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Assigns.sptool
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#!/bin/csh -f
#
#=================================================================================================
#===== =====
#===== Speciation Tool Version 4.5 Sep 2017 =====
#===== =====
#===== Description: =====
#===== This Assigns file defines the environment variables used by the Speciation Tool. =====
#===== =====
#===== Usage: =====
#===== source <AssignFile> =====
#===== =====
#=================================================================================================
#
# <SYSTEM INSTALLATION DEPENDENT>
# <PostgreSQL>
#
# In order to access PostgreSQL you may need to set a pathname, username, and/or password.
# This is installation dependent. If you have database connection errors when running
# the Speciation Tool see your system administrator for access to postgreSQL.
#
# POSTGRES_BIN can be set to override the default. The result of "which psql" will be used if
# the environment variable is not set.
# setenv POSTGRES_BIN /usr/local/pgsql # directory of postgreSQL execuatable
# LD_LIBRARY_PATH may be required if PosrgreSQL is not installed in your path.
# setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:fullpath_name
# SPTOOL_USER is the PostreSQL user name. This can be set to override the default.
# The results of "whoami" will be used if the environment variable is not set.
# (Not needed for a typical installation).
# setenv SPTOOL_USER userName # Postgres user name
# SPTOOL_PWD can be set if your PostgreSQL installation is password protected.
# Only set if required on your system.
# setenv SPTOOL_PWD dbPWD # PostgreSQL password
#<Perl>
#
# PERL_BIN can be set to override the default. The directory of "which perl" will be used if
# the environment variable is not set. (Not needed for a typical installation).
# setenv PERL_BIN /usr/bin # directory of Perl executable
# PERL_DBI must be set. This is the Perl database interface and is system dependent.
# Typical Postgres options include "PgPP" or "Pg" (case sensitive).
setenv PERL_DBI Pg # Perl/Postgres interface must be set !!!!!
#=================================================================================================
# <Speciation Tool INSTALLATION DEPENDENT>
#
# SPTOOL_HOME must be set to the location of the Speciation Tool home directory. This is the
# full pathname of where the Speciation Tool will be installed.
# (The directory where init_sptooldb_v3.2.csh resides).
setenv SPTOOL_HOME /opt/sptool # Speciation Tool top level directory
setenv SPTOOL_SRC_HOME $SPTOOL_HOME/src # Speciation Tool source code directory
setenv SPTOOL_DB sptoolv5_1 # Speciation Tool Database name
# <Speciation Tool 'shared' schema input directory and default data files>
#
setenv IDIR $SPTOOL_HOME/import_data # input data directory
#
setenv MECHANISM $IDIR/mechanism_forImport_11Feb2020_speciate5_0_withSOAALK_13mar2020_v0.csv
setenv MECHANISMPM $IDIR/mech_pm_ae5_ae6_ae8.txt
setenv MECHANISM_DESCRIPTION $IDIR/sptool_mechanism_description_speciate5_0_04mar2020_v0.csv
setenv CARBONS $IDIR/carbons_all_mechanisms_speciate5_0_04mar2020_v0.csv
setenv INVTABLE $IDIR/invtable_hapcap_cb05soa_25may2011_v13.txt
setenv PROFILES_STATIC $IDIR/static_19aug07.csv
setenv SPECIES_RENAME $IDIR/aqm_poll_rename.csv
setenv CAMX_FCRS $IDIR/camx_fcrs.profile.lst
setenv VBS_SVOC_FACTORS $IDIR/vbs_svoc.profile.26sep2016.csv
setenv VBS_IVOC_FACTORS $IDIR/vbs_ivoc.profile.30aug2016.csv
setenv IVOC_SPECIES $IDIR/ivoc_species.csv
setenv O2M_RATIOS $IDIR/oxygen_metal_Ratios.csv # added Sep 2018
# updated with SPECIATE 5.1
setenv PROFILES_RAW $IDIR/speciate5.1_exports/export_profiles.txt
setenv WEIGHTS_RAW $IDIR/speciate5.1_exports/export_species.txt
setenv SPECIES_PROPERTIES_RAW $IDIR/speciate5.1_exports/export_species_properties.txt