6
edits
Custom building Coot from source code: Difference between revisions
Jump to navigation
Jump to search
Custom building Coot from source code (edit)
Revision as of 23:48, 27 February 2011
, 27 February 2011Undo revision 1930 by Mok (talk)
mNo edit summary |
|||
| (12 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
Return to [[coot]] | |||
These instructions are current as of coot release 0.5. | 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. | 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 download a pre-compiled binary, or to use the autobuild scripts | '''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Please be aware that everything compiled below has been archived as [[Coot#Instalation_on_Debian.2FUbuntu_from_debian_archive_files | Debian archive files]] that you can easily install.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.== | ==Install gpp4 and other dependencies on Linux.== | ||
| Line 26: | Line 38: | ||
===gpp4=== | ===gpp4=== | ||
wget | 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 | ||
| Line 49: | Line 61: | ||
http://distfiles.msn.wi.us.finkmirrors.net/mirrors/fink/distfiles | http://distfiles.msn.wi.us.finkmirrors.net/mirrors/fink/distfiles | ||
==Make sure the other needed dependencies are installed== | ==Make sure the other needed dependencies are installed== | ||
| Line 129: | Line 140: | ||
===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 | ||
| Line 142: | Line 153: | ||
cd /tmp | cd /tmp | ||
wget http://www.ysbl.york.ac.uk/refmac/data/refmac_dictionary.tar.gz | |||
tar xvfz | 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 === | ||
| Line 154: | Line 165: | ||
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). | ||
| Line 177: | Line 188: | ||
<pre> | <pre> | ||
cd /usr/local/xtal/coot | 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 | sudo cp -i $dylib /usr/local/xtal/coot/lib/. | ||
end | end | ||
</pre> | </pre> | ||
| Line 186: | Line 197: | ||
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 | cp -R /usr/share/guile* /usr/local/xtal/coot/share/. | ||
Return to [[coot]] | |||