User:Tlinnet/Linux Install - Revision history

Pyadmin: 9 revisions

2014-03-28T01:20:15Z

9 revisions

Tlinnet: /* Install script */

2013-04-15T10:48:03Z

Install script

Tlinnet: /* Install script */

2013-04-15T10:34:08Z

Install script

Tlinnet: /* Install script */

2013-04-15T10:14:19Z

Install script

Tlinnet: /* Install script */

2013-04-15T10:11:42Z

Install script

Tlinnet: /* Install script */

2013-04-15T10:10:36Z

Install script

Tlinnet: /* Install script */

2013-04-15T10:10:18Z

Install script

Tlinnet: /* Install script */

2012-06-08T18:41:47Z

Install script

Tlinnet at 17:05, 26 May 2012

2012-05-26T17:05:32Z

Speleo3: moved from Linux_Install

2012-03-02T23:46:05Z

moved from Linux_Install

New page

These are customized installation scripts. For more general instructions, see [[Linux Install]].

== Ubuntu/Mint 12 compile and install with MPEG support ==
First install dependencies.
<source lang="bash">
sudo apt-get install subversion git
sudo apt-get install python-imaging python-pygame apbs
sudo apt-get install build-essential python-dev python-pmw libglew-dev freeglut3-dev libpng-dev libfreetype6-dev
bash installpymol.sh
</source>

== Red Hat Enterprise Linux RHEL 6 compile and install with MPEG support for x86_64 bit ==
Install the EPEL repository: The .rpm will be download from here 
http://fedoraproject.org/wiki/EPEL 
And the CentOS repository for additional .rpm are located here 
http://mirror.centos.org/centos/6/os/x86_64/Packages/ 
<source lang="bash">
bash
cd && wget http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-5.noarch.rpm
sudo rpm -i epel-release-6-5.noarch.rpm
rm epel-release-6-5.noarch.rpm</pre>
</source>
Then add Centos repository
<source lang="bash">
rpm --import http://mirror.centos.org/centos/6/os/x86_64/RPM-GPG-KEY-CentOS-6
sudo gedit /etc/yum.repos.d/centos.repo
</source>

Write these lines.
<source lang="text">
[centos]
name=Centos for RHEL/ CentOS $releasever - $basearch
baseurl=http://mirror.centos.org/centos/6/os/x86_64
enabled=1
</source>
Then check configuration. Do NOT UPGRADE PACKAGES from CentOS. It will replace RHEL packages. 
If you do upgrade packages, you will now see Centos login and such, but not much is problematic.
<source lang="bash">
sudo yum repolist all
sudo yum install subversion git
sudo yum install python-imaging pygame apbs
sudo yum install gcc-c++ python-devel python-pmw glew-devel freeglut-devel libpng-devel freetype-devel
</source>
Then disable centos repository. Set '''enabled=0'''
<source lang="bash">
sudo gedit /etc/yum.repos.d/centos.repo
</source>
Now install pymol
<source lang="bash">
bash installpymol.sh
</source>
Make sure, that you will have '''~/bin''' as part of your path
<source lang="bash">
gedit ~/.cshrc
</source>
Make sure this lines is in the file. Only if you use tcsh shell.
<source lang="text">
setenv PATH ${PATH}:{$HOME}/bin
</source>

== Install script ==
Make a text file "installpymol.sh" and make it executable
<source lang="bash">
chmod u+x installpymol.sh
</source>

Put this in the file, modify the first line
<source lang="bash">
#!/bin/bash -e
pymoldir=$HOME/software/pymol
modules=$pymoldir/modules
svnpymol=svnpymol
svnfreemol=svnfreemol
pymolplugins=pymolplugins
pymolscriptrepo=Pymol-script-repo

###################################################
[ -d $pymoldir ] || mkdir -p $pymoldir
[ -d $HOME/bin ] || mkdir $HOME/bin

