diff --git a/README.md b/README.md index 3c48bfb6..5551c5a3 100644 --- a/README.md +++ b/README.md @@ -435,6 +435,32 @@ using a combination of `bwa` and `samtools` to output a BAM file instead of a SA > NB: Build information for all tools within a multi-tool container can be obtained in the `/usr/local/conda-meta/history` file within the container. - It is also possible for a new multi-tool container to be built and added to BioContainers by submitting a pull request on their [`multi-package-containers`](https://github.com/BioContainers/multi-package-containers) repository. + - Fork the [multi-package-containers repository](https://github.com/BioContainers/multi-package-containers) + - Make a change to the `hash.tsv` file in the `combinations` directory see [here](https://github.com/aunderwo/multi-package-containers/blob/master/combinations/hash.tsv#L124) for an example where `pysam=0.16.0.1,biopython=1.78` was added. + - Commit the code and then make a pull request to the original repo, for [example](https://github.com/BioContainers/multi-package-containers/pull/1661) + - Once the PR has been accepted a container will get built and you can find it using a search tool in the `galaxy-tool-util conda` package + + ```console + mulled-search --destination quay singularity conda --search pysam biopython | grep "mulled" + quay mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f 185a25ca79923df85b58f42deb48f5ac4481e91f-0 docker pull quay.io/biocontainers/mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 + singularity mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f 185a25ca79923df85b58f42deb48f5ac4481e91f-0 wget https://depot.galaxyproject.org/singularity/mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 + ``` + + - You can copy and paste the `mulled-*` path into the relevant Docker and Singularity lines in the Nextflow `process` definition of your module + - To confirm that this is correct. Spin up a temporary Docker container + + ```console + docker run --rm -it quay.io/biocontainers/mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 /bin/sh + ``` + + And in the command prompt type + + ```console + $ grep specs /usr/local/conda-meta/history + # update specs: ['biopython=1.78', 'pysam=0.16.0.1'] + ``` + + The packages should reflect those added to the multi-package-containers repo `hash.tsv` file - If the software is not available on Bioconda a `Dockerfile` MUST be provided within the module directory. We will use GitHub Actions to auto-build the containers on the [GitHub Packages registry](https://github.com/features/packages).