tamanna Posted September 2, 2013 Share Posted September 2, 2013 I have a PHP script within which I have embedded a Perl program using system command. The Perl program is as under; <code> #!/usr/bin/perlsystem("perl /opt/lampp/htdocs/matepred/blast/bin/scriptforblastcompleterun.pl sequence.txt uniprot_sprot.fasta > out");system("perl /opt/lampp/htdocs/matepred/blast/bin/convert.pl");system("perl /opt/lampp/htdocs/matepred/blast/bin/format.pl > output");system("/opt/lampp/htdocs/matepred/blast/bin/svm-predict output pssm.scale.model pssm.predict >pssm.out"); <code> The first four commands of this program run correctly, but the last one does not run. This one contains an executable named "svm-predict". I guess this is because I need to grant special permissions to the PHP user for running executables. Please suggest. Quote Link to comment https://forums.phpfreaks.com/topic/281771-executable-not-running-in-php-script/ Share on other sites More sharing options...
requinix Posted September 2, 2013 Share Posted September 2, 2013 Are you sure svm-predict is marked as executable? Any warnings? Is pssm.out created? Quote Link to comment https://forums.phpfreaks.com/topic/281771-executable-not-running-in-php-script/#findComment-1447771 Share on other sites More sharing options...
tamanna Posted September 3, 2013 Author Share Posted September 3, 2013 Yes svm-predict is an executable. pssmout is created but it is an empty file. Quote Link to comment https://forums.phpfreaks.com/topic/281771-executable-not-running-in-php-script/#findComment-1447936 Share on other sites More sharing options...
requinix Posted September 3, 2013 Share Posted September 3, 2013 Then it looks like the shell is executing correctly. Try redirecting stdout someplace in case there are errors. system("/opt/lampp/htdocs/matepred/blast/bin/svm-predict output pssm.scale.model pssm.predict >pssm.out 2>pssm.err"); Quote Link to comment https://forums.phpfreaks.com/topic/281771-executable-not-running-in-php-script/#findComment-1447942 Share on other sites More sharing options...
tamanna Posted September 4, 2013 Author Share Posted September 4, 2013 Thanks!!! It works for me. Quote Link to comment https://forums.phpfreaks.com/topic/281771-executable-not-running-in-php-script/#findComment-1448075 Share on other sites More sharing options...
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