Cannot run system commands from matlab macOS catalina; zsh:1: command not found: blastp
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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?
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Ameer Hamza
le 30 Nov 2020
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
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Walter Roberson
le 4 Août 2021
It would be better to replace that link with an absolute link to /usr/local/Cellar/airspy/1.0.10/bin/airspy_info
Michael
le 4 Août 2021
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!
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