Provide documentation on how to build bioconda binaries for local / private use about bioconda-utils HOT 5 CLOSED

This should do:

cd bioconda-recipes
bioconda-utils build recipes config.yaml --packages $YOURPACKAGES

Adding this to the docs is a good idea, indeed.

from bioconda-utils.

Alternatively, you can also set https://github.com/bioconda/bioconda-recipes/blob/master/config.yml#L8 to a Docker container with CentOS-5 and run it with --docker. However, the real challenge is that BioConda depends on conda-forge and you also have to recompile all dependencies from them and in the worst also from defaults.

from bioconda-utils.

@johanneskoester thanks i did try that (should have specified).

bioconda-utils build recipes config.yml --packages pysam
06:55:56 BIOCONDA INFO blacklist: bioconductor-bubbletree, bioconductor-cexor, bioconductor-deseq2/1.10.1, bioconductor-genelendatabase/1.6.0, bioconductor-iranges/2.4.6, bioconductor-iranges/2.4.7, bioconductor-limma/3.26.7, bioconductor-limma/3.28.2, bioconductor-limma/3.28.6, bioconductor-mmdiff, bioconductor-s4vectors/0.8.7, bioconductor-summarizedexperiment/1.0.2, blast/2.2.21, cap-mirseq, denovogear, detonate, gdsctools, mothur/1.36.1, mysqlclient, perl-font-afm, r-hdrcde, r-knitr, r-ks, r-mutoss, r-phonr, r-rainbow, r-readr, r-sartools/1.2.0, triform2
06:55:56 BIOCONDA INFO Filtering recipes

Filtering 4 of 4 (100.0%) recipes/pysam/0.9.1
06:56:00 BIOCONDA INFO Nothing to be done.

It appears it attempts to determine whether the package has already been built and skips it?

from bioconda-utils.

There are a few other things scattered throughout that are specific to bioconda that make it not so straightforward to use for another channel, like encrypted tokens in the bioconda-recipes's travis config and hard-coded repos and branches to check. It is certainly possible to use this with another repo, and that's always been the intention. We just haven't documented it yet and pulled out all the config into a single place.

Here are some places that would need changing to a different repo/channel:

• bioconda-utils/bioconda_utils/utils.py

  Line 430 in 7d34d35

  def get_channel_packages(channel='bioconda', platform=None):

• bioconda-utils/bioconda_utils/linting.py

  Line 110 in 7d34d35

  def channel_dataframe(cache=None, channels=['bioconda', 'conda-forge',

• bioconda-utils/bioconda_utils/utils.py

  Line 382 in 7d34d35

  def get_channel_repodata(channel='bioconda', platform=None):

• bioconda-utils/bioconda_utils/docker_utils.py

  Line 141 in 7d34d35

  RUN /opt/conda/bin/conda config --add channels bioconda

• bioconda-utils/bioconda_utils/cli.py

  Line 144 in 7d34d35

  repo='bioconda-recipes', git_range=None, full_report=False,

from bioconda-utils.

Closing as the specific use case - building for Centos5 - is likely nigh impossible because of conda-forge dependencies.

from bioconda-utils.