d94f19ab9f
Standard kent userapps commands are installed under ${PREFIX}/userapps
because of multiple conflicts. The kent command turns the standard
commands into subcommands, so no special PATH is needed.
/usr/local/ucsc-userapps/bin/bigWigToBedGraph [args]
can be run as
kent bigWigToBedGraph [args]
59 lines
1.8 KiB
C
59 lines
1.8 KiB
C
/***************************************************************************
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* Description:
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* Wrapper to turn ucsc kent commands into subcommands. The kent suite
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* contains executables that conflict with multiple other software
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* packages and therefore cannot be safely installed directly under a
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* standard prefix. This wrapper can be installed under the standard
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* PATH and used to to execute kent commands installed under a
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* private prefix, without altering PATH, activating a special
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* environment, opening a container, etc. This sub-command paradigm
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* is already familiar to bioinformaticians thanks to other suites
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* like samtools, bedtools, etc.
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*
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* Example:
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*
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* kent bigWigToBedGraph args
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*
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* instead of one of the following:
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*
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* prefix/bin/bigWigToBedGraph args
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*
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* env PATH=prefix/bin:$PATH bigWigToBedGraph args
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*
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* conda activate kent
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* bigWigToBedGraph args
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*
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* Arguments:
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* The full kent utils command you would use if it were in PATH.
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*
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* Compile with UCSC_PREFIX set to the parent of the bin directory
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* containing the kent binaries.
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*
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* History:
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* Date Name Modification
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* 2021-09-13 Jason Bacon Begin
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***************************************************************************/
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#include <stdio.h>
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#include <sysexits.h>
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#include <limits.h>
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#include <unistd.h>
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#ifndef UCSC_PREFIX
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#define UCSC_PREFIX "/usr/local/userapps"
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#endif
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int main(int argc,char *argv[])
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{
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char cmd[PATH_MAX + 1];
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if ( argc < 2 )
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{
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fprintf(stderr, "Usage: %s UCSC-userapps-command [args]\n", argv[0]);
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return EX_USAGE;
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}
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snprintf(cmd, PATH_MAX, "%s/bin/%s", UCSC_PREFIX, argv[1]);
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execv(cmd, argv + 1);
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}
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