Manual compilation of BWA

[karel-brinda]

prophyle compile maybe does not (re)compile bwa (/home/kb219/miniconda/envs/p/lib/python3.8/site-packages/prophyle/prophyle_index/bwa/bwa)

[esteinig]

@karel-brinda

I might running into an issue with bwa compilation when trying to compile and test (make & make cleanall) a RASE skeleton database - the exact error relates to the command: make -j -s -C /path/to/conda/envs/rase/lib/python3.8/site-packages/prophyle on the latest prophyle version (v0.3.2, installed with conda through the commands outlined in theRASE repository)

Output is:

/usr/bin/ld: bwa/bwashm.o: unable to initialize decompress status for section .debug_info
/usr/bin/ld: bwa/bwashm.o: unable to initialize decompress status for section .debug_info
/usr/bin/ld: bwa/bwashm.o: unable to initialize decompress status for section .debug_info
/usr/bin/ld: bwa/bwashm.o: unable to initialize decompress status for section .debug_info
bwa/bwashm.o: file not recognized: File format not recognised
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:49: prophyle_index] Error 1
make: *** [Makefile:17: compile_index] Error 2

I'll update here if I find a solution but any pointers are appreciated.

Edit: same error occurs when running prophyle compile manually (outside the make files)
Edit: installing bwa into the environment does not solve it either
Edit: same error when regressing to version prophyle-0.3.1.0-py36h61628e2_7

Edit: as the title suggests manual compilation actually seems to solve it (make clean and make) 🥳

[karel-brinda]

@esteinig Thank you very much for the report!!

[karel-brinda]

TODO:

• Ensure that with prophyle compile everything gets recompiled
• If compilation fails, run make clean first