Subject: Re: ccp4.setup file for environment-modules?
From: Paul Mcewan Paul {- dot -} Mcewan {- at -} NOTTINGHAM {- dot -} AC {- dot -} UK
Date: 2009-05-29
RE: [ccp4bb] ccp4.setup file for environment-modules?
Hi Matt,
this is what we use in Nottingham for ccp4 6.1.1.
hope it's of use.
#%Module1.0################################################################
set sw "CCP4 version 6.1.1"
source /usr/remote/modulefiles/.template.tcl
conflict ccp4
# CCP4_MASTER is the location of the top-level directory containing `ccp4-<versi
on>'
set CCP4_MASTER /usr/remote/ccp4/6.1.1
setenv CCP4_MASTER $CCP4_MASTER
set CCP4 $CCP4_MASTER/ccp4-6.1.1
setenv CCP4 $CCP4
# CCP4_SCR: a per-user directory for run-time-generated scratch files.
# BINSORT_SCR: a scratch directory for binsort's use; normally same as CCP4_SCR
set CCP4_SCR /tmp/$env(USER)
setenv CCP4_SCR $CCP4_SCR
setenv BINSORT_SCR $CCP4_SCR
if { ! [ file exists $CCP4_SCR ] } {
file mkdir $CCP4_SCR
}
### CCP4i setup ###
# CCP4I_TOP - the top directory of the interface
# CCP4I_TCLTK - directory containing tclsh,wish and bltwish executables
# as used in $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
# For 'standard' installations this is /usr/local/bin
# but note the SGI distributed version of Tcl/Tk is not
# appropriate version
# CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help
set CCP4I_TOP $CCP4/ccp4i
setenv CCP4I_TOP $CCP4I_TOP
set CCP4I_TCLTK $CCP4_MASTER/tcltk++/bin
setenv CCP4I_TCLTK $CCP4I_TCLTK
setenv CCP4I_HELP $CCP4I_TOP/help
### Optional - setting http_proxy environment
setenv HTTP_PROXY wwwcache.nottingham.ac.uk:3128
# Set GFORTRAN_UNBUFFERED_ALL to either 1 or Y to ensure that the logfile
# output from programs compiled with Gfortran is in the correct order.
# Note that there will be some performance penalty for this.
setenv GFORTRAN_UNBUFFERED_ALL 1
# The significance of the environment variables is as follows:
# CBIN: location of the executables -- must be on your path (see below);
# CLIB: location of (binary) library files such as libccp4.a and libccp4.so;
# MANPATH: set this if your system's `man' looks at such an environment
# variable to determine where to look for man pages. By adding
# $CCP4/man to the normal path you get the CCP4 man pages
# with keyword searching as system ones.
# CCP4_BROWSER: set this if you intend to use the html documentation
# (recommended). It should have the path and name of a html browser eg
# /usr/bin/X11/mozilla or /usr/local/bin/lynx. The browser will be
# started with the alias ccp4help and will open the file
# $CHTML/INDEX.html.
set CBIN $CCP4/bin
setenv CBIN $CBIN
set CLIB $CCP4/lib
setenv CLIB $CLIB
set CCP4_BROWSER htmlview
setenv CCP4_BROWSER $CCP4_BROWSER
prepend-path MANPATH $CCP4/man
# The following are for all systems
set CCP4_LIB $CLIB
setenv CCP4_LIB $CCP4_LIB
setenv CCP4_BIN $CBIN
# CLASSPATH for Java
prepend-path CLASSPATH $CBIN
# Python path for the subprocess fixed module
prepend-path PYTHONPATH $CCP4/share/python
### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
setenv PLOT_COMMAND lpr
setenv PRINT_COMMAND lpr
