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Automatic build of linux containers

The aim of this project is to utilize mulled and with this involucro in an automatic way. Every new package in bioconda is build and packaged into a Linux Container (Docker, rkt) and available from quay.io.

We have developed small utilities around this technology stack which is currently included in galaxy-lib. Here is a short introduction:

Search for containers

mulled-search -s deeptools -o biocontainers

Build all packages from bioconda from the last 24h

mulled-build-channel --channel bioconda --namespace biocontainers \
    --involucro-path ./involucro --recipes-dir ./bioconda-recipes --diff-hours 25 build

Test all packages from bioconda from the last 24h

tests will be extracted from the recipes-dir - we need to improve it, if you have time get in touch with me :)

mulled-build-channel --channel bioconda --namespace biocontainers \
    --involucro-path ./involucro --recipes-dir ./bioconda-recipes --diff-hours 25 build

Building Docker containers for local Conda packages

we modified the samtools package to version 3.0 to make clear we are using a local version

  1. build your recipe
conda build recipes/samtools
  1. index your local builds
conda index /home/bag/miniconda2/conda-bld/linux-64/
  1. build a container for your local package
mulled-build build-and-test 'samtools=3.0--0' \
  --extra-channel file://home/bag/miniconda2/conda-bld/ --test 'samtools --help'

 The --0 indicates the build version of the conda package. It is recommended to specify this number otherwise  you will override already exsisting images. For python conda packages this extension might look like this --py35_1.

Build, test and push a conda-forge package to biocontainers

You need to have write access to the biocontainers repository

mulled-build build-and-test 'pandoc=1.17.2--0' --test 'pandoc --help' -n biocontainers
mulled-build push 'pandoc=1.17.2--0' --test 'pandoc --help' -n biocontainers

ToDo:

  • all bioconda precompiled conda-packages are mirrored to the Galaxy depot
  • extend this concept for conda-forge