From a3a6ca1c9850920ab68a0a9c73100bf64b0bfb0a Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Tue, 10 Sep 2024 13:13:54 -0400 Subject: [PATCH] refactor: use jobby & spooker from CCBR/Tools they are added to the path when ccbrpipeliner/7 is loaded --- workflow/Snakefile | 6 +- workflow/scripts/_jobby.py | 726 ------------------- workflow/scripts/_run_jobby_on_snakemake_log | 13 - workflow/scripts/_spooker | 98 --- 4 files changed, 2 insertions(+), 841 deletions(-) delete mode 100644 workflow/scripts/_jobby.py delete mode 100644 workflow/scripts/_run_jobby_on_snakemake_log delete mode 100644 workflow/scripts/_spooker diff --git a/workflow/Snakefile b/workflow/Snakefile index 75232e7..eef0478 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -256,10 +256,8 @@ rule all: unpack(get_enrichment) # create jobby tables -## command for jobby: bash scripts/_run_jobby_on_snakemake_log logs/snakemake.log _jobby.py | tee logs/snakemake.log.jobby | cut -f2,3,18 > logs/snakemake.log.jobby.short -## command for spooker: bash scripts/_spooker /data/sevillas2/carlisle/spook1 | tee logs/spooker.log -jobby_cmd = "bash " + join(SCRIPTSDIR, '_run_jobby_on_snakemake_log') + " " + join('logs', 'snakemake.log') + " " + join(SCRIPTSDIR, '_jobby.py') + " | tee " + join('logs', 'snakemake.log.jobby') + " | cut -f2,3,18 > " + join('logs', 'snakemake.log.jobby.short') -spook_cmd = "bash " + join(SCRIPTSDIR, '_spooker') + " " + WORKDIR + " | tee " + join('logs', 'spooker.log') +jobby_cmd = 'run_jobby_on_snakemake_log logs/snakemake.log | tee logs/snakemake.log.jobby | cut -f2,3,18 > logs/snakemake.log.jobby.short' +spook_cmd = f'spooker {WORKDIR} CARLISLE' onsuccess: print("OnSuccess") diff --git a/workflow/scripts/_jobby.py b/workflow/scripts/_jobby.py deleted file mode 100644 index 747183e..0000000 --- a/workflow/scripts/_jobby.py +++ /dev/null @@ -1,726 +0,0 @@ -#!/usr/bin/env python3 -# Thanks @skchronicles -# source: https://raw.githubusercontent.com/OpenOmics/mr-seek/2ecbbb2628b7102bf2cc23bc946858de2e09929f/workflow/scripts/jobby -# -*- coding: UTF-8 -*- - -""" -ABOUT: - `jobby` will take your past jobs and display their job information. - Why? We have pipelines running on several different clusters and - job schedulers. `jobby` is an attempt to centralize and abstract - the process of querying different job schedulers. On each supported - target system, `jobby` will attempt to determine the best method for - getting job information to return to the user in a standardized - format and unified cli. - -REQUIRES: - - python>=3.5 - -DISCLAIMER: - PUBLIC DOMAIN NOTICE - NIAID Collaborative Bioinformatics Resource (NCBR) - - National Institute of Allergy and Infectious Diseases (NIAID) - This software/database is a "United States Government Work" under - the terms of the United States Copyright Act. It was written as - part of the author's official duties as a United States Government - employee and thus cannot be copyrighted. This software is freely - available to the public for use. - - Although all reasonable efforts have been taken to ensure the - accuracy and reliability of the software and data, NCBR do not and - cannot warrant the performance or results that may be obtained by - using this software or data. NCBR and NIH disclaim all warranties, - express or implied, including warranties of performance, - merchantability or fitness for any particular purpose. - - Please cite the author and NIH resources like the "Biowulf Cluster" - in any work or product based on this material. - -USAGE: - $ jobby [OPTIONS] JOB_ID [JOB_ID ...] - -EXAMPLE: - $ jobby 18627545 15627516 58627597 -""" - -# Python standard library -from __future__ import print_function, division -import sys, os, subprocess, math, re -from subprocess import PIPE -import argparse # added in python/3.5 -import textwrap # added in python/3.5 -import tempfile # added in python/3.5 - -# Jobby metadata -__version__ = "v0.2.0" -__authors__ = "Skyler Kuhn" -__email__ = "skyler.kuhn@nih.gov" -__home__ = os.path.dirname(os.path.abspath(__file__)) -_name = os.path.basename(sys.argv[0]) -_description = "Will take your job(s)... and