tanghaibao/bio-pipeline

My collection of light bioinformatics analysis pipelines for specific tasks

bio-pipeline's Issues

Nim wrapper to kseq

Dear Haibao,

I came across this repo after a failed attempt to write a Nim wrapper for Heng Li's kseq. Awesome stuff! Native versions are all very slow, possibly due to reasons discussed in this post on the Nim forum. My plan was to modify your code and make it ready for Nimble submission, however I can't get it compiled because ../kseq.h is missing (running nimble test in klib/nim). You have a few versions of that file in the repo but I couldn't get either to work . Maybe that file is simply missing?

Could you help?

Many thanks!
Andreas

License for poaV2?

Hello,
I'm working on a tool that uses poaV2 to do partial order alignment. I've managed to bind your poaV2 library in nim, but just noticed that there is no stated license for poaV2 or the bio-pipeline repo in general. I wanted to check with you whether it is acceptable for me to bind your library and distribute the code from the poaV2 software in a nim software package.
I'd obviously credit you and this repo as the source of the library, and link to this repo in my README and any publication resulting from the completion of the tool.
Thanks for your time and the great software! Please let me know either way when you get the chance.

synonymous_calculation/bin/pal2nal.pl has no license, not distributable

Hello @tanghaibao

I found your repository because I'm trying to find a version of pal2nal that is licensed by the authors for redistribution.

fstrozzi/scalability-reproducibility-chapter#1

Alas you seem to be using the same version we're looking at, and the lack of license means that you can't even put a copy on GitHub.

If you happen to know the authors in any way, you could help us to petition them to add a license: https://lists.debian.org/debian-med/2017/10/msg00019.html

In the mean time I recommend that you remove this copy of pal2nal from GitHub as no one besides the authors have the legal right to distribute the code.

Sorry to be the bearer of bad news,

Move kseq nim out to make nimble package

Dear Haibao,

Would you be open to moving the kseq nim bits into its own repo and publish as a nimble package? This could either be a new repo (ideally having kseq in its name to make the roots clear) or simply using https://github.com/sdwfrost/nimkseq which is empty right now :) If you don't have the time I'm happy to help. I noticed you have no license added to your repo so guess I better ask.

PS: Sorry I thought could swear I asked you already, but I can't find any reference to it