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Singularity.def
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Bootstrap:docker
From:ubuntu:20.04
%labels
MAINTAINER Eike Matthias Wacker
DESCRIPTION Singularity image containing the finemap workflow
VERSION 0.1
%setup
%environment
PATH=/opt/conda/envs/finepipe/bin:/opt/locuszoom:/usr/local:/opt/conda/bin:$PATH
export PATH
%files
m2zfast.py /
m2zfast.conf /
%post
export DEBIAN_FRONTEND=noninteractive
echo "Installing basic build system"
apt -y update
apt -y dist-upgrade
apt -yq install build-essential locales wget unzip libgomp1 tclsh bash psmisc curl default-jre-headless gawk
#Installing Miniconda 3
wget -nc https://repo.anaconda.com/miniconda/Miniconda3-py39_4.9.2-Linux-x86_64.sh
/bin/bash Miniconda3-py39_4.9.2-Linux-x86_64.sh -bfp /opt/conda
chmod -R o+rX /opt/conda
export PATH="$PATH:/opt/conda/bin"
#Conda configuration of channels from .condarc file
conda config --file /.condarc --add channels defaults
conda config --file /.condarc --add channels bioconda
conda config --file /.condarc --add channels conda-forge
rm -f Miniconda3-py39_4.9.2-Linux-x86_64.sh
echo "Installing locuszoom"
cd /opt
mkdir -p locuszoom
cd locuszoom
wget -nc https://statgen.sph.umich.edu/locuszoom/download/locuszoom_1.4_srconly.tgz
tar zxf locuszoom_1.4_srconly.tgz
yes | cp -f /m2zfast.py /opt/locuszoom/locuszoom/src/m2zfast.py
mkdir -p locuszoom/conf
cp -f /m2zfast.conf /opt/locuszoom/locuszoom/conf/m2zfast.conf
ln -s /opt/locuszoom/locuszoom /usr/local/bin/locuszoom
rm -f locuszoom_1.4_srconly.tgz
echo "Installing Nextflow"
curl -s https://get.nextflow.io | bash
mv nextflow /usr/bin
chmod 0755 /usr/bin/nextflow
echo "name: finepipe
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
- _r-mutex=1.0.1=anacondar_1
- binutils_impl_linux-64=2.35.1=h193b22a_2
- binutils_linux-64=2.35=h67ddf6f_30
- bwidget=1.9.14=ha770c72_0
- bzip2=1.0.8=h7f98852_4
- c-ares=1.17.1=h7f98852_1
- ca-certificates=2020.12.5=ha878542_0
- cairo=1.16.0=h9f066cc_1006
- certifi=2019.11.28=py27h8c360ce_1
- curl=7.76.0=h979ede3_0
- fontconfig=2.13.1=hba837de_1005
- freetype=2.10.4=h0708190_1
- fribidi=1.0.10=h36c2ea0_0
- gcc_impl_linux-64=9.3.0=h70c0ae5_19
- gcc_linux-64=9.3.0=hf25ea35_30
- gettext=0.19.8.1=hf34092f_1004
- gfortran_impl_linux-64=9.3.0=hc4a2995_19
- gfortran_linux-64=9.3.0=hdc58fab_30
- graphite2=1.3.13=h58526e2_1001
- gsl=2.6=he838d99_2
- gxx_impl_linux-64=9.3.0=hd87eabc_19
- gxx_linux-64=9.3.0=h3fbe746_30
- harfbuzz=2.7.2=ha5b49bf_1
- icu=67.1=he1b5a44_0
- jpeg=9d=h36c2ea0_0
- kernel-headers_linux-64=2.6.32=h77966d4_13
