Pipeline improvements

[xileF1337]

This PR contains several improvements to the LazyB/MuCHSALSA pipeline. Changes include:

• prevent race condition during index creation of input files when running multiple instances
• use the recommended bloom filter mode of Abyss instead of the legacy mpi mode
• skip non-unique k-mers in Jellyfish, greatly reducing the memory requirements
• Conda environment and Vagrant files added to provide the dependencies for using / compiling MuCHSALSA
• many sanity checks added: argument count, existence of input files, availability of external tools, abort on errors, status messages
• allow setting thread count and memory size of Bloom filters from the command line
• use quotes for variables to support paths containing spaces
• require python3 in shebang lines
• extended .gitignore file

[xileF1337]

@TGatter, would you be so kind as to review and merge? Thank you so much!

[0x002A]

Thanks for the PR.

But before @TGatter merges, I'd like to give it a short review too. 😀

[xileF1337]

Sure, you're very welcome. My reference to Thomas was mainly due to the fact that I discussed those things with him already.

[xileF1337]

And just for clarification, this PR only contains technical improvements to the pipeline scripts, and no improvements to the actual assembly process. Thomas has to decide what exactly we will do about that.

[0x002A]

Only a single remark/question otherwise it lgtm. Will approve after clarification.

Nice code quality, good job

[xileF1337]

Only a single remark/question otherwise it lgtm. Will approve after clarification.

Nice code quality, good job

Thanks for the review, @0x002A ! I commented on the Cmake version requirement in your remark above. Looking forward for the merge!

[TGatter]

You may go ahead an merge. I approve of the pipeline changes.

[0x002A]

Your wish is my command.