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adamewing / bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers
MIT License
231 stars 86 forks source link

Bam surgeon installation error: Not Python3 #131

Closed yvazirabad closed 5 years ago

yvazirabad commented 5 years ago

This is the same issue as #118, but this has nothing to do with Python3 as in the previous thread.

sudo python2 setup.py install Traceback (most recent call last): File "setup.py", line 89, in if not check_bwa(): sys.exit('Dependency problem: bwa >= 0.7.12 not found') File "setup.py", line 16, in check_bwa p = subprocess.Popen(['bwa'], stderr=subprocess.PIPE) File "/usr/lib/python2.7/subprocess.py", line 711, in init errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory softgen@hqbreak:~/NGSTools/bamsurgeon-1.2$ which bwa /home/softgen/bin/bwa

BWA runs and is in the bin. Some direction on this would be appreciated.

adamewing commented 5 years ago

I seem to have overlooked this, my apologies. Is this still an issue? It looks like something to do with your linux environment.

yvazirabad commented 5 years ago

Thanks Adam, I moved to a fresh installation and it was resolved.