- krb5=1.17.2=h926e7f8_0
- ld_impl_linux-64=2.35.1=hea4e1c9_2
- libblas=3.9.0=8_openblas
- libcblas=3.9.0=8_openblas
- libcurl=7.76.0=hc4aaa36_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libffi=3.2.1=he1b5a44_1007
- libgcc-devel_linux-64=9.3.0=h7864c58_19
- libgcc-ng=9.3.0=h2828fa1_19
- libgfortran-ng=9.3.0=hff62375_19
- libgfortran5=9.3.0=hff62375_19
- libglib=2.66.3=hbe7bbb4_0
- libgomp=9.3.0=h2828fa1_19
- libiconv=1.16=h516909a_0
- liblapack=3.9.0=8_openblas
- libnghttp2=1.43.0=h812cca2_0
- libopenblas=0.3.12=pthreads_h4812303_1
- libpng=1.6.37=h21135ba_2
- libssh2=1.9.0=ha56f1ee_6
- libstdcxx-devel_linux-64=9.3.0=hb016644_19
- libstdcxx-ng=9.3.0=h6de172a_19
- libtiff=4.2.0=hdc55705_0
- libuuid=2.32.1=h7f98852_1000
- libwebp-base=1.2.0=h7f98852_2
- libxcb=1.13=h7f98852_1003
- libxml2=2.9.10=h68273f3_2
- lz4-c=1.9.3=h9c3ff4c_0
- make=4.3=hd18ef5c_1
- ncurses=6.2=h58526e2_4
- openssl=1.1.1k=h7f98852_0
- pandoc=2.12=h7f98852_0
- pango=1.42.4=h69149e4_5
- pcre=8.44=he1b5a44_0
- pcre2=10.36=h032f7d1_1
- pip=20.1.1=pyh9f0ad1d_0
- pixman=0.40.0=h36c2ea0_0
- plink=1.90b6.21=h779adbc_1
- pthread-stubs=0.4=h36c2ea0_1001
- python=2.7.15=h5a48372_1011_cpython
- python_abi=2.7=1_cp27mu
- r-askpass=1.1=r40hcdcec82_2
- r-assertthat=0.2.1=r40h6115d3f_2
- r-backports=1.2.1=r40hcfec24a_0
- r-base=4.0.3=ha43b4e8_3
- r-base64enc=0.1_3=r40hcdcec82_1004
- r-blob=1.2.1=r40h6115d3f_1
- r-brio=1.1.1=r40hcfec24a_0
- r-broom=0.7.6=r40hc72bb7e_0
- r-callr=3.6.0=r40hc72bb7e_0
- r-cellranger=1.1.0=r40h6115d3f_1003
- r-cli=2.4.0=r40hc72bb7e_0
- r-clipr=0.7.1=r40h142f84f_0
- r-colorspace=2.0_0=r40h9e2df91_0
- r-cpp11=0.2.7=r40hc72bb7e_0
- r-crayon=1.4.1=r40hc72bb7e_0
- r-curl=4.3=r40hcfec24a_1
- r-data.table=1.14.0=r40hcfec24a_0
- r-dbi=1.1.1=r40hc72bb7e_0
- r-dbplyr=2.1.1=r40hc72bb7e_0
- r-desc=1.3.0=r40hc72bb7e_0
- r-diffobj=0.3.3=r40hcfec24a_0
- r-digest=0.6.27=r40h1b71b39_0
- r-dplyr=1.0.5=r40h03ef668_0
- r-ellipsis=0.3.1=r40hcdcec82_0
- r-evaluate=0.14=r40h6115d3f_2
- r-fansi=0.4.2=r40hcfec24a_0
- r-farver=2.1.0=r40h03ef668_0
- r-forcats=0.5.1=r40hc72bb7e_0
- r-fs=1.5.0=r40h0357c0b_0
- r-generics=0.1.0=r40hc72bb7e_0
- r-ggplot2=3.3.3=r40hc72bb7e_0
- r-glue=1.4.2=r40hcfec24a_0
- r-gtable=0.3.0=r40h6115d3f_3
- r-haven=2.3.1=r40hde08347_0
- r-highr=0.8=r40h6115d3f_2
- r-hms=1.0.0=r40hc72bb7e_0
- r-htmltools=0.5.1.1=r40h03ef668_0
- r-httr=1.4.2=r40h6115d3f_0
- r-isoband=0.2.4=r40h03ef668_0
- r-jsonlite=1.7.2=r40hcfec24a_0
- r-knitr=1.31=r40hc72bb7e_0
- r-labeling=0.4.2=r40h142f84f_0
- r-lattice=0.20_41=r40hcfec24a_3
