# Fedora 64bit BUSTER version

# csh/tcsh version, ============================================================
# template for file $BDG_home/setup_local.csh that is sourced
# by the normal setup script $BDG_home/setup.csh and should be used
# to setup site specific settings necessary to run Global Phasing Software.
#
# This template should be used to prepare your own $BDG_home/setup_local.csh
# file (either directly or as a softlink). Instructions:
# (a) Use an editor to remove "##### " at the start of the line and edit
#     /location/of/... to the location of the required feature!
# (b) to test your setup_local.csh file works use commands:
#
#   source $BDG_home/setup.csh
#   checkdeps
#
# see $BDG_home/docs/installation/index.html

# imagemagick convert setup ====================================================
# required by buster-report, normally found from PATH
# see $BDG_home/docs/autobuster/manual/autoBUSTER9.html
# convert also used by autoPROC
##### setenv BDG_TOOL_CONVERT /location/of/imagemagick/convert 

# imagemagick identify setup ====================================================
# required by buster-report, normally found from PATH
# see $BDG_home/docs/autobuster/manual/autoBUSTER9.html
##### setenv BDG_TOOL_IDENTIFY /location/of/imagemagick/identify

# ps2pdf setup =================================================================
# required by buster-report, normally found from PATH
# see $BDG_home/docs/autobuster/manual/autoBUSTER9.html
##### setenv BDG_TOOL_PS2PDF /location/of/ps2pdf

# mogul setup ==================================================================
# if mogul not on PATH then set BDG_TOOL_MOGUL to full path of mogul exe or none
# see $BDG_home/docs/autobuster/manual/autoBUSTER9.html 
##### setenv BDG_TOOL_MOGUL /location/of/bin/mogul
# if you have corporate mogul database(s) then set
# BDG_MOGUL_LOCAL_DATABASE_FILE
# to the full path of the instruction file to be used
# see $BDG_home/docs/autobuster/manual/autoBUSTER9.html#mogulAdditionalLibrary
##### setenv BDG_MOGUL_LOCAL_DATABASE_FILE /location/of/corporate.ins

# MolProbity setup =============================================================
# optional for buster-report, required for hydrogenate.
# should be set to the full path of the root directory of the MolProbity 
# installation or none. The root directory contains files:
# "cmdline/reduce-nobuild", "cmdline/multichart" and "lib/hless.jar
##### setenv BDG_TOOL_MOLPROBITY_ROOT /location/of/molprobity/latest

# java for buster-report setup =================================================
# buster-report with MolProbity analysis requires java to work
# normally java should be on the user's PATH but if a different version
# is required by another application then set BDG_TOOL_BUSTERREPORT_JAVA
# to the full path of java executable
# see $BDG_home/docs/autobuster/manual/autoBUSTER9.html 
##### setenv BDG_TOOL_BUSTERREPORT_JAVA /location/of/java

# pymol setup ==================================================================
# if pymol not on PATH then set BDG_TOOL_PYMOL to full path of pymol exe or none
# see $BDG_home/docs/autobuster/manual/autoBUSTER9.html 
##### setenv BDG_TOOL_PYMOL none 

# latex setup ==================================================================
# if pdflatex not on PATH then set BDG_TOOL_PDFLATEX to full path of pdflatex
#                                                          executable or none
# see $BDG_home/docs/autobuster/manual/autoBUSTER9.html 
##### setenv BDG_TOOL_PDFLATEX none 

# curl setup ===================================================================
# grade_PDB_ligand needs curl or wget for full functionality 
# Normally curl used from users PATH but BDG_TOOL_CURL can be set to the full 
#                                                    path of curl exe or none.
# If your site uses a proxy to limit internet access then use 
#  BDG_TOOL_CURL_OPTIONS to supply curl options for downloads (see man curl)
# see $BDG_home/docs/grade/manual/index.html#acknowledgements
##### setenv BDG_TOOL_CURL none # do not use curl
##### setenv BDG_TOOL_CURL_OPTIONS "options" # curl command line options for proxy

# wget setup ===================================================================
# grade_PDB_ligand needs curl or wget for full functionality, if it is 
# impossible to get either to work then set both BDG_TOOL_CURL and BDG_TOOL_WGET
# to none and users will be prompted to manually download the files needed.
# see $BDG_home/docs/grade/manual/index.html#acknowledgements
##### setenv BDG_TOOL_WGET none # do not use wget
##### setenv BDG_TOOL_WGET_OPTIONS "options" # wget command line options for proxy

# temporary directory setup ====================================================
# By default # the directory /tmp will be used to write temporary files and 
# directories. This can be changed by setting enviroment variable:
# (expert option)
##### setenv autoBUSTER_scrdir /tmp 

# location of directory containing locally created macros for refine
# see $BDG_home/docs/autobuster/manual/autoBUSTER6.html#macro
# (expert option) for an example of use see
# https://www.globalphasing.com/buster/wiki/index.cgi?AutobusterLigandQMhelpers#macros
##### setenv autoBUSTER_MacroDirs /location/of/local/refine/macros

# -forcefield option setup =====================================================
# use the OpenEye provided MMFF94 helper by setting BDG_TOOL_OE_HELPER_BIN_DIR to
# the directory containing OpenEye provided buster_helper_mmff. Unless already 
# set you will also need to set environment variable OE_LICENSE to the location
# of the OpenEye license.
# see http://www.globalphasing.com/buster/wiki/index.cgi?AutobusterLigandForcefield
##### setenv BDG_TOOL_OE_HELPER_BIN_DIR /location/of/directory_contains_buster_helper_mmff/
##### setenv OE_LICENSE /location/of/file/oe_license.txt

# databaseid url setup for buster-report =======================================
# Use this for buster-report to provide a hyperlink rather than plain text for 
# ligands # with -databaseid defined. Set environment variables:
# 	BDG_BR_DATABASEID_MATCH a regular expression for the database id
# 	BDG_BR_DATABASEID_SUBSTITUTE a substitution pattern converting the id 
#                                    to url (normally a local intranet)
# For example to map -databaseid 'CID 11957412' tothe url 
# http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=11957412 use:
#
##### setenv BDG_BR_DATABASEID_MATCH 'CID ?(\d*)'
##### setenv BDG_BR_DATABASEID_SUBSTITUTE '"'"<a href='http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid="'$1'"'>CID "'$1</a>"'
#
# N.B., if you need help with the defining environment variables for your site
#      please email buster-develop@globalphasing.com.

# (optional) local PDB repository setup ========================================
# location of a local mirror of the PDB repository (used by fetch_PDB).
# set BDG_TOOL_LOCALPDBDIR to point to the directory containing the data/structures/all
# subdirectory
#### setenv BDG_TOOL_LOCALPDBDIR /data/PDB/v3


# For BUSTER only installation the autoPROC options below are not relevant 
# and should be left commented

# autoPROC uses XDS http://xds.mpimf-heidelberg.mpg.de/
# the location of the xds_par binary should be set as BDG_TOOL_XDS 
##### setenv BDG_TOOL_XDS /location/of/XDS-INTEL64_Linux_x86_64/xds_par

# location of directory containing locally created macros for autoPROC
# see $BDG_home/docs/autoproc/manual/autoPROC4.html
##### setenv autoPROC_MacroDirs /location/of/local/autoPROC/macros
