Improve runtime requirements, bundled 3rd-party code and a way to avoid that

[mmokrejs]

Hi,
I would like to add Sibelia to Gentoo Linux but it is a mix of many other tools, for some of them we already do have separate packages.

Please clarify why you include the many 3-rd-party tools and libs? Did you modify them? Why didn't you ask their respective authors to change them?

Can the tool use official lagan, snpEff? Which versions? I mean, would snpEff-4.3 work fine too?

Could you avoid the statically linked ./libdivsufsort-2.0.1/lib/libdivsufsort.a?

What is the "boost" thing in your source tree? That isn't a true boost library, isn't it? What version could that be, btw?

What version of seqan does it need?

Although I added https://github.com/gentoo/sci/tree/master/sci-biology/Sibelia I will soon get a slap from the gatekeepers for that. Please try to cleanup the compile&installation process so that it could cleanly re-use system-wide installed libraries and tools. Currently, you claim this is GPL-2 code but in real it is a mix. No matter in Readme.md you mention some additional licenses. It is not a complete listing anyway.
Thank you

[iminkin]

Please clarify why you include the many 3-rd-party tools and libs? Did you modify them? Why didn't you ask their respective authors to change them?

I wanted to make the distribution & compilation as easy as possible. For example, the reason why I extracted a subset of boost and included it in the distribution is that many people run into trouble when trying to compile code relying on a local installation of boost. For example, often systems have outdated version of boost (like really, really outdated) and the user may not be qualified to make a proper local installation. And it is often impossible to update the boost system-wide because whatever reason. The same fore seqan and some other things.

At this moment I am developing a successor for Sibelia and I don't know if it makes sense to reorganize old code. Probably it does, but I have to give it a thought.

[iminkin]

But I appreciate your efforts and agree that your concerns are valid.