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seq-lang / seq

A high-performance, Pythonic language for bioinformatics
https://seq-lang.org
Apache License 2.0
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conda packaging #224

Open Juke34 opened 3 years ago

Juke34 commented 3 years ago

Hi, I'm thinking to make it available through conda. see here https://github.com/bioconda/bioconda-recipes/pull/29660

I would need to know if deps.sh statically compiles dependencies in. Could you let me know?

arshajii commented 3 years ago

Hi @Juke34, thanks for undertaking this daunting task 😄 Let me know how I can help.

Everything in deps.sh is statically compiled and linked directly to libseqrt except for OpenMP, which we package and ship as a shared library. For the purposes of Conda, though, maybe we can just list (LLVM's) OpenMP as a dependency.

The Seq installation itself consists of the following components:

RasmusEdgar commented 2 years ago

I have created a conda package using the prebuilt binary. The recipe and dependent scripts can be found here: https://github.com/RasmusEdgar/seq-lang-conda-recipe

A problem I could not find a workaround to:

LD_LIBRARY_PATH needs to be set to include lib/seq when activating the environment where seq-lang is installed. If not set it was not possible to compile binaries from the seq code. See activate.sh and deactivate.sh.

Suggestions for improvements are welcome.

arshajii commented 2 years ago

Thanks a lot for this @RasmusEdgar -- will check it out soon.

The LD_LIBRARY_PATH issue should be resolvable on our end I believe when we're interfacing with clang. I'll look into this as well.