###### Checkout pymol svn
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol $pymoldir/$svnpymol
###### Build and install pymol
cd $pymoldir/$svnpymol
python setup.py build install --home=$pymoldir --install-purelib=$modules --install-platlib=$modules
export PYTHONPATH=$modules:$PYTHONPATH
python setup2.py install
install pymol $pymoldir/

########## Setup freemol - for MPEG support ############
svn co svn://bioinformatics.org/svnroot/freemol/trunk $pymoldir/$svnfreemol
cd $pymoldir/$svnfreemol/src/mpeg_encode
export FREEMOL=$pymoldir/$svnfreemol/freemol
./configure
make
make install

########## Install PluginArchitecture ############
git clone https://github.com/speleo3/pymolplugins.git $pymoldir/$pymolplugins
########## Install Pymol-script-repo ############
git clone git://github.com/Pymol-Scripts/Pymol-script-repo.git $pymoldir/$pymolscriptrepo

## Make a shortcut to an extended pymol execution
echo "#!/bin/bash" >> $pymoldir/pymolMPEG.sh
echo "if [ ! -f $HOME/.local/share/applications/pymolsvn.desktop ];" >> $pymoldir/pymolMPEG.sh
echo "then" >> $pymoldir/pymolMPEG.sh
echo "ln -s $pymoldir/pymolsvn.desktop $HOME/.local/share/applications/pymolsvn.desktop" >> $pymoldir/pymolMPEG.sh
echo "fi" >> $pymoldir/pymolMPEG.sh
echo "export FREEMOL=$pymoldir/$svnfreemol/freemol" >> $pymoldir/pymolMPEG.sh
echo "export PYMOL_GIT_MOD=$pymoldir/$pymolscriptrepo/modules" >> $pymoldir/pymolMPEG.sh
echo '#export PYTHONPATH=$PYTHONPATH:/path/to/shared/python/site-packages/PIL' >> $pymoldir/pymolMPEG.sh
echo '#export PYTHONPATH=$PYTHONPATH:/path/to/shared/python/site-packages/lib-dynload' >> $pymoldir/pymolMPEG.sh
echo "export PYTHONPATH=$pymoldir"':$PYTHONPATH' >> $pymoldir/pymolMPEG.sh
echo "export PYTHONPATH=$pymoldir/$pymolscriptrepo/modules"':$PYTHONPATH' >> $pymoldir/pymolMPEG.sh
echo "export PYTHONPATH=$pymoldir/$pymolscriptrepo"':$PYTHONPATH' >> $pymoldir/pymolMPEG.sh
echo "export PYMOL_PATH=$modules/pymol/pymol_path" >> $pymoldir/pymolMPEG.sh
echo '#export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/shared/lib/pymollib' >> $pymoldir/pymolMPEG.sh
echo '#export LIBGL_ALWAYS_INDIRECT=no' >> $pymoldir/pymolMPEG.sh
tail -n +2 $pymoldir/pymol >> $pymoldir/pymolMPEG.sh
chmod u+x $pymoldir/pymolMPEG.sh

## Make a link, so we execute pymol with the freemol env exported
ln -s $pymoldir/pymolMPEG.sh $HOME/bin/pymol

## Make a pymolsvn.desktop
echo "#!/bin/env xdg-open" >> $pymoldir/pymolsvn.desktop
echo "[Desktop Entry]" >> $pymoldir/pymolsvn.desktop
echo "Version=1.5.x" >> $pymoldir/pymolsvn.desktop
echo "Name=PyMOL Molecular Graphics System - Open source" >> $pymoldir/pymolsvn.desktop
echo "GenericName=Molecular Modeller" >> $pymoldir/pymolsvn.desktop
echo "Comment=Model molecular structures and produce high-quality images of them" >> $pymoldir/pymolsvn.desktop
echo "Type=Application" >> $pymoldir/pymolsvn.desktop
echo "Exec=env $pymoldir/pymolMPEG.sh" >> $pymoldir/pymolsvn.desktop
echo "Icon=$pymoldir/$pymolscriptrepo/files_for_examples/pymol.xpm" >> $pymoldir/pymolsvn.desktop
echo "MimeType=chemical/x-pdb" >> $pymoldir/pymolsvn.desktop
echo "Categories=Education;Science;Chemistry;" >> $pymoldir/pymolsvn.desktop
echo "Terminal=false" >> $pymoldir/pymolsvn.desktop

