Cannot run system commands from matlab macOS catalina; zsh:1: command not found: blastp

I am trying to run the bioinformatics software blast+ from within matlab environment.

>> addpath("/usr/local/ncbi/blast/bin")

>> ! blastp -h

zsh:1: command not found: blastp

The software runs fine when I run it from the terminal.

Initially I tried to run it with the system(command) function but it was not working. As suggested on other posts I tried to add it to the matlab path but still Matlab R2020b cannot locate it. Any suggestions?

Answer 1

[Ameer Hamza]

The command addpath() add the folder to MATLAB's path. ! or system() do not use MATLAB's path. You need to use setenv() to change the PATH variable as shows here: https://www.mathworks.com/matlabcentral/answers/10451-how-do-i-add-to-the-path-of-system

[kyllen87]

Yup, this works like a charm! Thank you very for your help!

setenv('PATH','/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/ncbi/blast/bin');

[Ameer Hamza]

I am glad to be of help!

[Michael]

@Ameer Hamza, I am having a similar issue. I can see that my PATH variable includes the folder /usr/local/bin. Within that folder is an alias to the executable that I need to call. I assume homebrew installed the alias in /usr/local/bin when it installed the package I need. The actual executable is burried deep in my /usr/local/ files. Do I need to add the path all the way down to the executable? Why is it that I can run the command in Termal just fine, but it doesn't work from the ! call in Matlab? I hope this is all clear. Sorry if it isn't.

[Walter Roberson]

In MATLAB what shows up for

getenv('PATH')
system('echo "$PATH"') 

[Michael]

@Walter Roberson Thanks for getting back to me on this. When I used those commands you suggested, here is what I got.

>> getenv('PATH')

ans =

    '/usr/bin:/bin:/usr/sbin:/sbin'

>> system('echo "$PATH"')
/usr/bin:/bin:/usr/sbin:/sbin

ans =

     0

In terminal though

echo $PATH

gives me

/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/laps

I don't think those other directories are critical, as the executable I need isn't in them. It is curious that the Matlab call and the terminal call each produce different results though, but hopefully besideds the point.

In terminal, I can navigate to '/usr/local/bin' and then do an 'ls' call and I can see the ailias of the executable I need. FYI - it is call 'airspy_info' and is a program that checks on a device I plugged in via USB.

Now I tried to explicitly call the executable from with the full path to the ailias and it works just fine. Calling

>> system(['/usr/local/bin/airspy_info'])

in Matlab returns:

airspy_lib_version: 1.0.10

Found AirSpy board 1
Board ID Number: 0 (AIRSPY)
Firmware Version: AirSpy NOS v1.0.0-rc10-0-g946184a 2016-09-19
Part ID Number: 0x6906002B 0x00000030
Serial Number: 0x910865C8258B53C3
Supported sample rates:
	10.000000 MSPS
	2.500000 MSPS
Close board 1

ans =

     0

But if I manually change the directory to '/usr/local/bin' with the system call and then try to call the executable, it doesn't seem to see the executable:

>> system(['cd /usr/local/bin ;','airspy_info'])
zsh:1: command not found: airspy_info

ans =

   127

This is the same output I get when I enter

system('airspy_info')

It is unclear to me what is going on, as using system.m with a call that uses the full path to the directory containing the alias works, but if you do a cd or rely on the PATH variable, it doesn't see the file.

[Walter Roberson]

It is normal for Terminal to show a different PATH. Some shell initialization file contains commands that are adding additional elements to the PATH, but that initialization file is not being executed for non-interactive shells.

See https://www.mathworks.com/matlabcentral/answers/740062-use-command-line-in-matlab-using-and-zsh-1-command-not-found-is-displayed#comment_1671562 where I show strategies to locate the executable.

Note:

I have a suspicion that /usr/local/bin/airspy_info is a malformed symbolic link. What shows up if you do

!readlink /usr/local/bin/airspy_info

[Michael]

Okay. I now understand that each shell instance is its own process, with potentially a different PATH depending on the initilization file. Thanks.

Here is what I get with the command you asked about.

>> !readlink /usr/local/bin/airspy_info
../Cellar/airspy/1.0.10/bin/airspy_info

I think this is okay because the full path to the executable airspy_info is

/usr/local/Cellar/airspy/1.0.10/bin/airspy_info

[Walter Roberson]

It would be better to replace that link with an absolute link to /usr/local/Cellar/airspy/1.0.10/bin/airspy_info

[Michael]

Okay. Thanks. I didn't make the link. It was created when I installed the package with homebrew. Your solution to the related issue is getting me along without needing to noodle with this link. Thanks so much!