meglab-metagenomics/amrplusplus_v2:latest
$ singularity pull shub://meglab-metagenomics/amrplusplus_v2:latest
Singularity Recipe
Bootstrap: docker
From: debian:jessie-slim
#Includes trimmomatic, samtools, bwa, bedtools, vcftools, htslib, kraken2, SNPfinder, freebayes, bbmap
%environment
export LC_ALL=C
%post
apt update \
&& apt install -y --no-install-recommends \
build-essential ca-certificates sudo tcsh\
git make automake autoconf openjdk-7-jre wget gzip unzip sed\
zlib1g-dev curl libbz2-dev locales libncurses5-dev liblzma-dev libcurl4-openssl-dev software-properties-common apt-transport-https\
python3-pip python3-docopt python3-pytest python-dev python3-dev\
libcurl4-openssl-dev libssl-dev zlib1g-dev fonts-texgyre \
gcc g++ gfortran libblas-dev liblapack-dev dos2unix libstdc++6\
r-base-core r-recommended hmmer\
&& rm -rf /var/lib/apt/lists/*
wget -c https://repo.continuum.io/archive/Anaconda3-2020.02-Linux-x86_64.sh
sh Anaconda3-2020.02-Linux-x86_64.sh -bfp /usr/local
# add bioconda channels
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
# install bulk of bioinformatic tools using conda
conda create -n AmrPlusPlus_env python=3 trimmomatic bwa samtools bedtools freebayes bbmap vcftools htslib kraken2
. /usr/local/bin/activate AmrPlusPlus_env
#ln -s /usr/local/envs/AmrPlusPlus_env/bin/* /usr/local/bin/
#Still experimenting with how to change $PATH location.
echo 'export PATH=$PATH:/usr/local/envs/AmrPlusPlus_env/bin/' >> $SINGULARITY_ENVIRONMENT
# SNPfinder
cd /usr/local
git clone https://github.com/cdeanj/snpfinder.git
cd snpfinder
make
cp snpfinder /usr/local/bin
cd /
# Make sure all the tools have the right permissions to use the tools
chmod -R 777 /usr/local/
%test
Collection
- Name: meglab-metagenomics/amrplusplus_v2
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/meglab-metagenomics-amrplusplus_v2-latest |
collection name | meglab-metagenomics/amrplusplus_v2 |
branch | master |
tag | latest |
commit | c3dad185f37462e85ea090358648a582cd7fb661 |
version (container hash) | b4cd8f6073072e2d0f1d671a2e9ccce7 |
build date | 2021-04-16T11:58:57.097Z |
size (MB) | 7441.0 |
size (bytes) | 3740483615 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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