## Make a startup files, which is always executed on startup.
t="'"
echo "import sys,os" >> $modules/pymol/pymol_path/run_on_startup.py
echo "import $pymolplugins" >> $modules/pymol/pymol_path/run_on_startup.py
echo "pymolplugins.preferences = {'instantsave': False, 'verbose': False}" >> $modules/pymol/pymol_path/run_on_startup.py
echo "pymolplugins.autoload = {'apbs_tools': False}" >> $modules/pymol/pymol_path/run_on_startup.py
echo "pymolplugins.set_startup_path( [$t$pymoldir/$pymolscriptrepo/plugins$t,$t$modules/pmg_tk/startup$t] )" >> $modules/pymol/pymol_path/run_on_startup.py
echo "pymolplugins.preferences = {'instantsave': True, 'verbose': False}" >> $modules/pymol/pymol_path/run_on_startup.py
echo "pymolplugins.preferences['instantsave'] = True" >> $modules/pymol/pymol_path/run_on_startup.py
</source>

=== Change MPEG settings ===
Change settings in
<source lang="bash">
$HOME/Software/pymol/svnfreemol/freemol/libpy/freemol/mpeg_encode.py
</source>
For example, change in line 205: 
FRAME_RATE 24 
(Note, only legal values is allowed: 23.976, 24, 25, 29.97, 30, 50 ,59.94, 60)

Then restart PyMOL.

[[Category:Installation|Linux Installation]]

@@ Line 107: / Line 107: @@
 echo '#export LIBGL_ALWAYS_INDIRECT=no' >> $prefix/pymolMPEG.sh
 tail -n +2 $prefix/pymol >> $prefix/pymolMPEG.sh
-chmod u+x $prefix/pymolMPEG.sh
+chmod ugo+x $prefix/pymolMPEG.sh
 ## Make a startup files, which is always executed on startup.

@@ Line 73: / Line 73: @@
 svnfreemol=svnfreemol
 pymolscriptrepo=Pymol-script-repo
+update=$prefix/updatepymol.sh
 ###################################################
 mkdir -p $prefix
@@ Line 83: / Line 84: @@
 cd $prefix/$svnpymol
 python setup.py build install --home=$prefix --install-lib=$modules --install-scripts=$prefix
 ########## Setup freemol - for MPEG support ############
@@ Line 97: / Line 97: @@
 ## Make a shortcut to an extended pymol execution
-echo "#!/bin/bash" >> $prefix/pymolMPEG.sh
+echo "#!/bin/bash" > $prefix/pymolMPEG.sh
 echo "export FREEMOL=$prefix/$svnfreemol/freemol" >> $prefix/pymolMPEG.sh
 echo "export PYMOL_GIT_MOD=$prefix/$pymolscriptrepo/modules" >> $prefix/pymolMPEG.sh
@@ Line 111: / Line 111: @@
 ## Make a startup files, which is always executed on startup.
 t="'"
-echo "import sys,os" >> $modules/pymol/pymol_path/run_on_startup.py
+echo "import sys,os" > $modules/pymol/pymol_path/run_on_startup.py
 echo "import pymol.plugins" >> $modules/pymol/pymol_path/run_on_startup.py
 echo "pymol.plugins.preferences = {'instantsave': False, 'verbose': False}" >> $modules/pymol/pymol_path/run_on_startup.py
@@ Line 117: / Line 117: @@
 echo "pymol.plugins.set_startup_path( [$t$prefix/$pymolscriptrepo/plugins$t,$t$modules/pmg_tk/startup$t] )" >> $modules/pymol/pymol_path/run_on_startup.py
 echo "pymol.plugins.preferences = {'instantsave': True, 'verbose': False}" >> $modules/pymol/pymol_path/run_on_startup.py
 </source>
 === Change MPEG settings ===

