Setup SMRTLink Dev ENV

setup-smrtlink-env-410.sh

#!/bin/env bash

#set -o
# This is the new >= 4.1.0 config setup

source /mnt/software/Modules/current/init/bash
module load jq
module load jdk/1.8.0_71

# Sets up SMRT Link System ENV

default="smrtlink-bihourly"

export PB_SYSTEM=${1:-"$default"}

export PB_SMRT_ROOT=/pbi/dept/secondary/siv/smrtlink/${PB_SYSTEM}/smrtsuite
export PB_USER_DATA=${PB_SMRT_ROOT}/userdata
export PB_SLAG_ROOT=${PB_SMRT_ROOT}/current/bundles/smrtlink-analysisservices-gui/current/private/pacbio/smrtlink-analysisservices-gui
export PB_CONFIG_JSON=${PB_USER_DATA}/config/smrtlink-system-config.json

# This are useful for pbservice to not have to explicitly pass --port and --host
export PB_SERVICE_HOST=$(cat ${PB_CONFIG_JSON} | jq --raw-output ' .smrtflow.server.dnsName')
export PB_SERVICE_PORT=$(cat ${PB_CONFIG_JSON} | jq --raw-output ' .smrtflow.server.port')
export PB_SERVICE_LOG_DIR=$(cat ${PB_CONFIG_JSON} | jq --raw-output '.pacBioSystem.logDir')

function smrtlink_server_log() {
  echo ${PB_SERVICE_LOG_DIR}/secondary-smrt-server.log
}

function smrtlink_server_summary() {
  echo "SMRT Link Config Summary"
  echo "System             ${PB_SYSTEM}"
  echo "Server Config.json ${PB_CONFIG_JSON}"
  echo "Jobs root          ${PB_JOB_ROOT}"
  echo ""
  python -m json.tool ${PB_CONFIG_JSON}
}

# Customized the PATH to have extra exes in the PATH
# - server admin for get-status
# - smrtcmds/bin
# - Add all other tools
# - Admin (to start, stop, get status)

export PATH=${PB_SMRT_ROOT}/smrtcmds/bin:${PB_SMRT_ROOT}/current/bundles/smrttools/current/private/otherbins/all/bin:${PB_SMRT_ROOT}/current/admin/bin:${PB_SLAG_ROOT}/bin:${PB_SLAG_ROOT}/tools/bin:$PATH

smrtlink_server_summary

setup-smrtlink-env.sh

#!/bin/env bash

#set -o

source /mnt/software/Modules/current/init/bash
module load jq

# Sets up SMRT Link System ENV

default="smrtlink-beta"

export PB_SYSTEM=${1:-"$default"}

export PB_SMRT_ROOT=/pbi/dept/secondary/siv/smrtlink/${PB_SYSTEM}/smrtsuite
export PB_USER_DATA=${PB_SMRT_ROOT}/userdata
export PB_CONFIG_JSON=${PB_USER_DATA}/config/config.json

# This are useful for pbservice to not have to explicitly pass --port and --host
export PB_SERVICE_HOST=$(cat ${PB_CONFIG_JSON} | jq --raw-output ' .HOST')
export PB_SERVICE_PORT=$(cat ${PB_CONFIG_JSON} | jq --raw-output ' .PB_SERVICES_ANALYSIS_PORT')


function smrtlink_server_log() {
  local logDir=$(cat ${PB_CONFIG_JSON} | jq --raw-output ' .PB_LOG_DIR')
  echo ${logDir}/secondary-smrt-server.log
}

function smrtlink_server_summary() {
  echo "SMRT Link Config Summary"
  echo "System             ${PB_SYSTEM}"
  echo "Server Config.json ${PB_CONFIG_JSON}"
  echo "Jobs root          ${PB_JOB_ROOT}"
  echo ""
  python -m json.tool ${PB_CONFIG_JSON}
}

# Customized the PATH to have extra exes in the PATH
# - server admin for get-status
# - smrtcmds/bin
# - Add all other tools
# - Admin (to start, stop, get status)
export PATH=${PB_SMRT_ROOT}/smrtcmds/bin:${PB_SMRT_ROOT}/current/bundles/smrttools/current/private/otherbins/all/bin:${PB_SMRT_ROOT}/current/admin/bin:$PATH