Hi Bjoern, Thank you for your direction and information. The post-link script is exactly what I was looking for. I am glad I asked the question here. Thank you.
Best regards, Jin On Wed, Jul 24, 2019 at 3:26 PM Björn Grüning <bjoern.gruen...@gmail.com> wrote: > > 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 > >> ___________________________________________________________ > >> Please keep all replies on the list by using "reply all" > >> in your mail client. To manage your subscriptions to this > >> and other Galaxy lists, please use the interface at: > >> %(web_page_url)s > >> > >> To search Galaxy mailing lists use the unified search at: > >> http://galaxyproject.org/search/ > >> > >> > >> Bradley W. Langhorst, Ph.D. > >> Development Group Leader > >> New England Biolabs > >> > >> > >> > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > %(web_page_url)s > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/ > > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
