wkpalan/pacbioapps:latest
$ singularity pull shub://wkpalan/pacbioapps:latest
Singularity Recipe
Bootstrap: docker
From: ubuntu:18.04
%labels
Maintainer Matthew Flister
Version v1.0
%help
This container runs includes several PacBio apps.
%environment
SHELL=/bin/bash
export PATH="/opt/miniconda3/bin:$PATH"
%post
# default mount points
mkdir -p /scratch/global /scratch/local /rcc/stor1/refdata /rcc/stor1/projects /rcc/stor1/depts
# Install necessary packages
apt-get update && apt-get install -y --no-install-recommends \
build-essential \
gcc-multilib \
libboost-all-dev \
libhdf5-serial-dev \
zlib1g-dev \
python3-pip \
pkg-config \
python3-dev \
python3-setuptools \
wget
apt-get clean
# install miniconda
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda3.sh
bash miniconda3.sh -b -p /opt/miniconda3
rm miniconda3.sh
export PATH="/opt/miniconda3/bin:$PATH"
# install pacbio apps
conda install -c bioconda pbccs bax2bam lima bam2fastx pbmm2
mkdir /media/data
Collection
- Name: wkpalan/pacbioapps
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/wkpalan-pacbioapps-latest |
collection name | wkpalan/pacbioapps |
branch | master |
tag | latest |
commit | 6eaffab64105f3e4c7db07e24b795530a93ba0e3 |
version (container hash) | 049485f25dab1606638b03cd672ccc45 |
build date | 2019-02-09T23:03:29.251Z |
size (MB) | 1405 |
size (bytes) | 545005599 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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