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multi-tool instructions (#376)

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* multi-tool instructions

Add instructions on how to build a bespoke multi-tool Docker container and Singularity image

* fix linting issues

* Change bash to console

* Update README.md

* Update README.md

* Update README.md

* Update README.md

* Update README.md

Co-authored-by: Ramon Rivera <ramon.rivera10@upr.edu>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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Anthony Underwood 2021-03-24 18:18:38 +00:00 committed by GitHub
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@ -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).