Custom building Coot from source code
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.
Install gpp4 and other dependencies on Linux.
Instead of using ccp4-onlylibs-dev, we want to use ssm, mmdb, gpp4 and clipper packages.
To keep things tidy, I suggest installing everything into /usr/local/xtal
Install these in the order described:
mmdb
wget http://www.ebi.ac.uk/~keb/cldoc/downloads/mmdb-1.19.tar.gz ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include make make install
ssm
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 make make install
gpp4
wget ftp://ftp.bioxray.au.dk/pub/mok/src/gpp4-1.0.4.tar.gz CPPFLAGS=-I/usr/local/xtal/include ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include make make install
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.
ftp://ftp.fftw.org/pub/fftw/old/fftw-2.1.5.tar.gz CPPFLAGS=-I/usr/local/xtal/include ./configure --prefix=/usr/local/xtal --includedir=/usr/local/xtal/include --enable-float make make install
clipper
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 make make install
Make sure the other needed dependencies are installed
These include at least the following dependencies:
Ubuntu packages
A list of coot dependencies that is probably only a subset
Others that you have to make yourself:
guile-lib (I had to compile this myself as described below)
goosh (I had to compile this myself)
guile-gui (I had to compile this myself)
guile-gtk-2.0 (I had to compile this myself)
net-htttp (I had to compile this myself)
To do so, I used
configure --prefix=/usr make sudo make install
Fourth, configure and build coot like this:
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
sudo zsh
(or whatever shell) to open a root shell, and issue the following commands as indicated.
Fix a configure bug
First, issue the following command to fix a configure bug when compiling with gpp4:
perl -pi -e 's|lccp4c|lgpp4|g' configure
Now configure this way:
PATH="/usr/local/xtal/bin:$PATH" \ CPPFLAGS="-I/usr/local/xtal/include -I/usr/local/xtal/include/clipper -I/usr/local/xtal/include/gpp4 -I/usr/local/xtal/include/mmdb -I/usr/local/xtal/include/ssm" \ ./configure --prefix=$PWD \ --with-gpp4=/usr/local/xtal \ --with-mmdb-prefix=/usr/local/xtal \ --with-ssmlib-prefix=/usr/local/xtal \ --with-clipper-prefix=/usr/local/xtal \ --with-fftw=/usr/local/xtal \ --with-glut-prefix=/usr --with-gl-prefix=/usr/X11R6 \ --with-gtk2 --with-gnomecanvas-prefix=/usr \ --with-imlib-prefix=/usr --with-gtkgl-prefix=/usr \ --with-glib-prefix=/usr --with-guile-gtk \ --with-guile-gtk-prefix=/usr --with-gsl-prefix=/usr \ --with-guile --with-python
Then, remake the src/coot_wrap_python.cc and src/coot_wrap_guile.cc files:
/bin/rm -f **/coot_wrap_**.cc cd src touch c-interface-database.hh make coot_wrap_guile.cc make coot_wrap_python.cc cp coot_wrap_guile_pre.cc coot_wrap_guile.cc cd ..
Now compile coot:
make make -i install
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 cp src/coot.py python/. cp src/coot.py share/coot/python/.
Now add the reference structures:
cd share/coot 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
Now add the refmac dictionaries
(eg using coot-0.5 and refmac 5.4; change as required):
cd /tmp wget wget http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz tar xvfz refmac5.4_dictionary.tar.gz mkdir -p /usr/local/xtal/coot-0.5/lib/data cp -r dic /usr/local/xtal/coot-0.5/lib/data/monomers
Export the COOT_REFMAC_LIB_DIR variable
(you can edit bin/coot):
export COOT_REFMAC_LIB_DIR=$COOT_PREFIX/lib
Notes on the above:
The configure command is all one line; I've escaped the return. Using --prefix=$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 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
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 can see what dynamic libraries coot needs to load by issuing the command
ldd coot-real
or, if you just want to see the full path to the libraries, issue
ldd coot-real | awk '{print $3}' | grep -v fff | sort -u
You can use additional grep filters to select the ccp4 libs, clipper libs, eliminate coot's own libaries (that are already in the lib directory) and so forth.
(The ldd command is equivalent to otool -L on Mac OS X.) Then you can copy these into coot's lib directory. I used the following commands in zsh to copy in the needed directories (this is overkill, but wtf).
cd /usr/local/xtal/coot-0.1.2/bin
foreach dylib in $(ldd coot-real | awk '{print $3}' | grep -v fff | grep -v "usr/local/xtal/coot" | sort -u )
print copying $dylib
sudo cp -i $dylib /usr/local/xtal/coot-0.1.2/lib/.
end
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/.
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).