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Published 20 hours ago • verified publisher icon hhg7

Tagged release

Open npavlovikj opened this issue 6 years ago • 6 comments

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

npavlovikj avatar Mar 16 '19 19:03 npavlovikj

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.

epruesse avatar Apr 28 '19 23:04 epruesse

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 avatar Apr 29 '19 13:04 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 avatar Apr 29 '19 14:04 hhg7

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.

npavlovikj avatar Apr 29 '19 16:04 npavlovikj

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

hhg7 avatar May 01 '19 01:05 hhg7

@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.

npavlovikj avatar May 01 '19 08:05 npavlovikj