@@ Line 102: / Line 102: @@
 echo "export PYTHONPATH=$prefix/$pymolscriptrepo/modules"':$PYTHONPATH' >> $prefix/pymolMPEG.sh
 echo "export PYTHONPATH=$prefix/$pymolscriptrepo"':$PYTHONPATH' >> $prefix/pymolMPEG.sh
-#echo 'export PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/PIL' >> $prefix/pymolMPEG.sh
+echo '#export PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/PIL' >> $prefix/pymolMPEG.sh
-#echo 'export PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/lib-dynload' >> $prefix/pymolMPEG.sh
+echo '#export PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/lib-dynload' >> $prefix/pymolMPEG.sh
-#echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/sbinlab2/software/x64/lib/pymollib' >> $prefix/pymolMPEG.sh
+echo '#export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/sbinlab2/software/x64/lib/pymollib' >> $prefix/pymolMPEG.sh
-#echo 'export LIBGL_ALWAYS_INDIRECT=no' >> $prefix/pymolMPEG.sh
+echo '#export LIBGL_ALWAYS_INDIRECT=no' >> $prefix/pymolMPEG.sh
 tail -n +2 $prefix/pymol >> $prefix/pymolMPEG.sh
 chmod u+x $prefix/pymolMPEG.sh

@@ Line 100: / Line 100: @@
 echo "export FREEMOL=$prefix/$svnfreemol/freemol" >> $prefix/pymolMPEG.sh
 echo "export PYMOL_GIT_MOD=$prefix/$pymolscriptrepo/modules" >> $prefix/pymolMPEG.sh
 echo "export PYTHONPATH=$prefix/$pymolscriptrepo/modules"':$PYTHONPATH' >> $prefix/pymolMPEG.sh
 echo "export PYTHONPATH=$prefix/$pymolscriptrepo"':$PYTHONPATH' >> $prefix/pymolMPEG.sh
-echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/sbinlab2/software/x64/lib/pymollib' >> $prefix/pymolMPEG.sh
+#echo 'export PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/PIL' >> $prefix/pymolMPEG.sh
-echo 'export LIBGL_ALWAYS_INDIRECT=no' >> $prefix/pymolMPEG.sh
+#echo 'export PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/lib-dynload' >> $prefix/pymolMPEG.sh
 tail -n +2 $prefix/pymol >> $prefix/pymolMPEG.sh
 chmod u+x $prefix/pymolMPEG.sh

@@ Line 135: / Line 135: @@
 t="'"
 echo "import sys,os" >> $modules/pymol/pymol_path/run_on_startup.py
-echo "import $pymol.plugins" >> $modules/pymol/pymol_path/run_on_startup.py
+echo "import pymol.plugins" >> $modules/pymol/pymol_path/run_on_startup.py
 echo "pymol.plugins.preferences = {'instantsave': False, 'verbose': False}" >> $modules/pymol/pymol_path/run_on_startup.py
 echo "pymol.plugins.autoload = {'apbs_tools': False}" >> $modules/pymol/pymol_path/run_on_startup.py

← Older revision	Revision as of 01:20, 28 March 2014
(No difference)

