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brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
139 stars 53 forks source link

Installation problem #8

Closed ikron closed 10 years ago

ikron commented 10 years ago

Hi,

I'm trying to install bwa-meth but I get the following error when trying to run sudo python setup.py install

Traceback (most recent call last): File "setup.py", line 5, in import bwameth File "/home/ilkka/biologia/bwa-meth-0.09/bwameth.py", line 42, in checkX('samtools') File "/home/ilkka/biologia/bwa-meth-0.09/bwameth.py", line 40, in checkX raise Exception("executable for '%s' not found" % cmd) Exception: executable for 'samtools' not found

It seems that the installer cannot find samtools. However, I have samtools in my $PATH. Any ideas?

Cheers, Ilkka

brentp commented 10 years ago

is samtools in the path when you run sudo? which does which samtools show?

ikron commented 10 years ago

Okay, I did not realize that in Ubuntu sudo resets the $PATH for security reasons. Sorry, my bad. I have it working now.