We need to find a way to be able to copy binary files into our backup system

[ypriverol]

@osallou

One of the ideas of having the ftp binary folder is to find a way to copy all the binaries needed to generate the containers into our internal file system. We need to find out a way to allow users or administrators of Biocontainers upon request to copy to the binary folder https://containers.biocontainers.pro/s3/ the binary files.

Best Regards
Yasset

[bgruening]

to copy to the binary folder https://containers.biocontainers.pro/s3/ the binary files.

You mean copy tarballs and binaries into this folder?

[ypriverol]

We have now the backup from your side, which is what we aim at the very beginning. However, we don't have a way to copy a tarball or binary in that folder in the s3. one possible option is that you @bgruening give us access to copy in the original folder and this will be finally reflected in the s3.

[bgruening]

This already exists for years. Its called cargo-port and you can find it here: https://github.com/galaxyproject/cargo-port

[ypriverol]

How can I copy a binary to the ftp using cargo?

Thanks @bgruening for the feedback

[bgruening]

There is documentation in this repo. You need to edit a tsv file add a temporary location of your binary and create a PR. On merge cargo-port will download the binary and archive it.

This is done in this way to give all people the same change to add files and to prevent uploading malicious content. GitHub acts here as a review place for the links and binaries.

[ypriverol]

Ok, we can formally use this mechanism to add the binaries/ tarballs to the system thanks. Can we give to @BioContainers/core members rights to merge there?

[bgruening]

Can we give to @BioContainers/core members rights to merge there?

I think so. If it turns out to be useful and Biocontainers/core keeps maintaining it, why not. Please note it is not my project.

[ypriverol]

Quick Question. I have seen that the url.tsv file hasn't been modified in 3 months. How the bioconda that rely on binaries has been released recently?

Yasset

[ypriverol]

@bgruening I have check one recently added container and you use this path https://github.com/bgruening/download_store/raw/master/thermorawfileparser/thermorawfileparser2018_09_07.zip

Why you didn't use the cargo project? Any special reason?

[bgruening]

Because you told me its not official :-)

[ypriverol]

Then, we go for that PR in that system.

[osallou]

@ypriverol, sorry but i do not understand what you mean here by 'binaries needed to generate the containers'
What do you need to save here for biocontainers?
Admin (we) can upload things there, using s3 cmds...
Users, who and what would they upload there?