Bio::Grid::Run::SGE::Util - Utility functions for Bio::Grid::Run::SGE
use Bio::Grid::Run::SGE::Util qw( my_glob delete_by_regex expand_path my_mkdir concat_files my_glob_non_fatal timer expand_path_rel );
Provides utility functions for the Bio::Grid::Run::SGE module.
See File::Glob::bsd_glob for an explanation of the $pattern. This function is for convenience only and takes care of some quirks of bsd_glob.
$pattern
Same as my_glob, but does not die if glob result is empty.
my_glob
Expands a path to its absoulte equivalent. Taks also care of paths beginning with '~'.
Expands the '~' at the beginning of a path to the home directory.
Creates $path and dies if something goes wrong. See also "mkpath" in File::Path.
$path
Opens $dir and deletes all files that match $file_regex. If simulate is true, then just print the files that would be deleted.
$dir
$file_regex
Concatenates all result files in one file $c-{result_dir}/$c->{job_name}.j${job_id}.result.concat and deletes the single result files. Result files are determined by following regex:
qr/\Q$c->{job_name}\E #job name \.j$c->{job_id} #the job id \.[0-9]+ #the sge task id \.c[\-0-9]+(?:\.[\w\-.#]+)? #combination idx (?:\..*)? #suffix $/x;
If your toolwrapper makes use of it, you can also invoke it by hand. In the working dir of your job run:
~/script/<toolwrapper>.pl -p <job_id> <tmp>/<job_name>.config
TAKE CARE, IT DELETES THE RESULT FILES AND OVERWRITES THE LAST RESULT.CONCAT FILE
Time something. Usage:
# get a timer my $timer = timer(); # start my $start_time = $timer->(); # stop my $stop_time = $timer->(); my ($stop_time, $elapsed_time_as_string) = $timer->();
Bio::Grid::Run::SGE
jw bargsten, <joachim.bargsten at wur.nl>
<joachim.bargsten at wur.nl>
To install Bio::Grid::Run::SGE, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Grid::Run::SGE
CPAN shell
perl -MCPAN -e shell install Bio::Grid::Run::SGE
For more information on module installation, please visit the detailed CPAN module installation guide.