display their information!" - - -# Classes -class Colors: - """Class encoding for ANSI escape sequeces for styling terminal text. - Any string that is formatting with these styles must be terminated with - the escape sequence, i.e. `Colors.end`. - """ - - # Escape sequence - end = "\33[0m" - # Formatting options - bold = "\33[1m" - italic = "\33[3m" - url = "\33[4m" - blink = "\33[5m" - higlighted = "\33[7m" - # Text Colors - black = "\33[30m" - red = "\33[31m" - green = "\33[32m" - yellow = "\33[33m" - blue = "\33[34m" - pink = "\33[35m" - cyan = "\33[96m" - white = "\33[37m" - # Background fill colors - bg_black = "\33[40m" - bg_red = "\33[41m" - bg_green = "\33[42m" - bg_yellow = "\33[43m" - bg_blue = "\33[44m" - bg_pink = "\33[45m" - bg_cyan = "\33[46m" - bg_white = "\33[47m" - - -# Helper Functions -def which(cmd, path=None): - """Checks if an executable is in $PATH - @param cmd : - Name of executable to check - @param path : - Optional list of PATHs to check [default: $PATH] - @return : - True if exe in PATH, False if not in PATH - """ - if path is None: - path = os.environ["PATH"].split(os.pathsep) - - for prefix in path: - filename = os.path.join(prefix, cmd) - executable = os.access(filename, os.X_OK) - is_not_directory = os.path.isfile(filename) - if executable and is_not_directory: - return True - - return False - - -def err(*message, **kwargs): - """Prints any provided args to standard error. - kwargs can be provided to modify print functions - behavior. - @param message : - Values printed to standard error - @params kwargs - Key words to modify print function behavior - """ - print(*message, file=sys.stderr, **kwargs) - - -def fatal(*message, **kwargs): - """Prints any provided args to standard error - and exits with an exit code of 1. - @param message : - Values printed to standard error - @params kwargs - Key words to modify print function behavior - """ - err(*message, **kwargs) - sys.exit(1) - - -def get_toolkit(tool_list): - """Finds the best suited tool from a list of - possible choices. Assumes tool list is already - ordered from the best to worst choice. The first - tool found in a user's $PATH is returned. - @param tool_list list[]: - List of ordered tools to find - @returns best_choice : - First tool found in tool_list - """ - best_choice = None - for exe in tool_list: - if which(exe): - best_choice = exe - break - - # Did not find any tools - # to potentially use - if not best_choice: - err("Error: Did not find any tools to get job information!") - fatal( - "Expected one of the following tools to be in $PATH:" - "\t{0}".format(tool_list) - ) - - return best_choice - - -def add_missing(linelist, insertion_dict): - """Adds missing information to a list. This can be used - to add missing job information fields to the results of - job querying tool. - @param linelist list[]: - List containing job information for each field of interest - @param insertion_dict dict[] = str - Dictionary used to insert missing information to a given - index, where the keys are indices of the `linelist` and the - values are information to add. Please note that the indices - should be zero based. Note that multiple consequetive values - should be inserted at once as a list, see example below: - Example: - add_missing([0,1,2,3,4], {3:['+','++'], 1:'-', 4:'@'}) - >> [0, '-', 1, 2, '+', '++', 3, '@', 4] - """ - # Get the order of indices - # add missing information - # starting from largest to - # smallest, if we insert - # missing values in this - # order we do not need to - # calculate the offset of - # new indices - tmp_list = linelist - indices = sorted(list(insertion_dict.keys()), reverse=True) - for i in indices: - # Check if multiple values - # need to be inserted at a - # given index - if isinstance(insertion_dict[i], list): - for v in reversed(insertion_dict[i]): - tmp_list.insert(i, v) - else: - tmp_list.insert(i, insertion_dict[i]) - return tmp_list - - -def convert_size(size_bytes): - """Converts bytes to a human readable format.""" - # Sizes range from B to YiB, - # warning larger sizes storage - # may results in blackhole - size_name = ("B", "KiB", "MiB", "GiB", "TiB", "PiB", "EiB", "ZiB", "YiB") - if size_bytes == 0: - return "0B" - i = int(math.floor(math.log(size_bytes, 1024))) - p = math.pow(1024, i) - s = round(size_bytes / p, 2) - return "{0}{1}".format(s, size_name[i]) - - -def to_bytes(size): - """Convert a human readable size unit into bytes. - Returns None if cannot convert/parse provided size.""" - size2bytes = { - "b": 1, - "bytes": 1, - "byte": 1, - "k": 1024, - "kib": 1024, - "kb": 1000, - "m": 1024**2, - "mib": 1024**2, - "mb": 1000**2, - "g": 1024**3, - "gib": 1024**3, - "gb": 1000**3, - "t": 1024**4, - "tib": 1024**4, - "tb": 1000**4, - "p": 1024**5, - "pib": 1024**5, - "pb": 1000**5, - "e": 1024**6, - "eib": 1024**6, - "eb": 1000**6, - "z": 1024**7, - "zib": 1024**7, - "zb": 1000**7, - "y": 1024**8, - "yib": 1024**8, - "yb": 1000**8, - } - - size = size.replace(" ", "") - match = re.search("(?P[0-9.]+)(?P[a-zA-Z]+)$", size) - - if match: - human_units = match.group("units").lower() - human_units = human_units.lstrip().rstrip() - scaling_factor = size2bytes[human_units] - bytes = int(math.ceil(scaling_factor * float(match.group("size")))) - else: - # Cannot parse units, - # cannot convert value - # into bytes - return None - - return bytes - - -# Core logic for getting -# job information -def sge(jobs, threads, tmp_dir): - """Displays SGE job information to standard output. - @param sub_args : - Parsed command-line arguments - @return None - """ - # NOTE: add later for SGE cluster - pass - - -def uge(jobs, threads, tmp_dir): - """Displays UGE job information to standard output. - @param sub_args : - Parsed command-line arguments - @return None - """ - # NOTE: add later for LOCUS cluster - pass - - -def dashboard_cli(jobs, threads=1, tmp_dir=None): - """Biowulf-specific tool to get SLURM job information. - HPC staff recommend using this over the default slurm - `sacct` command for performance reasons. By default, - the `dashboard_cli` returns information for the following - fields: - jobid state submit_time partition nodes - cpus mem timelimit gres dependency - queued_time state_reason start_time elapsed_time end_time - cpu_max mem_max eval - Runs command: - $ dashboard_cli jobs \\ - --joblist 12345679,12345680 \\ - --fields FIELD,FIELD,FIELD \\ - --tab --archive - """ - fields = [ - "jobid", - "jobname", - "state", - "partition", - "gres", - "cpus", - "mem", - "cpu_max", - "mem_max", - "timelimit", - "queued_time", - "start_time", - "end_time", - "elapsed_time", - "nodelist", - "user", - "std_out", - "std_err", - "work_dir", - ] - - # Display header information, - # --tab option does not print - # the header - print("\t".join(fields)) - # Display job information - cmd = subprocess.run( - "dashboard_cli jobs --archive --tab --joblist {0} --fields {1}".format( - ",".join(jobs), ",".join(fields) - ), - stdout=PIPE, - stderr=PIPE, - universal_newlines=True, - shell=True, - ) - - # Check for failure - # of the last command - if cmd.returncode != 0: - err("\nError: Failed to get job information with 'dashboard_cli'!") - err("Please see error message below:") - fatal(" └── ", cmd.stderr) - - print(cmd.stdout.rstrip("\n")) - - -def sacct(jobs, threads=1, tmp_dir=None): - """Generic tool to get SLURM job information. - `sacct` should be available on all SLURM clusters. - The `dashboard_cli` is prioritized over using `sacct` - due to perform reasons; however, this method will be - portable across different SLURM clusters. To get maximum - memory usage for a job, we will need to parse the MaxRSS - field from the `$SLURM_JOBID.batch` lines. - Returns job information for the following fields: - jobid jobname state partition reqtres - alloccpus reqmem maxrss timelimit reserved - start end elapsed nodelist user - workdir - To get maximum memory usage for a job, we will need to parse - the MaxRSS fields from the `$SLURM_JOBID.batch` lines. - Runs command: - $ sacct -j 12345679,12345680 \\ - --fields FIELD,FIELD,FIELD \\ - -P --delimiter $'\t' - """ - header = [ - "jobid", - "jobname", - "state", - "partition", - "gres", - "cpus", - "mem", - "cpu_max", - "mem_max", - "timelimit", - "queued_time", - "start_time", - "end_time", - "elapsed_time", - "nodelist", - "user", - "std_out", - "std_err", - "work_dir", - ] - fields = [ - "jobid", - "jobname", - "state", - "partition", - "reqtres", - "alloccpus", - "reqmem", - "maxrss", - "timelimit", - "reserved", - "start", - "end", - "elapsed", - "nodelist", - "user", - "workdir", - ] - - # Missing std_out and std_err - missing_fields = {15: ["-", "-"]} - # Display header information, - print("\t".join(header)) - # Display job information - cmd = subprocess.run( - "sacct -j {0} -P --delimiter $'\\t' --format={1}".format( - ",".join(jobs), ",".join(fields) - ), - stdout=PIPE, - stderr=PIPE, - universal_newlines=True, - shell=True, - ) - - # Check for failure - # of the last command - if cmd.returncode != 0: - err("\nError: Failed to get job information with 'dashboard_cli'!") - err("Please see error message below:") - fatal(" └── ", cmd.stderr) - - # Get max memory information, - # Stored as $SLURM_JOBID.batch - # in the MaxRSS field - j2m = {} - # Remove trailing newline from - # standard output and split lines - # on remaining newline characters - job_information = cmd.stdout.rstrip("\n").split("\n") - for i, line in enumerate(job_information): - if i < 1: - # skip over header - continue - linelist = line.lstrip().rstrip().split("\t") - if linelist[0].endswith(".batch"): - jobid = linelist[0].strip().split(".")[0] - maxmem = linelist[7].replace(" ", "") - mem_bytes = to_bytes(maxmem) - if not mem_bytes: - # Could not convert - # max_mem value into - # bytes - j2m[jobid] = "-" - continue # goto next line - - human_readable_mem = convert_size(mem_bytes) - j2m[jobid] = human_readable_mem - - # Display the results - for i, line in enumerate(job_information): - if i < 1: - # skip over header - continue - linelist = line.lstrip().rstrip().split("\t") - jobid = linelist[0].strip() - if "." not in jobid: - try: - max_mem = j2m[jobid] - except KeyError: - # Job maybe still be - # running or in a non- - # completed state. - max_mem = "-" - status = linelist[2].split(" ")[0] - linelist[2] = status - missing_fields[8] = max_mem - linelist = add_missing(linelist, missing_fields) - linelist = [info if info else "-" for info in linelist] - print("\t".join(linelist)) - - -def slurm(jobs, threads, tmp_dir): - """Displays SLURM job information to standard output. - @param sub_args : - Parsed command-line arguments - @return None - """ - # Try to use the following tools in this - # order to get job information! - # [1] `dashboard_cli` is Biowulf-specific - # [2] `sacct` should always be there - tool_priority = ["dashboard_cli", "sacct"] - job_tool = get_toolkit(tool_priority) - # Get information about each job - # must use eval() to make string - # to callable function - eval(job_tool)(jobs=jobs, threads=threads, tmp_dir=tmp_dir) - - -def jobby(args): - """ - Wrapper to each supported job scheduler: slurm, etc. - Each scheduler has a custom handler to most effectively - get and parse job information. - @param sub_args : - Parsed command-line arguments - @return None - """ - # Get command line options - abstract_handler = None - job_ids = args.JOB_ID - scheduler = args.scheduler - threads = args.threads - tmp_dir = args.tmp_dir - - # Set handler for each - # supported scheduler - if scheduler == "slurm": - abstract_handler = slurm - else: - # Unsupported job scheduler, - # needs to be implemented - fatal('Error: "{0}" is an unsupported job scheduler!'.format(scheduler)) - - # Display job(s) information - # to standard output - abstract_handler(jobs=job_ids, threads=threads, tmp_dir=tmp_dir) - - -# Parse command-line arguments -def parsed_arguments(name, description): - """Parses user-provided command-line arguments. This requires - argparse and textwrap packages. To create custom help formatting - a text wrapped docstring is used to create the help message for - required options. As so, the help message for require options - must be suppressed. If a new required argument is added to the - cli, it must be updated in the usage statement docstring below. - @param name : - Name of the pipeline or command-line tool - @param description : - Short description of pipeline or command-line tool - """ - # Add styled name and description - c = Colors - styled_name = "{0}{1}{2}{3}{4}".format(c.bold, c.bg_black, c.cyan, name, c.end) - description = "{0}{1}{2}".format(c.bold, description, c.end) - temp = tempfile.gettempdir() - - # Please note: update the usage statement - # below if a new option is added! - usage_statement = textwrap.dedent( - """\ - {0}: {1} - - {3}{4}Synopsis:{5} - $ {2} [--version] [--help] \\ - [--scheduler {{slurm | ...