Custom building Coot from source code: Difference between revisions

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Custom building Coot from source code (edit)

Revision as of 23:48, 27 February 2011

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This is an advanced task. Don't attempt it unless you are a Unix expert. The normal method installing Coot is to download a binary, or to use the autobuild scripts: [[Coot]].
Return to [[coot]]


====Install gpp4 and other dependencies on Linux.====
These instructions are current as of coot release 0.5.
 
The following is specific to Ubuntu linux, but should be generalizable to any recent linux distribution.
 
'''This is a so-called "advanced" task. Don't attempt it unless you would rather compile your own software than use pre-compiled versions. The standard (supported) method for installing Coot is to [[Coot#Installation_from_a_distributed_binary_tarball_package |download a pre-compiled binary]], or to use [[Coot#Installation_from_source_code_via_autobuild_scripts |the autobuild scripts]].'''
 
==Installing pre-compiled Coot binaries==
 
===Avoiding manual installation===
 
This page describes full manual installation, for those who want (or need) to do it.  It is not necessary on most systems. For autobuild and for installation of precompiled Coot binaries, see [[Coot#Installing_Coot | Installing Coot]]
 
===Debian packages for Coot and its Dependencies===
 
Please be aware that everything compiled below has been archived as [[Coot#Instalation_on_Debian.2FUbuntu_from_debian_archive_files | Debian archive files]] that you can easily install.
 
==Install gpp4 and other dependencies on Linux.==


Instead of using ccp4-onlylibs-dev, we want to use ssm, mmdb, gpp4 and clipper packages.     
Instead of using ccp4-onlylibs-dev, we want to use ssm, mmdb, gpp4 and clipper packages.     
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Install these in the order described:
Install these in the order described:


=====mmdb=====
===mmdb===
  wget http://www.ebi.ac.uk/~keb/cldoc/downloads/mmdb-1.19.tar.gz
  wget http://www.ebi.ac.uk/~keb/cldoc/downloads/mmdb-1.19.tar.gz
  ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include
  ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include
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  make install
  make install


=====ssm=====
===ssm===
  wget ftp://ftp.bioxray.au.dk/pub/mok/src/ssm-0.1.tar.gz
  wget ftp://ftp.bioxray.au.dk/pub/mok/src/ssm-0.1.tar.gz
  CPPFLAGS=-I/usr/local/xtal/include ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include
  CPPFLAGS=-I/usr/local/xtal/include ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include
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  make install
  make install


=====gpp4=====
===gpp4===
  wget ftp://ftp.bioxray.au.dk/pub/mok/src/gpp4-1.0.4.tar.gz
  wget http://launchpad.net/gpp4/1.3/1.3.1/+download/gpp4-1.3.1.tar.gz
  CPPFLAGS=-I/usr/local/xtal/include ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include
  CPPFLAGS=-I/usr/local/xtal/include ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include
  make
  make
  make install
  make install


=====fftw=====
===fftw===
We need to compile fftw in a way that differs from that used to make the standard linux distribution of fftw. So to do that, we will install our own in /usr/local/xtal/lib, so it will remain hidden from the rest of the system, unless directed to look for it there.
We need to compile fftw in a way that differs from that used to make the standard linux distribution of fftw. So to do that, we will install our own in /usr/local/xtal/lib, so it will remain hidden from the rest of the system, unless directed to look for it there.
  ftp://ftp.fftw.org/pub/fftw/old/fftw-2.1.5.tar.gz
  ftp://ftp.fftw.org/pub/fftw/old/fftw-2.1.5.tar.gz
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  make install
  make install


=====clipper=====
===clipper===
  wget http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper20ac.latest.tar.gz
  wget http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper20ac.latest.tar.gz
  CPPFLAGS=-I/usr/local/xtal/include ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include -enable-shared --with-gpp4=/usr/local/xtal --with-mmdb=/usr/local/xtal --with-fftw=/usr/local/xtal --enable-mmdb --enable-minimol --enable-cif --enable-cns --enable-gpp4
  CPPFLAGS=-I/usr/local/xtal/include ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include -enable-shared --with-gpp4=/usr/local/xtal --with-mmdb=/usr/local/xtal --with-fftw=/usr/local/xtal --enable-mmdb --enable-minimol --enable-cif --enable-cns --enable-gpp4
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====Make sure the other needed dependencies are installed====
Note that if the primary server for the source code is down, you can often find what you need mirrored elsewhere, eg:
 
http://distfiles.msn.wi.us.finkmirrors.net/mirrors/fink/distfiles
 
==Make sure the other needed dependencies are installed==


These include at least the following dependencies:
These include at least the following dependencies:


=====Ubuntu packages=====
===Ubuntu packages===


A [[list of coot dependencies]] that is probably only a subset
A [[list of coot dependencies]] that is probably only a subset


=====Others that you have to make yourself: =====
===Others that you have to make yourself: ===
[http://download.gna.org/guile-lib guile-lib] (I had to compile this myself as described below)
[http://download.gna.org/guile-lib guile-lib] (I had to compile this myself as described below)


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This puts stuff into /usr, rather than /usr/local or /usr/local/xtal, which you might not want to do.  The aim is to eventually get these into the standard system distribution, in which case they will reside in /usr with the other guile extensions. All of these should work with guile-1.8.
This puts stuff into /usr, rather than /usr/local or /usr/local/xtal, which you might not want to do.  The aim is to eventually get these into the standard system distribution, in which case they will reside in /usr with the other guile extensions. All of these should work with guile-1.8.


