[Bioc-devel] Submission of packages located at within a repository

Turaga, Nitesh N|te@h@Tur@g@ @end|ng |rom Ro@we||P@rk@org
Wed Feb 6 18:11:07 CET 2019

Hi Britta,

You could use submodules in git. I took some time to create an example use case for you, at 


The “main_repository” contains a README.md file which you might find useful to go about creating the submodule for your packages/

The example there, shows,

main_repository, (parent repo) located at https://github.com/nturaga/main_repository

	submodule_one (as submodule) located at https://github.com/nturaga/submodule_one

To give you a gist of what you could do:

Main repository is “MOFA_main”, located at https://github.com/bioFAM/MOFA_main

	submodule 1: MOFA software package located at https://github.com/bioFAM/MOFA

	submodule 2: MOFA data package located at https://github.com/bioFAM/MOFAdata

They would both live in the MOFA_main repository but would act as submodules within their own independent repos. This will allow you to submit from their separate repos.

https://github.com/nturaga/main_repository/blob/master/README.md gives you details on how to create submodules, if you need any assistance. But, I’ll highlight some steps,

Step 0: Rename the main MOFA directory which already exists to MOFA_main.

Step 1: Create two new repos in the bioFAM username, with MOFA, and MOFAdata. 

Step 2: Create submodules in MOFA_main, 

	git submodule init

	git submodule add git using github.com:bioFAM/MOFA MOFA

	git submodule add git using github.com:bioFAM/MOFAdata MOFAdata

Step 3: Add the submodules to MOFA_main

	git commit -m “Add MOFA and MOFAdata as submodules”.

The “.gitmodules” should show,

	$ cat .gitmodules

	[submodule “MOFA"]
		path = MOFA
		url = git using github.com:bioFAM/MOFA

	[submodule “MOFAdata”]
		path  = MOFAdata
		url = git using github.com:bioFAM/MOFAdata

But to answer your question, bioconductor doesn’t have a way to submit multiple packages from within one repository. 

I can assist you in creating submodules, and submitting the repos as required to Bioconductor. Please let me know if you have any questions. Please check the example and the documentation I wrote up in the README.md at https://github.com/nturaga/main_repository.



> On Feb 4, 2019, at 11:24 AM, Britta Velten <britta.velten using embl.de> wrote:
> Dear Bioconductor team,
> we would like to submit two R packages (software and accompanying data package) that are located in a git repository jointly with a Python package that one of them depends upon.
> These two R packages are located at 
> - https://github.com/bioFAM/MOFA/tree/master/MOFA
> - https://github.com/bioFAM/MOFA/tree/master/MOFAdata
> within the repository https://github.com/bioFAM/MOFA.
> However, the submission via the git submission system fails as it requires the package to sit at https://github.com/yourusername/yourpackagename <https://github.com/yourusername/yourpackagename>.
> We would like to avoid breaking up the repository https://github.com/bioFAM/MOFA into separate repositories for each package as they are inter-dependent and new developments or fixes often involve changes to both the python package (mofapy) and the R package (MOFA) (e.g. having common branches for the two packages is very useful).
> Is there a way to submit the packages at their current paths, i.e. make the submission system look at https://github.com/bioFAM/MOFA/tree/master/MOFA and /MOFAdata instead of https://github.com/bioFAM/MOFA? If not, do you have other suggestions how to solve this without breaking up the repository?
> Thanks for your help!
> Best,
> Britta Velten
> 	[[alternative HTML version deleted]]
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