}}] \\ - [--threads THREADS] [--tmp-dir TMP_DIR] \\ - - - {3}{4}Description:{5} - {2} will take your past jobs and display their job information - in a standardized format. Why???! We have pipelines running on several - different clusters (using different job schedulers). {2} centralizes - and abstracts the process of querying different job schedulers within - a unified command-line interface. - - For each supported scheduler, jobby will determine the best method - on a given target system for getting job information to return to the - user in a common output format. - - {3}{4}Required Positional Arguments:{5} - - Identiers of past jobs. One or more JOB_IDs - can be provided. Multiple JOB_IDs should be - seperated by a space. Information for each - of the JOB_IDs will be displayed to standard - output. Please see example section below for - more information. - - {3}{4}Options:{5} - -s,--scheduler {{slurm | ...}} - @Default: slurm - Job scheduler. Defines the job scheduler - of the target system. Additional support - for more schedulers coming soon! - @Example: --scheduler slurm - -n, --threads THREADS - @Default: 1 - Number of threads to query the scheduler - in parallel. - @Example: --threads: 8 - -t, --tmp-dir TMP_DIR - @Default: {7}/ - Temporary directory. Path on the filesystem - for writing temporary output files. Ideally, - this path should point to a dedicated space - on the filesystem for writing tmp files. If - you need to inject a variable into this path - that should NOT be expanded, please quote the - options value in single quotes. The default - location of this option is set to the system - default via the $TMPDIR environment variable. - @Example: --tmp-dir '/scratch/$USER/' - - -h, --help Shows help and usage information and exits. - @Example: --help - - -v, --version Displays version information and exits. - @Example: --version - """.format( - styled_name, description, name, c.bold, c.url, c.end, c.italic, temp - ) - ) - - # Display example usage in epilog - run_epilog = textwrap.dedent( - """\ - {2}{3}Example:{4} - # Please avoid running jobby - # on a cluster's head node! - ./jobby -s slurm -n 4 18627542 13627516 58627597 48627666 - - {2}{3}Version:{4} - {1} - """.format( - name, __version__, c.bold, c.url, c.end - ) - ) - - # Create a top-level parser - parser = argparse.ArgumentParser( - usage=argparse.SUPPRESS, - formatter_class=argparse.RawDescriptionHelpFormatter, - description=usage_statement, - epilog=run_epilog, - add_help=False, - ) - - # Required Positional Arguments - # List of JOB_IDs, 1 ... N_JOB_IDS - parser.add_argument("JOB_ID", nargs="+", help=argparse.SUPPRESS) - - # Options - # Adding verison information - parser.add_argument( - "-v", - "--version", - action="version", - version="%(prog)s {}".format(__version__), - help=argparse.SUPPRESS, - ) - - # Add custom help message - parser.add_argument("-h", "--help", action="help", help=argparse.SUPPRESS) - - # Base directory to write - # temporary/intermediate files - parser.add_argument( - "-t", - "--tmp-dir", - type=str, - required=False, - default=temp, - help=argparse.SUPPRESS, - ) - - # Number of threads for the - # pipeline's main proceess - # This is only applicable for - # local rules or when running - # in local mode. - parser.add_argument( - "-n", "--threads", type=int, required=False, default=1, help=argparse.SUPPRESS - ) - - # Job scheduler to query, - # available: SLURM, ... - # More coming soon! - parser.add_argument( - "-s", - "--scheduler", - type=lambda s: str(s).lower(), - required=False, - default="slurm", - choices=["slurm"], - help=argparse.SUPPRESS, - ) - - # Define handlers