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Custom building Coot from source code: Difference between revisions
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Custom building Coot from source code (edit)
Revision as of 21:03, 15 November 2008
, 15 November 2008organized section better with subheadings
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====Fourth, configure and build coot like this:==== | ====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 | 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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(or whatever shell) to open a root shell, and issue the following commands as indicated. | (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: | 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: ===== | |||
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 (eg using coot-0.5 and refmac 5.4; change as required): | ===== Now add the refmac dictionaries===== | ||
(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 wget http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz | ||
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cp -r dic /usr/local/xtal/coot-0.5/lib/data/monomers | 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 the COOT_REFMAC_LIB_DIR variable ===== | ||
(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: ===== | |||
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). | ||