Creating containers is easy! All you need to do is add a combination of packages to the hash.tsv file.
To assemble the required string of package combinations you can use the little helper service which we provide for you. This service will also tell you the name of the container that will be created.
Currently, this will create you Docker and rkt containers hosted at https://quay.io/organization/biocontainers and Singularity images hosted at https://depot.galaxyproject.org/singularity/ (Hosting sponsors and mirrors welcome!).
You can list and search for existing conda packages and container images as well as build multi-package container images locally
using the command line mulled-* tools available as part of galaxy-tool-util, which source
code is hosted as part of the Galaxy repo.
These can be installed using conda
conda create -n mulled galaxy-tool-util -c conda-forge -c bioconda
conda activate mulled
Multi-tool containers have hashed names to make them uniquely identifiable. You usually don't search for containers you construct the hash and pull them down. However, if you have the need to search for them, we have a CLI tool that helps you.
(planemo) bag@bag:~$ mulled-search --destination quay singularity -s deeptools samtools
The query returned the following result(s).
LOCATION NAME VERSION COMMAND
quay samtools 1.3.1--4 docker pull quay.io/biocontainers/samtools:1.3.1--4
quay samtools 1.3.1--3 docker pull quay.io/biocontainers/samtools:1.3.1--3
quay samtools 1.3.1--2 docker pull quay.io/biocontainers/samtools:1.3.1--2
quay samtools 1.0--0 docker pull quay.io/biocontainers/samtools:1.0--0
quay samtools 1.3--1 docker pull quay.io/biocontainers/samtools:1.3--1
...
singularity deeptools 3.4.2--py_0 wget https://depot.galaxyproject.org/singularity/deeptools:3.4.2--py_0
singularity deeptools 3.4.3--py_0 wget https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0
singularity deeptools 3.5.0--py_0 wget https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0
singularity deeptools 3.5.1--py_0 wget https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0
singularity deeptools 3.5.1--pyhdfd78af_1 wget https://depot.galaxyproject.org/singularity/deeptools:3.5.1--pyhdfd78af_1
singularity deeptools 3.5.2--pyhdfd78af_0 wget https://depot.galaxyproject.org/singularity/deeptools:3.5.2--pyhdfd78af_0
...
singularity samtools 1.9--h8571acd_10 wget https://depot.galaxyproject.org/singularity/samtools:1.9--h8571acd_10
singularity samtools 1.9--h8571acd_11 wget https://depot.galaxyproject.org/singularity/samtools:1.9--h8571acd_11
singularity samtools 1.9--h8ee4bcc_1 wget https://depot.galaxyproject.org/singularity/samtools:1.9--h8ee4bcc_1
singularity samtools 1.9--h91753b0_2 wget https://depot.galaxyproject.org/singularity/samtools:1.9--h91753b0_2
singularity samtools 1.9--h91753b0_3 wget https://depot.galaxyproject.org/singularity/samtools:1.9--h91753b0_3
singularity samtools 1.9--h91753b0_4 wget https://depot.galaxyproject.org/singularity/samtools:1.9--h91753b0_4
singularity samtools 1.9--h91753b0_5 wget https://depot.galaxyproject.org/singularity/samtools:1.9--h91753b0_5
singularity samtools 1.9--h91753b0_8 wget https://depot.galaxyproject.org/singularity/samtools:1.9--h91753b0_8
...
singularity mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a 9796fae7f3dc33539425911572b1af41da23d71c-0 wget https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:9796fae7f3dc33539425911572b1af41da23d71c-0
singularity mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a b7b2dac42861f5ad3a6dcbf1626378de27694869-0 wget https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:b7b2dac42861f5ad3a6dcbf1626378de27694869-0
singularity mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a d4ca6cb58c17558e45d789d552f8d20c2f0cf912-0 wget https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:d4ca6cb58c17558e45d789d552f8d20c2f0cf912-0
singularity mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a d67d021ff194d58c15cca934dd3dfe948d1c7145-0 wget https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:d67d021ff194d58c15cca934dd3dfe948d1c7145-0
singularity mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a e4be5f66213daef5a53e2a179b7e0c1d22016afe-0 wget https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:e4be5f66213daef5a53e2a179b7e0c1d22016afe-0
- Fork this repository or copy the github workflow.
- Create quay.io oauth token in an organization.
- Change the MULLED_NAMESPACE variable to point to your quay.io organization.
- Add QUAY_OAUTH_TOKEN, MY_USER MY_PASSWORD and MY_EMAIL to the repository secrets.