for each sub-parser - parser.set_defaults(func=jobby) - # Parse command-line args - args = parser.parse_args() - - return args - - -def main(): - # Sanity check for usage - if len(sys.argv) == 1: - # Nothing was provided - fatal("Invalid usage: {} [-h] [--version] ...".format(_name)) - - # Collect args for sub-command - args = parsed_arguments(name=_name, description=_description) - - # Display version information - err("{} ({})".format(_name, __version__)) - # Mediator method to call the - # default handler function - args.func(args) - - -if __name__ == "__main__": - main() diff --git a/workflow/scripts/_run_jobby_on_snakemake_log b/workflow/scripts/_run_jobby_on_snakemake_log deleted file mode 100644 index 3ca3356..0000000 --- a/workflow/scripts/_run_jobby_on_snakemake_log +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env bash -# input: -## intake snakemake log -## full path to jobby.py script - -# prep the logs by pulling IDs -snakemakelog=$1 -jobids=$(grep --color=never "^Submitted .* with external jobid" $snakemakelog | awk '{print $NF}' | sed "s/['.]//g" | sort | uniq | tr "\\n" " ") -jobidswc=$(echo $jobids | wc -c) - -# run jobby script -module load python -if [ "$jobidswc" != "1" ];then python $2 $jobids; fi diff --git a/workflow/scripts/_spooker b/workflow/scripts/_spooker deleted file mode 100644 index 3a9a0d1..0000000 --- a/workflow/scripts/_spooker +++ /dev/null @@ -1,98 +0,0 @@ -#!/usr/bin/env bash -# if running on Biowulf -# create a zip of essential files like dryrun and tree -# use spook to push the file to secret location on /scratch -# -# This scripts is created using _zip_tar_copy script from permfix as template -# - -set -o pipefail -PIPELINE_OUTDIR=$1 - -SCONTROL=$(type -P scontrol) -if [[ "$SCONTROL" == "" ]];then - echo "scontrol not in PATH!" - exit -fi - -nbiowulf=$(scontrol show config | grep -i -c biowulf) -if [[ "$nbiowulf" > 0 ]];then ISBIOWULF=true; else ISBIOWULF=false;fi -nfrce=$(scontrol show config | grep -i -c fsitgl) -if [[ "$nfrce" > 0 ]];then ISFRCE=true; else ISFRCE=false;fi - -if [[ $ISBIOWULF == true || $ISFRCE == true ]];then - if [[ $ISBIOWULF == true ]];then - SPOOK=$(type -P spook) - if [[ "$SPOOK" == "" ]];then - echo "spook is not in PATH." - echo "... trying to add it." - # setup SPACESAVERS2DIR PERMFIXDIR PATHs etc. - . "/data/CCBR_Pipeliner/cronjobs/scripts/setup" - SPOOK=$(type -P spook) - if [[ "$SPOOK" == "" ]];then - echo "spook is still not in PATH!" - exit - fi - fi - echo "spook is now in PATH:$SPOOK" - SPOOK_COPY2DIR="/scratch/ccbrpipeliner" - fi - if [[ $ISFRCE == true ]];then - SPOOK_COPY2DIR="/mnt/projects/CCBR-Pipelines/pipelines/userdata/ccbrpipeliner" - fi - - DT=$(date +%y%m%d%H%M%S) - archivefile="${HOME}/${USER}.${DT}.tar" - treefile="${HOME}/${USER}.${DT}.tree" - - dryrunlogfile="" - if [[ -d "$PIPELINE_OUTDIR" ]];then - dryrunlogfile=$(ls -rt ${PIPELINE_OUTDIR}/dryrun*log 2>/dev/null |tail -n1 || echo "") - cmd="tar cvf ${archivefile}" - if [[ "$dryrunlogfile" != "" ]];then - cmd="$cmd $dryrunlogfile" - fi - # gather some info - echo "PIPELINE_OUTDIR:$PIPELINE_OUTDIR" > $treefile - echo "USER:$USER" >> $treefile - #GROUPS=$(groups 2>/dev/null) - echo "GROUPS:" $(groups) >> $treefile - CARLISLE=$(which CARLISLE) - echo "CARLISLE:$CARLISLE" >> $treefile - echo "DATE:$DT" >> $treefile - tree $PIPELINE_OUTDIR >> $treefile - cmd="$cmd $treefile" - - if [[ -d "${PIPELINE_OUTDIR}/logs" ]];then - logdir="${PIPELINE_OUTDIR}/logs" - for thisfile in "snakemake.log" "snakemake.log.jobby" "master.log" "runtime_statistics.json";do - absthisfile="${logdir}/${thisfile}" - if [[ -f "$absthisfile" ]];then - cmd="$cmd $absthisfile" - fi - done - fi - - echo $cmd - $cmd - - # copy over the archive to secrete location and delete it - if [ -f "${archivefile}" ];then - gzip -f $archivefile - if [[ $ISBIOWULF == true ]]; then - cmd="$SPOOK -f ${archivefile}.gz -d $SPOOK_COPY2DIR" - echo $cmd - $cmd - fi - if [[ $ISFRCE == true ]];then - cmd="cp -rv ${archivefile}.gz $SPOOK_COPY2DIR" - echo $cmd - $cmd - fi - rm -f ${archivefile}.gz $treefile - fi - fi - -else # not biowulf or frce ... so exit - exit 0 -fi