Calling bowtie2 from matlab

I am trying to run bowtie2 from matlab: [a,b]=unix('bowtie2 -h') the output is: a =127 b='bin/bash not such command' so I copied all the executables to usr/bin and then it gave me: a = 127 b = 'env: perl: No such file or directory'

And in my startup.m I have: setenv('PATH','usr/bin:/usr/local/bin'); Where bowtie2 is defined, and when I type the same bowtie2 command from terminal it works. It used to work in matlab too, in an earlier version, but now i am using 2017a, and it's not working anymore. I would love to get some answers. Thank you

Answer 1

[Ramnarayan Krishnamurthy]

Can you try running bowtie2 from matlab using the 'system' command. That is,

[a,b] = system('bowtie2 -h')

Also, there is a possibility that the startup.m is being shadowed. Try running to check if there are multiple startup files:

which -all startup

[Guy Nir]

Hi Ramnarayan,

Apparently I somehow deleted a backslash from my startup.m, and thus, didn't have PATH well-defined. It works well now!

Thanks, Guy