Name: auto-mulled
Owner: BioContainers
Description: Generating Docker containers from bioconda on the fly with Travis cron-job feature.
Created: 2016-07-10 18:00:52.0
Updated: 2017-02-07 16:59:02.0
Pushed: 2017-06-23 08:57:08.0
Homepage: null
Size: 33
Language: null
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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:
ed-search -s deeptools -o biocontainers
ed-build-channel --channel bioconda --namespace biocontainers \
--involucro-path ./involucro --recipes-dir ./bioconda-recipes --diff-hours 25 build
tests will be extracted from the
recipes-dir
- we need to improve it, if you have time get in touch with me :)
ed-build-channel --channel bioconda --namespace biocontainers \
--involucro-path ./involucro --recipes-dir ./bioconda-recipes --diff-hours 25 build
we modified the samtools package to version 3.0 to make clear we are using a local version
build your recipe
a build recipes/samtools
index your local builds
a index /home/bag/miniconda2/conda-bld/linux-64/
build a container for your local package
ed-build build-and-test 'samtools=3.0--0' \
tra-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
ed-build build-and-test 'pandoc=1.17.2--0' --test 'pandoc --help' -n biocontainers
ed-build push 'pandoc=1.17.2--0' --test 'pandoc --help' -n biocontainers