969036f80b7c7dddbe7d1cf99ee', dependencies = TRUE)"
# colorblind friendly palettes
RUN R -e "devtools::install_url('https://cran.r-project.org/src/contrib/Archive/colorspace/colorspace_1.4-0.tar.gz')"
RUN R -e "devtools::install_github('clauswilke/colorblindr', ref = '1ac3d4d62dad047b68bb66c06cee927a4517d678', dependencies = TRUE)"
# FastQC
RUN apt update && apt install -y fastqc
ENV PACKAGES git gcc make g++ libboost-all-dev liblzma-dev libbz2-dev \
ca-certificates zlib1g-dev curl unzip autoconf
ENV SALMON_VERSION 0.13.1
# salmon binary will be installed in /home/salmon/bin/salmon
# don't modify things below here for version updates etc.
WORKDIR /home
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
# Apt doesn't have the latest version of cmake, so install it using their script.
RUN apt remove cmake cmake-data -y
RUN wget --quiet https://github.com/Kitware/CMake/releases/download/v3.13.3/cmake-3.13.3-Linux-x86_64.sh && \
mkdir /opt/cmake && \
sh cmake-3.13.3-Linux-x86_64.sh --prefix=/opt/cmake --skip-license && \
sudo ln -s /opt/cmake/bin/cmake /usr/local/bin/cmake
RUN curl -k -L https://github.com/COMBINE-lab/salmon/archive/v${SALMON_VERSION}.tar.gz -o salmon-v${SALMON_VERSION}.tar.gz && \
tar xzf salmon-v${SALMON_VERSION}.tar.gz && \
cd salmon-${SALMON_VERSION} && \
mkdir build && \
cd build && \
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local && make && make install
# fastp
RUN git clone https://github.com/OpenGene/fastp.git
RUN cd fastp && \
make && \
sudo make install
WORKDIR /home
# MultiQC
RUN apt update && apt install -y python-pip
RUN pip install multiqc