Hi Jin,
you can use a post-link script in conda.
Like here:
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picrust2/post-link.sh
This way the data can be fetch during tool installation.
See more information here:
https://docs.conda.io/projects/conda-build/en/latest/resources/link-scripts.html
Ciao,
Bjoern
Am 24.07.19 um 18:43 schrieb Jin Li:
Hi Brad,
Thank you for your quick reply. I can put the data file to Zenodo so
that I will have a permanent location for it.
As for re-computing the data file locally, it may need several days to
run, so it may be quite inefficient to do the computing. I am
expecting an automatic download of the data file when installing the
package. Do we have a convention to do that? Thank you.
Best regards,
Jin
On Wed, Jul 24, 2019 at 11:31 AM Langhorst, Brad <langho...@neb.com> wrote:
Hi:
I’d be concerned about that file changing or disappearing and causing
irreproducibility.
If the URL were to a permanent location (e.g. NCBI or zenodo) maybe it’s ok.
Could it be re-computed locally if necessary (like a genome index)?
Maybe others know of examples where this is done.
Brad
On Jul 24, 2019, at 12:24 PM, Jin Li <lijin....@gmail.com> wrote:
Hi all,
I am not sure if this mailing list is a good place to ask a bioconda
question. Sorry to bother if not. I want to ask how to include a large
data file when publishing a bioconda package. Our program depends on a
pre-computed data file, which is too large to be included in the
source code package. The data file can be accessed via a public URL.
Can I put the downloading command in `build.sh` when publishing a
bioconda package? If not, do we have a convention to deal with
dependent large datafiles? Thank you.
Best regards,
Jin
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Bradley W. Langhorst, Ph.D.
Development Group Leader
New England Biolabs
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