github-ci/Singularity.StephensLab at master · Travyse/github-ci · GitHub

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
Bootstrap: docker
From: gaow/base-notebook


%labels
MAINTAINER Hao Sun <hs3163@cumc.columbia.edu>
%post
su -  root # USER root
apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends libgsl0-dev

cd /tmp && wget https://github.com/samtools/htslib/releases/download/1.12/htslib-1.12.tar.bz2 -O htslib-1.12.tar.bz2 && \
tar -xjvf htslib-1.12.tar.bz2 && \
cd htslib-1.12 && \
./configure --prefix=/usr/local/bin && \
make && \
make install && \
cp tabix bgzip htsfile /usr/local/bin && cd ../ && rm -rf /tmp/htslib*

R --slave -e "for (p in c('abind','rlang', 'RcppEigen', 'BiocManager', 'tidyr', 'data.table', 'tibble','modelr','purrr')) if (!(p %in% rownames(installed.packages()))) install.packages(p, repos = 'http://cran.rstudio.com')"

R --slave -e "BiocManager::install('VariantAnnotation')"
# https://github.com/gabraham/plink2R/issues/10
R --slave -e "Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS"=TRUE); remotes::install_github('gabraham/plink2R', subdir='plink2R', ref='d74be015e8f54d662b96c6c2a52a614746f9030d')"
R --slave -e "remotes::install_github('stephenslab/flashr')"
R --slave -e "remotes::install_github('willwerscheid/flashier')"
R --slave -e "remotes::install_github('stephenslab/mashr')"
R --slave -e "remotes::install_github('stephenslab/udr')"
R --slave -e "remotes::install_github('stephenslab/susieR', build_vignettes=FALSE)"
R --slave -e "remotes::install_github('stephenslab/mvsusieR')"
R --slave -e "remotes::install_github('chr1swallace/coloc@main')"
R --slave -e "install.packages('Rfast')"
R --slave -e "install.packages('cowplot')"
R --slave -e "install.packages('gwasrapidd')"
R --slave -e "install.packages('UpSetR')"
R --slave -e "install.packages('ComplexUpset')"
R --slave -e "install.packages('readr')"
R --slave -e "install.packages('wavethresh')"
R --slave -e "install.packages('L0Learn')"


python -m pip install -U pip
pip install scipy scikit-learn backports.zoneinfo
pip install rpy2
pip install https://files.pythonhosted.org/packages/a8/fd/f98ab7dea176f42cb61b80450b795ef19b329e8eb715b87b0d13c2a0854d/ldstore-0.1.9.tar.gz

## Install susiF and mvsusieF
R --slave -e "remotes::install_github('stephenslab/susiF.alpha')"
R --slave -e "remotes::install_github('william-denault/mvf.susie.alpha')"

echo "cd /tmp" >> /entrypoint.sh
echo "exec /bin/bash "$@"" >> /entrypoint.sh
chmod u+x /entrypoint.sh
%runscript
exec /bin/bash exec /bin/bash /bin/bash /entrypoint.sh "$@"
%startscript
exec /bin/bash exec /bin/bash /bin/bash /entrypoint.sh "$@"