### CCP4_OPEN ###
# CCP4_OPEN may be set to 'UNKNOWN' to stop open failures for files opened
# as NEW that already exist. Novices should use 'NEW' to avoid inadvertant
# over-writing of existing files, which is then treated as a fatal error.
setenv CCP4_OPEN UNKNOWN
# LD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.so) at
runtime
prepend-path LD_LIBRARY_PATH $CLIB
# DYLD_LIBRARY_PATH specifies where to find dynamic libraries (e.g. libccp4.dyli
b) at runtime (used on Mac OS X)
prepend-path DYLD_LIBRARY_PATH $CLIB
### XAPPLRESDIR ###
setenv XUSERFILESEARCHPATH $CCP4_LIB/X11/app-defaults/%N:/usr/lib/X
11/app-defaults
### dbCCP4i database handler setup ###
set DBCCP4I_TOP $CCP4/share/dbccp4i
setenv DBCCP4I_TOP $DBCCP4I_TOP
### IMOSFLM environment is now defined here
setenv MOSFLM_EXEC $CBIN/ipmosflm
setenv MOSFLM_WISH $CCP4I_TCLTK/wish
setenv IMOSFLM_VERSION 0.6.1
### MMCIFDIC is now defined here. cif_mmdic.lib is a binary file ===
# so on multiple installs it need to be unique and not in $CLIBD
setenv MMCIFDIC $CLIB/cif_mmdic.lib
### MOLREPLIB Point to the location of the files bs-zeros.dat ps.resource syml
ib.blc
# They are distributed with CCP4 in $CLIBD. This env must have the trailing or
/
setenv MOLREPLIB $CCP4/lib/data/monomers/
### CRANK points to location of Crank automation suite within ccp4i
setenv CRANK $CCP4/ccp4i/crank
setenv CCP4_CRANK 1
### XIA2 setup
# XIAROOT directory (default is under the share folder)
set XIA2_HOME $CCP4/share/XIAROOT
setenv XIA2_HOME $XIA2_HOME
set XIA2CORE_ROOT $XIA2_HOME/xia2core/
setenv XIA2CORE_ROOT $XIA2CORE_ROOT
set XIA2_ROOT $XIA2_HOME/xia2/
setenv XIA2_ROOT $XIA2_ROOT
setenv platform [exec uname]
setenv besthome $XIA2_ROOT/binaries/best
setenv XIA2_CCP4_61 1
append-path PATH $XIA2CORE_ROOT/Test
append-path PATH $XIA2CORE_ROOT/Test/Compiled/linux_386
prepend-path PATH $XIA2_ROOT/binaries/linux_386
append-path PATH $XIA2_ROOT/Applications
### PISA_CONF_FILE is the config file needed to run the stand-alone PISA, though
this can be set on the command line too.
setenv PISA_CONF_FILE $CCP4/share/pisa/pisa.cfg
### CLIBD_MON Point to the location of the dictionary files for REFMAC5
# They are distributed with CCP4 in $CLIBD/monomers. This env must have the trai
ling or /
setenv CLIBD_MON $CCP4/lib/data/monomers/
### PUBLIC_FONT84, CCP4_HELPDIR, HELPDIR, MOSHELPFILE ###
# (essential for the relevant programs)
setenv PUBLIC_FONT84 $CLIB/font84.dat
# location of VMS-style help files required for mosflm [used by hlplib, chelp, c
hlp, (ip)mosflm]:
setenv CCP4_HELPDIR $CCP4/help/
# Rasmol path. Needed for prog. to find rasmol.hlp
setenv RASMOLPATH $CCP4/x-windows/RasMol/src
# CCP4 executables and scripts live in $CBIN and $CETC respectively; put them
# on the path in an appropriate order for scripts to be used as wrappers for
# binaries of the same name. Put ccp4 stuff after the current path to avoid
# confusion with `.' or whatever in the path:
prepend-path PATH $CCP4/etc
prepend-path PATH $CCP4I_TOP/bin
prepend-path PATH $DBCCP4I_TOP/bin
# Optional (useful) additional environment variables
set CDOC $CCP4/doc
