qsubtools is a suite of shell scripts to automate PBS submissions
qsubi automates the submission of creating and activating an interactive node
------------------------------ QSUB INTERACTIVE HELP
---------- PROGRAM == qsubi (qsub interactive)
---------- VERSION == 2.0.3
---------- DATE == 2022_06_24
---------- CONTACT == lee.marshall@vai.org
---------- DESCRIPTION == automates creation of PBS interactive job
---------- PATH == export PATH=\$PATH:/path/to/qsubi/directory
-------------------- COMMANDS
---------- USAGE == qsubs [options]* -s "command"
---------- FLAGS
[ -d | --debug ] == creates job script but does not execute
[ -h | --help ] == help function
---------- OPTIONS
[ -c | --cores <int> ] == number of cores per job 1 to 80, default 1 core
[ -n | --node <node> ] == name of specific node, default any node
[ -N | --name <name> ] == name specific to job, default STDIN
[ -q | --queue <name> ] == specify queue name, default any queue
[ -w | --walltime <int> ] == number of hours per job 1 to 744, default 24 hours
-------------------- EXAMPLES
qsubi
qsubi -c 4 -q shortq
qsubs automates the submission of creating and activating of job submissions. qsubs will automate single and array based submissions as well as linux and R based submissions.
------------------------------ QSUB SUBMITTER HELP
---------- PROGRAM == qsubs (qsub submitter)
---------- VERSION == 2.0.3
---------- DATE == 2022_06_24
---------- CONTACT == lee.marshall@vai.org
---------- DESCRIPTION == automates creation and submission of PBS qsub scripts
---------- PATH == export PATH=\$PATH:/path/to/qsubs/directory
-------------------- COMMANDS
---------- USAGE == qsubs [options]* -s "command"
---------- FLAGS
[ -d | --debug ] == creates job script but does not execute
[ -h | --help ] == help function
[ --no_info ] == suppress PBS description info on output scripts
---------- OPTIONS
[ -a | --array <file> ] == file containing column of sample names for array,
use SAMPLE as variable for sample name in command or script
[ -c | --cores <int> ] == number of cores per job 1 to 80, default 1 core
[ -n | --name <name> ] == name specific to job, default user name and date
[ -q | --queue <name> ] == specify queue name, default any queue
[ -r | --rscript <"command"> or <file> ] == command enclosed in double quotes or script file
[ -s | --script <"command"> or <file> ] == command enclosed in double quotes or script file
[ --script_args <args> ] == positional arguments passed to your bash script file
[ -u | --umask <umask>] == umask value, default 0022 (group read)
[ -w | --walltime <int> ] == number of hours per job 1 to 744, default 24 hours
-------------------- MULTIPLE COMMANDS
---------- USAGE == contain multiple commands with double quotes,
with each command on separate line, see example
---------- COMMAND VARIABLES == must start with a backslash \$1
-------------------- EXAMPLES
touch sample_data.txt
qsubs -n gzip_file -s "gzip sample_data.txt"
touch sample1_data.txt
touch sample2_data.txt
echo sample1 > sample_names
echo sample2 >> sample_names
qsubs -n zip_command -a sample_names -s "zip SAMPLE_data.zip SAMPLE_data.txt"
echo "zip SAMPLE_data.zip SAMPLE_data.txt" > sample_script
qsubs -n zip_script -a sample_names -s sample_script -d