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/***************************************************************************
* Description:
* Wrapper to turn emboss commands into subcommands. The emboss suite
* contains executables that conflict with multiple other software
* packages and therefore cannot be safely installed directly under a
* standard prefix. This wrapper can be installed under the standard
* PATH and used to to execute emboss commands installed under a
* private prefix, without altering PATH, activating a special
* environment, opening a container, etc. This sub-command paradigm
* is already familiar to bioinformaticians thanks to other suites
* like samtools, bedtools, etc.
*
* Example:
*
* emboss seqret args
*
* instead of one of the following:
*
* prefix/bin/seqret args
*
* env PATH=prefix/bin:$PATH seqret args
*
* conda activate emboss
* seqret args
*
* Arguments:
* The full emboss command you would use if it were in PATH.
*
* Compile with EMBOSS_PREFIX set to the parent of the bin directory
* containing the emboss binaries.
*
* History:
* Date Name Modification
* 2021-09-13 Jason Bacon Begin
***************************************************************************/
#include <stdio.h>
#include <sysexits.h>
#include <limits.h>
#include <unistd.h>
#ifndef EMBOSS_PREFIX
#define EMBOSS_PREFIX "/usr/local/emboss"
#endif
int main(int argc,char *argv[])
{
char cmd[PATH_MAX + 1];
if ( argc < 2 )
{
fprintf(stderr, "Usage: %s emboss-command [args]\n", argv[0]);
return EX_USAGE;
}
snprintf(cmd, PATH_MAX, "%s/bin/%s", EMBOSS_PREFIX, argv[1]);
execv(cmd, argv + 1);
}
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