I think the bash-compatible startup script has disappeared from CNS
distribution at some point. The one that was distributed with cns 1.1
still works though, and I attach my copy of it.
On 07/12/2012 11:24 AM, Dirk Kostrewa wrote:
Dear Fulvio Saccoccia,
along the lines of Ian Tickle's reply: there should be a script
"cns_solve_env_sh" using /bin/sh, which is usually a soft-link to
/bin/bash. I use this script for setup of CNS under bash.
Best regards,
Dirk.
Am 12.07.12 16:49, schrieb fulvio saccoccia:
Dear ccp4 users,
I tried to install CNS under Debian 64bit. I followed the
installation
giude as reported by CNS developers but I received the following
message when souurcing cns_solve_env:
bash: setenv: command not found
bash: setenv: command not found
bash: cns_solve_env: line 32: syntax error near unexpected token
`setenv'
bash: cns_solve_env: line 32: ` if ( ! $?CNS_ARCH ) setenv CNS_ARCH `
$CNS_SOLVE/bin/getarch`'
I know that the script would set all variables; it is indicated for csh
(or tcsh) shell. I tried to run the script under a csh shell but I
received a different error:
Word too long
The above statement is also received if a bash-optimized script is run.
Does anyone have experience in CNS installation and environment setting?
Any advice?
Thanks in advance
Fulvio Saccoccia
Dept. of Biochemical Sciences
Sapienza University of Rome, Italy
#!/bin/sh
#
# This file sets up the appropriate environmental variables and paths
# for CNSsolve. In the case of the same machines with different versions
# of the OS, backward compatibility is assumed - ie. a later version will
# be setup for a previous version of the OS if nothing else is available.
#
# written by: Paul Adams
#
# copyright Yale University
#
# ==========================================================================
#
# >>>>>> Important: define the location of the CNSsolve directory <<<<<<
#
# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY
CNS_SOLVE='/sware/cns'
#
# ==========================================================================
#
# full expansion of the CNS_SOLVE variable prior to use.
#
export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE
#
# ==========================================================================
#
# set the number of threads for SGI multiprocessors
# if this causes a problem on other systems it can be commented out
#
export MP_SET_NUMTHREADS; MP_SET_NUMTHREADS=1
#
# ==========================================================================
#
# get the machine architecture
#
if [ -d $CNS_SOLVE ]; then
if [ ! "$CNS_ARCH" ]; then
export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch`
fi
else
export CNS_ARCH; CNS_ARCH='unknown'
fi
#
# ==========================================================================
#
# general environmental variables
#
export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries
export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules
export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar
export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb
export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal
export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr
export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray
export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal
export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr
export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib
#
# general user aliases
#
cns_web () { $CNS_SOLVE/bin/cns_web; }
cns_header () { $CNS_SOLVE/bin/cns_header; }
cns_info () { cat $CNS_SOLVE/bin/cns_info; }
cns_transfer () { $CNS_SOLVE/bin/cns_transfer; }
if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then
cns_edit () { $CNS_SOLVE/bin/cns_edit_local; }
else
cns_edit () { $CNS_SOLVE/bin/cns_edit; }
fi
run_tutorial () { "csh -f tutorial.csh"; }
#
# g77 compilation and use
#
g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; }
g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; }
#
# developer aliases
#
run_tests () { $CNS_SOLVE/bin/run_tests; }
run_diffs () { $CNS_SOLVE/bin/run_diffs; }
maketar () { $CNS_SOLVE/bin/maketar; }
create_patch () { $CNS_SOLVE/bin/create_patch; }
#
#
# ==========================================================================
#
# to do expansions - unset noglob just in case user has it otherwise
#
set +f
#
# try to set up appropriate path
#
# first strip off any trailing information (eg. _g77)
#
CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'`
#
cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'`
cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'`
cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'`
cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'`
cns_minor=`echo $cns_major | sed -e 's/\./ /g'`
#
# if we are looking for a specific type of setup then limit search
#
cns_dirs=""
if [ ! "$CNS_G77" ]; then
if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then
cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk
'BEGIN{FS="/"}{print $NF}' | sort -t\- +3 -4 -n -r`"
fi
else
CNS_ARCH="${CNS_ARCH}_g77"
if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then
cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk
'BEGIN{FS="/"}{print $NF}' | sort -t\- +3 -4 -n -r`"
fi
fi
#
# first look for an exact match (with os version)
#
#
cns_found=0
if [ -n "$cns_dirs" ]; then
for cns_dir in $cns_dirs ; do
cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'`
if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \
$cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ];
then
cns_archenv=$cns_dir
cns_found=1
fi
fi
done
#
#
# now look for an exact match (without os version)
#
if [ $cns_found -eq 0 ]; then
for cns_dir in $cns_dirs ; do
if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \
$cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then
cns_archenv=$cns_dir
cns_found=1
fi
fi
done
fi
#
# now look for a backwards compatible match (with os version major/minor)
#
if [ $cns_found -eq 0 ]; then
for cns_dir in $cns_dirs ; do
if [ $cns_found -eq 0 ]; then
cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed
's/_g77//g'`
if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then
osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print
1}'`
if [ $osv_test -eq 1 ]; then
cns_archenv=$cns_dir
cns_found=1
fi
fi
fi
fi
done
fi
#
# now look for a wildcard match on cpu
#
if [ $cns_found -eq 0 ]; then
cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'`
cpu_ver=`echo $cns_cpu | sed 's/[A-z]*//'`
for cns_dir in $cns_dirs ; do
if [ $cns_found -eq 0 ]; then
cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed
's/[0-9]*\.*[0-9]*$//'`
cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed
's/[A-z]*//'`
if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \
$cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77
]; then
cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'`
if [ $cpu_test -eq 1 ]; then
cns_archenv=$cns_dir
cns_found=1
fi
fi
fi
fi
done
fi
fi
#
# if found set environment
#
if [ $cns_found -eq 1 ]; then
#
# set installation and source directory
#
export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv
export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source
#
# path for CNSsolve utility programs
#
if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then
export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh
$CNS_SOLVE/$cns_archenv/utils`
fi
#
# path for CNSsolve executable if installed
#
if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then
export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh
$CNS_SOLVE/$cns_archenv/bin`
fi
fi
#
unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor
unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same
unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test
#
