touala/smtm:latest
$ singularity pull shub://touala/smtm:latest
Singularity Recipe
Bootstrap: docker
From: rocker/r-ver:3.5.3
%help
For more information, please consult https://github.com/touala/nanodisco
# Add files to the container
%files
postInstall /
code /tmp/code
# Install dependencies
%post
# Install basic dependencies
apt-get update && apt-get install -y --no-install-recommends \
"vim" \
"git" \
"wget" \
"bzip2" \
"parallel" \
"python" \
"ghostscript" \
"libcurl4-openssl-dev" \
"libssl-dev" \
"libxml2-dev" \
"libxslt1-dev" \
"zlib1g-dev" \
"libncurses5-dev" \
"libncursesw5-dev" \
"libexpat1-dev" \
"libjson-perl" \
"libhtml-tree-perl" \
"libbz2-dev" \
"liblzma-dev" \
"openmpi-bin" \
"libopenmpi-dev" \
"openssh-client" \
"openssh-server" \
&& rm -rf /var/lib/apt/lists/*
# Include nanodisco toolbox
mkdir /home/nanodisco
mv /tmp/code /home/nanodisco/code
# Install remaining dependencies from sources (nanopolish, bwa, samtools, R packages, MEME, bedtools)
bash /postInstall
# Define working directory
cd /home/nanodisco
# Create folders for analysis
mkdir /home/nanodisco/analysis
mkdir /home/nanodisco/dataset
# Set default behavior
cat > /.singularity.d/env/99-custom.sh <<EOF
export PS1="\[\033[36m\]\u\[\033[m\]@\[\033[32m\]nanodisco:\[\033[33;1m\]\w\[\033[m\]$ "
SINGULARITY_SHELL=/bin/bash
EOF
%environment
export HOME=/home/nanodisco
%runscript
cd /home/nanodisco
exec /bin/bash
Collection
- Name: touala/smtm
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/touala-smtm-latest |
collection name | touala/smtm |
branch | master |
tag | latest |
commit | 5911b80fec72bf6d11de15ea9835b1db8031ab36 |
version (container hash) | 8d222b87294de1f027d54c329d944b6d |
build date | 2020-02-15T16:31:40.498Z |
size (MB) | 3559.0 |
size (bytes) | 1975193631 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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