Installation - Revision history

Edit: /* Troubleshooting */

2009-07-06T18:28:15Z

Troubleshooting

Feig: /* Troubleshooting */

2006-08-12T12:35:10Z

Troubleshooting

Feig at 12:34, 12 August 2006

2006-08-12T12:34:39Z

Feig at 12:34, 12 August 2006

2006-08-12T12:34:05Z

Feig at 12:32, 12 August 2006

2006-08-12T12:32:47Z

New page

== Unpacking ==

To install, go to the directory where you want to install
the package (e.g. /usr/local) and unpack with

gzip -d <package>.tar.gz
tar xvf <package>.tar

This will create all files in the current directory

Now start the installation with

./install.sh

After running the installation script compiled binaries are available
in ./bin and self-starting perl scripts are in ./perl. Related data
files are in ./data and examples for each perl script are under
./bench.

== Setup ==

Every user planning to use the MMTSB tools should set the
environment variable MMTSBDIR to the directory where the MMTSB
tools are installed (e.g. /usr/local) and include $MMTSBDIR/bin
and $MMTSBDIR/perl in the file search path as follows:

For csh/tcsh:

setenv MMTSBDIR <installation-dir>
set path = ( $path $MMTSBDIR/perl $MMTSBDIR/bin )

and for sh/bash:

export MMTSBDIR = <installation-dir>
export PATH = $PATH:$MMTSBDIR/perl:$MMTSBDIR/bin

For parallel execution, you may also specify the program
for remote login without passwords in REMOTESHELL, e.g.:

setenv REMOTESHELL rsh

== Integration with other packages ==
The MMTSB Tool Set benefits from the availability of other
software packages, in particular CHARMM, Amber, Modeller,
DSSP, SCWRL, NCBI-BLAST, PSIPRED.

The following environment variables are related to these
packages and should be set accordingly:

CHARMMEXEC CHARMM executable
CHARMMDATA CHARMM data files
AMBERHOME Amber installation directory
SANDEREXEC Amber sander executable
LEAPEXEC Amber tLeap executable
MODELLEREXEC Modeller executable
PSIPREDDIR PSIPRED installation directory
PDBDIR Directory with local copy of PDB

== Troubleshooting ==

Perl:

Perl 5.004 or newer is required to run the perl scripts. All perl scripts
check whether this (or a newer) version is available and and will
abort with a message if not. /usr/bin/env is used to find the location
of perl. This works only if perl can be found in the search path.
An error like

env: perl: No such file or directory

indicates that perl is either not installed or its location is not
included in the search path. Binary and source code distributions of
latest perl versions are available through http://www.cpan.org

Compiling:

The provided Makefile uses gcc, g++, and g77 to compile
the binaries. If that is not appropriate for your platform
or special linker options are needed, the file src/Makefile
needs to be modified accordingly. Please consult your
local system administrator if necessary.

Running:

If problems occur with running the scripts or programs please
consult the documentation at
http://mmtsb.scripps.edu/software/mmtsbtoolset.html
and check your input data.
If problems persist, help is available at the address below.

@@ Line 82: / Line 82: @@
 needs to be modified accordingly. Please consult your
 local system administrator if necessary.
 === Running ===

@@ Line 75: / Line 75: @@
-Compiling:
+=== Compiling ===
 The provided Makefile uses gcc, g++, and g77 to compile
@@ Line 83: / Line 83: @@
 local system administrator if necessary.
-Running:
+=== Running ===
 If problems occur with running the scripts or programs please

@@ Line 1: / Line 1: @@
 == Unpacking ==
@@ Line 59: / Line 60: @@
 == Troubleshooting ==
-Perl:
+=== Perl ===
 Perl 5.004 or newer is required to run the perl scripts. All perl scripts

@@ Line 27: / Line 27: @@
 For csh/tcsh:
-setenv MMTSBDIR <installation-dir>
+  setenv MMTSBDIR <installation-dir>
-set path = ( $path $MMTSBDIR/perl $MMTSBDIR/bin )
+  set path = ( $path $MMTSBDIR/perl $MMTSBDIR/bin )
 and for sh/bash:
-export MMTSBDIR = <installation-dir>
+  export MMTSBDIR = <installation-dir>
-export PATH = $PATH:$MMTSBDIR/perl:$MMTSBDIR/bin
+  export PATH = $PATH:$MMTSBDIR/perl:$MMTSBDIR/bin
 For parallel execution, you may also specify the program
 for remote login without passwords in REMOTESHELL, e.g.:
-setenv REMOTESHELL rsh
+  setenv REMOTESHELL rsh
 == Integration with other packages ==
@@ Line 48: / Line 48: @@
 packages and should be set accordingly:
-CHARMMEXEC    CHARMM executable
+  CHARMMEXEC    CHARMM executable
-CHARMMDATA    CHARMM data files
+  CHARMMDATA    CHARMM data files
-AMBERHOME     Amber installation directory
+  AMBERHOME     Amber installation directory
-SANDEREXEC    Amber sander executable
+  SANDEREXEC    Amber sander executable
-LEAPEXEC      Amber tLeap executable
+  LEAPEXEC      Amber tLeap executable
-MODELLEREXEC  Modeller executable
+  MODELLEREXEC  Modeller executable
-PSIPREDDIR    PSIPRED installation directory
+  PSIPREDDIR    PSIPRED installation directory
-PDBDIR        Directory with local copy of PDB
+  PDBDIR        Directory with local copy of PDB
 == Troubleshooting ==
@@ Line 86: / Line 86: @@
 If problems occur with running the scripts or programs please
 consult the documentation at
-http://mmtsb.scripps.edu/software/mmtsbtoolset.html
+http://feig.bch.msu.edu/mmtsb
 and check your input data.