I need to execute a program using php, the file in question is ClustalW (clustalw2). My apache user is http using fish shell, so I moved clustalw2 to
/srv/http/Clustal and added the dir to fish path.
If I log in into http using terminal and run
clustalw2 -INFILE=input_file -OUTFILE=output_file everything works as expected.
But every time I run
shell_exec('clustalw2 -INFILE=input_file -OUTFILE=output_file'); nothing happens and I get this error log:
sh: line 1: clustalw2: command not found
If I run:
<?php echo "USER: ".shell_exec('whoami')."<br>"; echo "SHELL: ".shell_exec('echo "$SHELL"')."<br>"; echo "WHICH clustalw2: ".shell_exec('which clustalw2');
If I run
which clustalw2 in terminal using http user: