samtools required as dependency

[sihellem]

Dear,

I recently installed MinYS v1.1 from source and all mentioned dependencies (bwa.gcc/0.7.10, minia-v3.2.4, MindTheGap-v2.2.2).

When executing the test, I got the following error:

MinYS.py -1 test_data/reads.1.fq -2 test_data/reads.2.fq -ref test_data/ref.fa -out MinYS_results
2020-08-31 16:54:25,282 [MainThread  ] [INFO ]  Indexing reference genome
2020-08-31 16:54:25,315 [MainThread  ] [INFO ]  Starting mapping
2020-08-31 16:54:25,315 [MainThread  ] [INFO ]      Call : bwa mem -t 40 test_data/ref.fa test_data/reads.1.fq test_data/reads.2.fq
Traceback (most recent call last):
  File "/home/Programs/MinYS/MinYS.py", line 183, in <module>
    p3 = subprocess.Popen(sam2bamCommand.split(),stdin=p1.stdout,stdout=open(bamFile,"w"),stderr=out)
  File "/apps/python/3.7.3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/apps/python/3.7.3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'

When adding samtools/1.9 to my PATH, the test could complete.

Maybe samtools should be added as a dependency on the doc page?

Best, Simon