Tagged release

[npavlovikj]

Hi @hhg7 ,

I am a contributor to "bioconda", https://bioconda.github.io/, that packages bioinformatics tools for easier installation and distribution. I would like to create a conda package for "defiant". However, one of the requirements for this, is to have a tagged release. Therefore, can you please tag a release and create a tarball for it so I can proceed?

Thank you in advance, and please let me know if you have any questions regarding this request.

--
Natasha

[epruesse]

It would suffice for us if you just created a release via the web interface here with an official version number. You can upload files manually, so attaching a defiant-x.y.zip to that release would make things easier for us.

[hhg7]

Hi @epruesse @npavlovikj there is now a file defiant-1.1.4.zip on the main repository. Please let me know if this works

[hhg7]

Hi @epruesse @npavlovikj there is now a file defiant-1.1.4.zip on the main repository. Please let me know if this works

[npavlovikj]

Thanks for the update @hhg7 . Is it possible to add regions_of_interest and LICENSE in defiant-1.1.4.zip as well? As of now, the bioconda recipe builds defiant and roi, and the latter one fails because regions_of_interest is not in defiant-1.1.4.zip.

[hhg7]

@npavlovikj @epruesse I've now included roi.c in the main release zip file. Is there anything else that I should do?

[npavlovikj]

@hhg7 , many thanks for updating the tarball!

We created the recipe, and now defiant is available as a bioconda package, https://anaconda.org/bioconda/defiant, for both Linux and Mac. Since there is a conda package llvm-openmp that allows multi-processing for OSX, we were able to include the -fopenmp option for the OSX build of defiant. This package includes both "defiant" and "roi" executables.

If you are interested in the recipe itself, please check https://github.com/bioconda/bioconda-recipes/tree/ce971e44db3bb61e8c66c3151be64fcae7193e10/recipes/defiant. "bioconda" checks for package updates, but you are more than welcome to update the recipe with new releases and/or bug fixes. "bioconda" is an open community, and volunteers are always welcome.

You can read more about installing Anaconda/Miniconda and creating environments here, https://bioconda.github.io/. Briefly, after you install Anaconda/Miniconda and properly configure the channels, you can use conda create -n defiant-1.1.4 defiant=1.1.4 to create environment for "defiant". Next, whenever you want to use the environment you need to do conda activate defiant-1.1.4, and after you are done, you can type conda deactivate.

I hope you and your users find the conda package useful, and please let us know if you have any questions or issues with the package.