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Issues with modules that require binaries (wrappers) #29
@yannickwurm: "Some major work is required for modules which require binaries. Currently using samtools (etc) involves download & compiling... this is extremely prone to fail & a big maintenance effort. Instead, rely on local docker install (so each module relies on a single docker file. (thus each module would include a dockerfile)."
So, either we:
referenced this issue
Apr 6, 2015
combine 1 and 2:
but in case they have a docker install, provide a dockerfile that includes the versions you've explicitly tested on. (not a dependency but an easy option)
changed the title from
Issues with modules that require binaries
Issues with modules that require binaries (wrappers)
Nov 8, 2015
added a commit
Nov 8, 2015
Another project that is wrapping bioinformatic tools is the Common Workflow Language, and after chatting with @tetron at #biohack15 he added to the current implementation of the specification some support for piping in/out NDJSON. This is the main requirement for using CWL with bionode pipelines. However, it's still an early project and there's very few tools wrapped (mostly just examples).
As for getting bioinformatics tools deployed/installed, Docker is great but still has issues (e.g., security), and there's a lot of alternatives popping up (e.g., vagga, hyperos.io, Rocket) so we probably don't want to commit yet to one solution. Plus, this might be out of scope for bionode in any case (we don't want to do package management...)
Alternatives to containers are package managers like Homebrew linux (lots of bioinformatics tools, but some won't install depending on host machine toolchain) and GUIX (functional package manager that is completely isolated and independent of root filesystem, plus containers support is coming for extra isolation).