setenv CDOC $CDOC
set CHTML $CCP4/html
setenv CHTML $CHTML
set CETC $CCP4/etc
setenv CETC $CETC
set CEXAM $CCP4/examples
setenv CEXAM $CEXAM
set CINCL $CCP4/include
setenv CINCL $CINCL
set CLIBD $CCP4/lib/data
setenv CLIBD $CLIBD
set CLIBS $CCP4/lib/src
setenv CLIBS $CLIBS
set CPROG $CCP4/src
setenv CPROG $CPROG
# useful aliases, at least for developers
set-alias ccp4 "pushd $CCP4>/dev/null"
set-alias xtal "pushd $CCP4_MASTER>/dev/null"
set-alias cbin "pushd $CBIN>/dev/null"
set-alias cetc "pushd $CETC>/dev/null"
set-alias cprog "pushd $CPROG>/dev/null"
set-alias cincl "pushd $CINCL>/dev/null"
set-alias clib "pushd $CLIB>/dev/null"
set-alias clibd "pushd $CLIBD>/dev/null"
set-alias clibs "pushd $CLIBS>/dev/null"
set-alias cbin "pushd $CBIN>/dev/null"
set-alias cexam "pushd $CEXAM>/dev/null"
set-alias cdoc "pushd $CDOC>/dev/null"
set-alias chtml "pushd $CHTML>/dev/null"
set-alias ccp4help "$CCP4_BROWSER $CHTML/INDEX.html &"
#BALBES root configuration
setenv BALBES_ROOT $CCP4/share/balbes/BALBES_0.0.1
#SET UP ADDITIONAL SOFTWARE
prepend-path PATH $CCP4_MASTER/Coot-0.5.2/bin
prepend-path PATH $CCP4_MASTER/ccp4-6.1.1//bin
prepend-path PATH $CCP4_MASTER/Python-2.4.5/bin
prepend-path PATH $CCP4_MASTER/tcltk++/bin
prepend-path PATH $CCP4_MASTER/clustalw-2.0.9/bin
prepend-path PATH $CCP4_MASTER/fasta-35.4.1/bin
prepend-path PATH $CCP4_MASTER/graphviz-2.20.2/bin
#prepend-path PATH $CCP4/src/phaser/phaser-2.1.4/build/intel
-linux/bin
prepend-path PATH /usr/local/Linux-x86_64/ccp4/6.1.1/ccp4-6
.1.1/src/phaser/phaser-2.1.4/build/intel-linux/bin
prepend-path LD_LIBRARY_PATH $CCP4_MASTER/Python-2.4.5/lib
prepend-path LD_LIBRARY_PATH $CCP4_MASTER/tcltk++/lib
prepend-path LD_LIBRARY_PATH $CCP4_MASTER/graphviz-2.20.2/lib
prepend-path LD_LIBRARY_PATH $CCP4_MASTER/chooch/lib
prepend-path MANPATH $CCP4_MASTER/Python-2.4.5/man
prepend-path MANPATH $CCP4_MASTER/tcltk++/man
prepend-path MANPATH $CCP4_MASTER/graphviz-2.20.2/man
prepend-path MANPATH $CCP4_MASTER/chooch/man
###################################
Dr. Paul A. McEwan
Office B55
Centre for Biomolecular Science
University of Nottingham
Nottingham
NG7 2RD
UK
Tel: 0115 8232010 (office)
Tel: 0115 8232011 (lab)
http://www.nottingham.ac.uk/pharmacy/research/medicinal-chemistry-structural-biology/structbio.php
###################################
-----Original Message-----
From: CCP4 bulletin board on behalf of Matt Harrington
Sent: Fri 29/05/2009 1:30 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ccp4.setup file for environment-modules?
I'd rather not reinvent the wheel if I don't have to. Does anyone
have a version of ccp4.setup which has been converted to Tcl for use
with environment-modules?
More info:
http://modules.sourceforge.net
Sample commands:
module load ccp4 # setup your environment for latest version
module unload ccp4 # resets environment
module load ccp4/6.0.2 # setup environment for old version
module switch ccp4 ccp4/6.1.1 # switch to a newer version with one command
module avail # list modules (i.e. applications) available on your system
Matt
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