Cannot run system commands from matlab macOS catalina; zsh:1: command not found: blastp
45 Ansichten (letzte 30 Tage)
Ältere Kommentare anzeigen
kyllen87
am 30 Nov. 2020
Kommentiert: Michael
am 4 Aug. 2021
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?
0 Kommentare
Akzeptierte Antwort
Ameer Hamza
am 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
9 Kommentare
Walter Roberson
am 4 Aug. 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
am 4 Aug. 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!
Weitere Antworten (0)
Siehe auch
Kategorien
Mehr zu File Operations finden Sie in Help Center und File Exchange
Community Treasure Hunt
Find the treasures in MATLAB Central and discover how the community can help you!
Start Hunting!