millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-11-14 21:53:10 +00:00
Code Issues Releases Packages Activity

build(spaceranger): Add initial dockerfile

Browse source 
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
This commit is contained in:
Edmund Miller 2021-10-29 07:29:14 -05:00
parent 2959b4ba07
commit d40cbb5e58
No known key found for this signature in database
GPG key ID: BD387FF7BC10AA9D
3 changed files with 40 additions and 0 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

1
modules/spaceranger/.gitignore vendored Normal file
View file

@ -0,0 +1 @@
spaceranger-*.tar.gz

21
modules/spaceranger/Dockerfile Normal file
View file

@ -0,0 +1,21 @@
FROM continuumio/miniconda3:4.9.2
LABEL authors="Gisela Gabernet <gisela.gabernet@gmail.com>,Edmund Miller <edmund.a.miller@gmail.com>" \
description="Docker image containing Space Ranger"
# Disclaimer: this container is not provided nor supported by 10x Genomics.
# Install procps and clean apt cache
RUN apt-get update --allow-releaseinfo-change \
&& apt-get install -y procps \
&& apt-get clean -y && rm -rf /var/lib/apt/lists/*
# Copy pre-downloaded spaceranger file
ENV SPACERANGER_VER 1.3.0
COPY spaceranger-$SPACERANGER_VER.tar.gz /opt/spaceranger-$SPACERANGER_VER.tar.gz
# Install spaceranger
RUN \
cd /opt && \
tar -xzvf spaceranger-$SPACERANGER_VER.tar.gz && \
export PATH=/opt/spaceranger-$SPACERANGER_VER:$PATH && \
ln -s /opt/spaceranger-$SPACERANGER_VER/spaceranger /usr/bin/spaceranger && \
rm -rf /opt/spaceranger-$SPACERANGER_VER.tar.gz

18
modules/spaceranger/README.md Normal file
View file

@ -0,0 +1,18 @@
# Updating the docker container and making a new module release
Space Ranger is a commercial tool by 10X Genomics. The container provided for the spaceranger nf-core module is not provided nor supported by 10x Genomics. Updating the Space Ranger version in the container and pushing the update to Dockerhub needs to be done manually.
1. Navigate to the [Space Ranger download page](https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest) and download the tar ball of the desired Space Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
2. Edit the Dockerfile: update the Cell Ranger version in this line:
```bash
ENV SPACERANGER_VER <VERSION>
```
3. Create the container:
```bash
docker build . -t nfcore/spaceranger:<VERSION>
docker push nfcore/spaceranger:<VERSION>
```