akward build process

[cmeesters]

Hi,

rmats-turbo has a build routine, which is totally broken into separate parts, which should work together:

• bamtools is a library (and command line tools), why ship it with rmats_turbo, the other libs are also not shipped with rmats_turbo? If everything is the the LD_LIBRARY_PATH, rmats_turbo should build
• then there is a makefile which invokes a genuine makefile and runs setup.py, should this not be the other way around? A setup.py which build everything?

Best regards, Christian Meesters

[EricKutschera]

The bamtools header files are referenced in the rmats cython code: https://github.com/Xinglab/rmats-turbo/blob/v4.1.1/rMATS_pipeline/rmatspipeline/nogilbam.pxd#L10 . The developer who originally worked on the cython implementation of rmats no longer works on the project, but my guess is that including the bamtools source code was an easy way to get things working

The makefile in the main rmats directory runs the build commands for bamtools, the rmats statistical model, and the rmats cython code (which is imported by the main rmats.py script). Since rmats is intended to be run on the command line rather than imported by other code, a top-level setup.py doesn't seem necessary

[cmeesters]

my guess is that including the bamtools source code was an easy way to get things working

Indeed, yet in cluster environments, we rather install optimized code (no conda at all) and provide libraries as dependencies. Shipping 3rd party libraries along with any software has an additional disadvantage: Whenever the library developers change anything upstream, the application developer has to reflect that change in the application trunk or risks not to be able to do that, when there is a severe change.

Whether or not there is a global makefile or a setup.py does not really matter. Having both, governed by a master script is a little cumbersome. I'll give you a link to an easyconfig (easybuild is a build framework for HPC systems) on Compute Canada, I am about to submit a similar easyconfig to easybuild, soon: https://github.com/ComputeCanada/easybuild-easyconfigs/blob/computecanada-main/easybuild/easyconfigs/r/rMATS/rMATS-4.1.1-gmkl-2020a.eb As you can see, it looks odd. And there is a patch file. I have one too, telling rmats-turbo to be compiled against OpenBlas and Scalapack instead of BLAS and Lapack. Imposing such requirements in a hard-coded fashion is unnecessary, too.

I hope that my rather blunt remarks, help improving the distribution and reach of your project.

Cheers, Christian Meesters