- r-lifecycle=1.0.0=r40hc72bb7e_0
- r-lubridate=1.7.10=r40h03ef668_0
- r-magrittr=2.0.1=r40hcfec24a_1
- r-markdown=1.1=r40hcfec24a_1
- r-mass=7.3_53.1=r40hcfec24a_0
- r-matrix=1.3_2=r40he454529_0
- r-mgcv=1.8_34=r40he454529_0
- r-mime=0.10=r40hcfec24a_0
- r-modelr=0.1.8=r40h6115d3f_0
- r-munsell=0.5.0=r40h6115d3f_1003
- r-nlme=3.1_152=r40h859d828_0
- r-openssl=1.4.3=r40he5c4762_0
- r-pillar=1.5.1=r40hc72bb7e_0
- r-pkgconfig=2.0.3=r40h6115d3f_1
- r-pkgload=1.2.1=r40h03ef668_0
- r-plyr=1.8.6=r40h0357c0b_1
- r-praise=1.0.0=r40h6115d3f_1004
- r-prettyunits=1.1.1=r40h6115d3f_1
- r-processx=3.5.1=r40hcfec24a_0
- r-progress=1.2.2=r40h6115d3f_2
- r-ps=1.6.0=r40hcfec24a_0
- r-purrr=0.3.4=r40hcdcec82_1
- r-r6=2.5.0=r40hc72bb7e_0
- r-rcolorbrewer=1.1_2=r40h6115d3f_1003
- r-rcpp=1.0.6=r40h03ef668_0
- r-readr=1.4.0=r40h1b71b39_0
- r-readxl=1.3.1=r40hde08347_4
- r-rematch=1.0.1=r40h6115d3f_1003
- r-rematch2=2.1.2=r40h6115d3f_1
- r-reprex=1.0.0=r40hc72bb7e_0
- r-reshape2=1.4.4=r40h0357c0b_1
- r-rlang=0.4.10=r40hcfec24a_0
- r-rmarkdown=2.7=r40hc72bb7e_0
- r-rprojroot=2.0.2=r40hc72bb7e_0
- r-rstudioapi=0.13=r40hc72bb7e_0
- r-rvest=1.0.0=r40hc72bb7e_0
- r-scales=1.1.1=r40h6115d3f_0
- r-selectr=0.4_2=r40h6115d3f_1
- r-stringi=1.5.3=r40hca8494e_0
- r-stringr=1.4.0=r40h6115d3f_2
- r-sys=3.4=r40hcdcec82_0
- r-testthat=3.0.2=r40h03ef668_0
- r-tibble=3.1.0=r40hcfec24a_1
- r-tidyr=1.1.3=r40h03ef668_0
- r-tidyselect=1.1.0=r40h6115d3f_0
- r-tidyverse=1.3.0=r40h6115d3f_2
- r-tinytex=0.31=r40hc72bb7e_0
- r-utf8=1.2.1=r40hcfec24a_0
- r-vctrs=0.3.7=r40hcfec24a_0
- r-viridislite=0.3.0=r40h6115d3f_1003
- r-waldo=0.2.5=r40hc72bb7e_0
- r-withr=2.4.1=r40hc72bb7e_0
- r-xfun=0.20=r40hcfec24a_0
- r-xml2=1.3.2=r40h0357c0b_1
- r-yaml=2.2.1=r40hcfec24a_1
- r-zeallot=0.1.0=r40h6115d3f_1002
- readline=8.0=he28a2e2_2
- sed=4.8=he412f7d_0
- setuptools=44.0.0=py27_0
- sqlite=3.35.4=h74cdb3f_0
- sysroot_linux-64=2.12=h77966d4_13
- tk=8.6.10=h21135ba_1
- tktable=2.10=hb7b940f_3
- wheel=0.36.2=pyhd3deb0d_0
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.0.10=h7f98852_0
- xorg-libsm=1.2.3=hd9c2040_1000
- xorg-libx11=1.7.0=h7f98852_0
- xorg-libxau=1.0.9=h7f98852_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h7f98852_1
- xorg-libxrender=0.9.10=h7f98852_1003
- xorg-libxt=1.2.1=h7f98852_2
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h7f98852_1002
- xorg-xproto=7.0.31=h7f98852_1007
- xz=5.2.5=h516909a_1
- zlib=1.2.11=h516909a_1010
- zstd=1.4.9=ha95c52a_0" >> /environment.yml
conda env create -f /environment.yml
conda clean -a
mkdir -p /ifs
apt-get -y install procps