12-16-2019
The id contains the unique prefix of each bam, so the
s1,s2,s3,s4.
I am trying to insert each of those into the command in post 3. That is make the command dependent or conditional on id. So if there are 4 id then there are 4
--bam ${id} \ inserted and if there are 7 id then 7
--bam ${id} \ inserted in the command. There may be a better way that I am not thinking of. Thank you
.
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LEARN ABOUT REDHAT
system
SYSTEM(3) Linux Programmer's Manual SYSTEM(3)
NAME
system - execute a shell command
SYNOPSIS
#include <stdlib.h>
int system(const char *string);
DESCRIPTION
system() executes a command specified in string by calling /bin/sh -c string, and returns after the command has been completed. During
execution of the command, SIGCHLD will be blocked, and SIGINT and SIGQUIT will be ignored.
RETURN VALUE
The value returned is -1 on error (e.g. fork failed), and the return status of the command otherwise. This latter return status is in the
format specified in wait(2). Thus, the exit code of the command will be WEXITSTATUS(status). In case /bin/sh could not be executed, the
exit status will be that of a command that does exit(127).
If the value of string is NULL, system() returns nonzero if the shell is available, and zero if not.
system() does not affect the wait status of any other children.
CONFORMING TO
ANSI C, POSIX.2, BSD 4.3
NOTES
As mentioned, system() ignores SIGINT and SIGQUIT. This may make programs that call it from a loop uninterruptable, unless they take care
themselves to check the exit status of the child. E.g.
while(something) {
int ret = system("foo");
if (WIFSIGNALED(ret) &&
(WTERMSIG(ret) == SIGINT || WTERMSIG(ret) == SIGQUIT))
break;
}
Do not use system() from a program with suid or sgid privileges, because strange values for some environment variables might be used to
subvert system integrity. Use the exec(3) family of functions instead, but not execlp(3) or execvp(3). system() will not, in fact, work
properly from programs with suid or sgid privileges on systems on which /bin/sh is bash version 2, since bash 2 drops privileges on
startup. (Debian uses a modified bash which does not do this when invoked as sh.)
The check for the availability of /bin/sh is not actually performed; it is always assumed to be available. ISO C specifies the check, but
POSIX.2 specifies that the return shall always be non-zero, since a system without the shell is not conforming, and it is this that is
implemented.
It is possible for the shell command to return 127, so that code is not a sure indication that the execve() call failed.
SEE ALSO
sh(1), signal(2), wait(2), exec(3)
2001-09-23 SYSTEM(3)