gitpod

In certain regions, pulling Docker images directly or cloning GitHub repositories can be challenging. As a straightforward alternative, creating Docker or Singularity images is an efficient solution. This repositories outlines general methods for seamlessly building functional Docker/SIF images using Gitpod’s cloud servers (e.g., Google Compute Engine).

Register

create an account in gitpod(https://www.gitpod.io/flex-or-classic) follow the guide, choose Gitpod Classic as workspace, the host connect the real international inernet by default.

Save docker image tallball

pull docker image from dockhub create tarball file

BIN_VERSION="1.6.1"
sudo docker pull google/deepvariant:"${BIN_VERSION}"
docker image save google/deepvariant:"${BIN_VERSION}" -o deepvariant-"${BIN_VERSION}".tar

download docker image

get SSH "access token" like 'ssh "xxxxxxxxx@xxxxxx"' in WorkSpace then login local host

scp -r "xxxxxxxxx@xxxxxx":/workspace/gitpod/deepvariant-"${BIN_VERSION}".tar .

build sif iamge in local host

singularity build deepvariant-"${BIN_VERSION}" docker-archive://deepvariant-"${BIN_VERSION}".tar

Build singularity sif image directly

install singularity in gitpod

git clone git@github.com:dozhun/gitpod.git 
cd gitpod/singularity
bash install 

de novo config def file et al.

a demo (not recommend for newfish)

mkdir nf-LO && cd nf-LO
curl -O https://raw.githubusercontent.com/evotools/nf-LO/main/singularity.def
curl -O https://raw.githubusercontent.com/evotools/nf-LO/main/environment.yml
singularity build nflo.sif singularity.def

or build sif from docker hub directly

BIN_VERSION="1.6.1"
singularity build deepvariant-"${BIN_VERSION}".sif docker://google/deepvariant:"${BIN_VERSION}"

download sif image

login local machine

BIN_VERSION="1.6.1"
scp -r "xxxxxxxxx@xxxxxx":/workspace/gitpod/deepvariant-"${BIN_VERSION}".sif .

A network bridge to clone github repo

git clone https://github.com/chaozhi/PolyOriginR 
tar -czf PolyOriginR.tar.gz PolyOriginR

then login local machine

scp -r "xxxxxxxxx@xxxxxx":/workspace/gitpod/PolyOriginR.tar.gz .

Contact

dozhun@outlook.com(Zhang Jun)