granek/crne_transposon:canu
$ singularity pull shub://granek/crne_transposon:canu
Singularity Recipe
BootStrap: docker
From: debian:buster
%runscript
exec "${@}"
%environment
export PATH=/usr/lib/rstudio-server/bin:${PATH}
export CONDA_DIR=/opt/conda
export PATH=$CONDA_DIR/bin:$PATH
export SHELL=/bin/bash
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8
export LANGUAGE=en_US.UTF-8
%post
# Install extra stuff
apt-get update
apt-get install -y --no-install-recommends \
curl \
wget \
bzip2 \
parallel \
sra-toolkit \
canu \
bwa \
samtools \
ncbi-blast+ \
python-biopython \
mafft \
&& apt-get clean && \
rm -rf /var/lib/apt/lists/*
# other aligners: t-coffee, muscle, dialign-tx, kalign
##------------------------------------------------------------
CONDA_DIR=/opt/conda
cd /tmp && \
mkdir -p $CONDA_DIR && \
wget --quiet https://repo.continuum.io/miniconda/Miniconda3-4.4.10-Linux-x86_64.sh && \
echo "bec6203dbb2f53011e974e9bf4d46e93 Miniconda3-4.4.10-Linux-x86_64.sh" | md5sum -c - && \
/bin/bash Miniconda3-4.4.10-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
rm Miniconda3-4.4.10-Linux-x86_64.sh && \
$CONDA_DIR/bin/conda clean -tipsy
$CONDA_DIR/bin/conda install -c bioconda pilon biopython && \
$CONDA_DIR/bin/conda clean -tipsy
#--------------------------------------------------------------------------------
# Helpful:
#------------------
# https://gitlab.oit.duke.edu/mccahill/jupyter-HTS-2017/blob/master/Dockerfile
# https://github.com/nickjer/singularity-r/blob/master/Singularity.3.4.3
# https://github.com/nickjer/singularity-rstudio/blob/master/Singularity
# https://www.singularity-hub.org/collections/174
# https://www.singularity-hub.org/collections/463
# sudo singularity build canu_rstudio.simg singularity_canu_rstudio
%labels
Maintainer Josh Granek
Version v0.007
Collection
- Name: granek/crne_transposon
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/granek-crne_transposon-canu |
collection name | granek/crne_transposon |
branch | master |
tag | canu |
commit | 233b0990d8100e14b620b9b06864ecd87d8b1dd7 |
version (container hash) | d059a295a92f3df1205b6d2ff1e4f8e9 |
build date | 2018-05-16T11:13:33.252Z |
size (MB) | 2065 |
size (bytes) | 768196639 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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