====Configuring and building coot ====
==Configuring and building coot ==


=====Start a root shell session=====
===Start a root shell session===


If root is enabled, log into a root shell, or else if you have sudo (debian, ubuntu, etc), use the command
If root is enabled, log into a root shell, or else if you have sudo (debian, ubuntu, etc), use the command
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=====Fix a configure bug=====
===Fix a configure bug===


First, issue the following command to fix a configure bug when compiling with gpp4:
First, issue the following command to fix a configure bug when compiling with gpp4:
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  perl -pi -e 's|lccp4c|lgpp4|g' configure  
  perl -pi -e 's|lccp4c|lgpp4|g' configure  


=====Now configure this way: =====
===Now configure this way: ===


<pre>
<pre>
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</pre>
</pre>


=====Then, remake the  src/coot_wrap_python.cc and src/coot_wrap_guile.cc files: =====
===Then, remake the  src/coot_wrap_python.cc and src/coot_wrap_guile.cc files: ===


  /bin/rm -f **/coot_wrap_**.cc
  /bin/rm -f **/coot_wrap_**.cc
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  cd ..
  cd ..


=====Now compile coot:=====
===Now compile coot:===
  make  
  make  
  make -i install
  make -i install


=====To make it play nice with python, I have had to do the following: =====
===To make it play nice with python, I have had to do the following: ===
  perl pi -e 's|PYTHONHOME=\$COOT_PREFIX|\#PYTHONHOME=\$COOT_PREFIX|g' bin/coot
  perl -pi -e 's|PYTHONHOME=\$COOT_PREFIX|\#PYTHONHOME=\$COOT_PREFIX|g' bin/coot
  cp src/coot.py python/.
  cp src/coot.py python/.
  cp src/coot.py share/coot/python/.
  cp src/coot.py share/coot/python/.
 
=====Now add the reference structures: =====
===Now add the reference structures: ===
  cd share/coot
  cd share/coot
  wget http://www.ysbl.york.ac.uk/~emsley/software/coot-reference-structures.tar.gz
  wget http://www.ysbl.york.ac.uk/~emsley/software/coot-reference-structures.tar.gz
  tar xvfz coot-reference-structures.tar.gz ; rm coot-reference-structures.tar.gz
  tar xvfz coot-reference-structures.tar.gz ; rm coot-reference-structures.tar.gz


===== Now add the refmac dictionaries=====
=== Now add the refmac dictionaries===
(eg using coot-0.5 and refmac 5.4; change as required):
(eg using coot-0.5 and refmac 5.4; change as required):


  cd /tmp
  cd /tmp
wget wget http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz
  wget http://www.ysbl.york.ac.uk/refmac/data/refmac_dictionary.tar.gz
  tar xvfz refmac5.4_dictionary.tar.gz
  tar xvfz refmac_dictionary.tar.gz
  mkdir -p  /usr/local/xtal/coot-0.5/lib/data
  mkdir -p  /usr/local/xtal/coot-0.5.2/lib/data
  cp -r dic /usr/local/xtal/coot-0.5/lib/data/monomers
  cp -r dic /usr/local/xtal/coot-0.5.2/lib/data/monomers


=====Export the COOT_REFMAC_LIB_DIR variable =====
===Export the COOT_REFMAC_LIB_DIR variable ===
(you can edit bin/coot):  
(you can edit bin/coot):  
   export COOT_REFMAC_LIB_DIR=$COOT_PREFIX/lib
   export COOT_REFMAC_LIB_DIR=$COOT_PREFIX/lib


=====Notes on the above: =====
===Notes on the above: ===
The configure command is all one line; I've escaped the return. Using --prefix=$PWD simply keeps everything self-contained.  You can use any install prefix you want to (it defaults to /usr/local; another sensible choice is /usr/local/xtal.  Avoid /usr as a prefix, as it can mess with your system).
The configure command is all one line; I've escaped the return. Using --prefix=$PWD simply keeps everything self-contained.  You can use any install prefix you want to (it defaults to /usr/local; another sensible choice is /usr/local/xtal.  Avoid /usr as a prefix, as it can mess with your system).


The make -i install is needed if you choose --prefix=$PWD because it tries to install some files where they are presently situated.
The''' make -i install''' is needed if you choose --prefix=$PWD because it tries to install some files where they are presently situated.


----
----


====If you want to make it portable====
==If you want to make it more portable==


You don't need to do this to run coot; this is only handy if you need to redistribute it (or make say a debian package).
You don't need to do this to run coot; this is only handy if you need to redistribute it (or make say a debian package).
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<pre>
<pre>
  cd /usr/local/xtal/coot-0.1.2/bin
  cd /usr/local/xtal/coot/bin
  foreach dylib in $(ldd coot-real | awk '{print $3}' | grep -v fff | grep -v "usr/local/xtal/coot" | sort -u )
  foreach dylib in $(ldd coot-real | awk '{print $3}' | grep -v fff | grep -v "usr/local/xtal/coot" | sort -u )
       print copying $dylib  
       print copying $dylib  
       sudo cp -i $dylib /usr/local/xtal/coot-0.1.2/lib/.
       sudo cp -i $dylib /usr/local/xtal/coot/lib/.
  end
  end
</pre>
</pre>
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In addition, the guile modules can all be put in one centralized location:
In addition, the guile modules can all be put in one centralized location:


  cp -R /usr/share/guile* /usr/local/xtal/coot-0.1.2/share/.
  cp -R /usr/share/guile* /usr/local/xtal/coot/share/.
 


Finally, you can give coot its own copy of the refmac monomers library:


mkdir -p /usr/local/xtal/coot-0.1.2/share/coot/lib/data
cp -R /usr/local/xtal/ccp4-6.0/lib/data/monomers /usr/local/xtal/coot-0.1.0-pre-3/share/coot/lib/data/.


Then edit /usr/local/xtal/coot-0.1.2/bin/coot and un-comment the appropriate environment variable lines (there are 2).
Return to [[coot]]
Mok
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