mheiges

#### required MACRO Substitutions #######
#  %SERVERNAME% - server host name, e.g. adhemar.schistodb.org
    # manually add a ServerAlias if needed, e.g. www.shistodb.org
#  %WEBAPP% - name of Tomcat webapp. e.g. schisto.adhemar
#  %PROJECT% - project name, e.g. SchistoDB
#  %ADMIN_EMAIL% - administrative email for server, e.g. root@schistodb.org
#  %TC_PORT% - Tomcat HTTP port
#  %ORACLE_HOME% - same as $ORACLE_HOME
#  %LD_LIBRARY_PATH% - $ORACLE_HOME/lib plus any other paths as appropriate
##########################################

mheiges

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mheiges

if [ -z "$PS1" ]; then
  # non-interactive shell
  export LSB_DEFAULTPROJECT="810086221_jcklab__10-21-RR374-062"
fi

. /iob_home/jcklab/.bashrc.rcluster

mheiges

#
# bash tab completion functions and assignments for the ApiDB project
#
# $Id: apidb-tab-completion.sh 1314 2009-11-12 22:49:57Z mheiges $

_instance_manager() {
  COMPREPLY=()

  local verbs="manage start stop restart status"
  local man_tasks="start stop reload redeploy undeploy list deploy"

mheiges

10378 ?        S      0:00  \_ /usr/bin/perl /iob_home/jcklab/mheiges/GUS/gus_home/bin/nodeSocketServer.pl rcluster 7901
10380 ?        S      0:00      \_ bash -s
10640 ?        S      0:00          \_ /bin/sh /iob_home/jcklab/mheiges/GUS/gus_home/bin/subtaskInvoker /tmp/170544.1.mri-q64-30d/slot_2 /iob_home/jcklab/mheiges/GUS/gus_home/test/DJob/master/running/subtask_9/result 170544 rcluster 7901 samplecmd /tmp/170544.1.mri-q64-30d/slot_2/inputset hello
10642 ?        S      0:00          |   \_ /usr/bin/perl /iob_home/jcklab/mheiges/GUS/gus_home/bin/samplecmd /tmp/170544.1.mri-q64-30d/slot_2/inputset hello
10649 ?        S      0:00          \_ /bin/sh /iob_home/jcklab/mheiges/GUS/gus_home/bin/subtaskInvoker /tmp/170544.1.mri-q64-30d/slot_4 /iob_home/jcklab/mheiges/GUS/gus_home/test/DJob/master/running/subtask_10/result 170544 rcluster 7901 samplecmd /tmp/170544.1.mri-q64-30d/slot_4/inputset hello
10650 ?        S      0:00          |   \_ /usr/bin/perl /iob_home/jcklab/mheiges/GUS/gus_home/bin/samplecmd /

mheiges

/* Groovy script for Jenkins' puppet-client-manager job
   to trigger downstream execution of puppet clients.
    https://ci.apidb.org/job/puppet-client-manager
*/
import hudson.model.*
import hudson.FilePath
import hudson.FilePath.FileCallable
import hudson.remoting.VirtualChannel
import java.io.OutputStream

mheiges

/**
 Checks the last build status of a sentinel job and if worse than expected,
 aborts the job running this script.
 
 Example usage. Use this script in a pre-scm build step (using pre-scm plugin) for
 qa.eupathdb.org . Configure the qa.eupathdb.org job to use the integrate.eupathdb.org
 job as a sentinel_job. If the last build of integrate.eupathdb.org is worse than 
 expected when a qa.eupathdb.org build is started then abort the qa.eupathdb.org
 build so it doesn't pick up the bad code that failed the sentinel job.
 

mheiges

#!/bin/sh
set -u -e

admin_path=$1;

if [ -d "$admin_path/bin" ]; then
  mv "$admin_path/bin" "$admin_path/bin.bak"
fi

mkdir "$admin_path/bin"

mheiges

#!/usr/bin/perl

# Scrape Oracle JDK web pages for RPM links. Download those RPM files.
# Deletes downloaded files that do not pass rpm checksum (e.g. incomplete downloads).
# Skips downloading files already on the local filesystem.

use strict;

use sigtrap qw(handler exit_handler normal-signals error-signals);

mheiges

#!/bin/sh
set -e

# Usage: workflow-software-sysadmin-init.sh [/path/to/workflow-software]
# were [/path/to/workflow-software] is where to install the sysadmin
# directory. Defaults to $HOME.
#
# This script nitializes and bootstraps the `${wfs_dir}/sysadmin`
# directory with required infrastructure. The end result is an
# environment where the workpuppet script can be run to maintain