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:
mulled-search -s deeptools -o biocontainersmulled-build-channel --channel bioconda --namespace biocontainers \
--involucro-path ./involucro --recipes-dir ./bioconda-recipes --diff-hours 25 buildtests 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 buildwe modified the samtools package to version 3.0 to make clear we are using a local version
- build your recipe
conda build recipes/samtools- index your local builds
conda index /home/bag/miniconda2/conda-bld/linux-64/- 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.
You need to have write access to the biocontainers repository
mulled-build build-and-test 'pandoc=1.17.2--0' --test 'pandoc --help' -n biocontainersmulled-build push 'pandoc=1.17.2--0' --test 'pandoc --help' -n biocontainers- all bioconda precompiled conda-packages are mirrored to the Galaxy depot
- extend this concept for conda-forge