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Calling bowtie2 from matlab

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Guy Nir
Guy Nir on 15 Sep 2017
Closed: MATLAB Answer Bot on 20 Aug 2021
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

Answers (1)

Ramnarayan Krishnamurthy
Ramnarayan Krishnamurthy on 21 Sep 2017
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
  1 Comment
Guy Nir
Guy Nir on 21 Sep 2017
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

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