@@ Line 68: / Line 68: @@
 <source lang="bash">
 #!/bin/bash -e
-pymoldir=$HOME/software/pymol
+prefix=$PWD/pymol
-modules=$pymoldir/modules
+modules=$prefix/modules
 svnpymol=svnpymol
 svnfreemol=svnfreemol
 pymolscriptrepo=Pymol-script-repo
 ###################################################
-[ -d $pymoldir ] || mkdir -p $pymoldir
+mkdir -p $prefix
-[ -d $HOME/bin ] || mkdir $HOME/bin
+mkdir -p $HOME/bin
 ###### Checkout pymol svn
-svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol $pymoldir/$svnpymol
+svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol $prefix/$svnpymol
 ###### Build and install pymol
-cd $pymoldir/$svnpymol
+cd $prefix/$svnpymol
-python setup.py build install --home=$pymoldir --install-lib=$modules
+python setup.py build install --home=$prefix --install-lib=$modules --install-scripts=$prefix
-export PYTHONPATH=$modules:$PYTHONPATH
+#install pymol $prefix/
 ########## Setup freemol - for MPEG support ############
-svn co svn://bioinformatics.org/svnroot/freemol/trunk $pymoldir/$svnfreemol
+svn co svn://bioinformatics.org/svnroot/freemol/trunk $prefix/$svnfreemol
-cd $pymoldir/$svnfreemol/src/mpeg_encode
+cd $prefix/$svnfreemol/src/mpeg_encode
-export FREEMOL=$pymoldir/$svnfreemol/freemol
+export FREEMOL=$prefix/$svnfreemol/freemol
 ./configure
 make
 make install
-−
 ########## Install Pymol-script-repo ############
-git clone git://github.com/Pymol-Scripts/Pymol-script-repo.git $pymoldir/$pymolscriptrepo
+git clone git://github.com/Pymol-Scripts/Pymol-script-repo.git $prefix/$pymolscriptrepo
-−
 ## Make a shortcut to an extended pymol execution
-echo "#!/bin/bash" >> $pymoldir/pymolMPEG.sh
+echo "#!/bin/bash" >> $prefix/pymolMPEG.sh
-echo "if [ ! -f $HOME/.local/share/applications/pymolsvn.desktop ];" >> $pymoldir/pymolMPEG.sh
+echo "export FREEMOL=$prefix/$svnfreemol/freemol" >> $prefix/pymolMPEG.sh
-echo "then" >> $pymoldir/pymolMPEG.sh
+echo "export PYMOL_GIT_MOD=$prefix/$pymolscriptrepo/modules" >> $prefix/pymolMPEG.sh
-echo "ln -s $pymoldir/pymolsvn.desktop $HOME/.local/share/applications/pymolsvn.desktop" >> $pymoldir/pymolMPEG.sh
+echo 'export PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/PIL' >> $prefix/pymolMPEG.sh
-echo "fi" >> $pymoldir/pymolMPEG.sh
+echo 'export PYTHONPATH=$PYTHONPATH:/sbinlab2/software/x64/lib64/python2.6/site-packages/lib-dynload' >> $prefix/pymolMPEG.sh
-echo "export FREEMOL=$pymoldir/$svnfreemol/freemol" >> $pymoldir/pymolMPEG.sh
+echo "export PYTHONPATH=$prefix/$pymolscriptrepo/modules"':$PYTHONPATH' >> $prefix/pymolMPEG.sh
-echo "export PYMOL_GIT_MOD=$pymoldir/$pymolscriptrepo/modules" >> $pymoldir/pymolMPEG.sh
+echo "export PYTHONPATH=$prefix/$pymolscriptrepo"':$PYTHONPATH' >> $prefix/pymolMPEG.sh
-echo '#export PYTHONPATH=$PYTHONPATH:/path/to/shared/python/site-packages/PIL' >> $pymoldir/pymolMPEG.sh
+echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/sbinlab2/software/x64/lib/pymollib' >> $prefix/pymolMPEG.sh
-echo '#export PYTHONPATH=$PYTHONPATH:/path/to/shared/python/site-packages/lib-dynload' >> $pymoldir/pymolMPEG.sh
+echo 'export LIBGL_ALWAYS_INDIRECT=no' >> $prefix/pymolMPEG.sh
-echo "export PYTHONPATH=$pymoldir/$pymolscriptrepo/modules"':$PYTHONPATH' >> $pymoldir/pymolMPEG.sh
+tail -n +2 $prefix/pymol >> $prefix/pymolMPEG.sh
-echo "export PYTHONPATH=$pymoldir/$pymolscriptrepo"':$PYTHONPATH' >> $pymoldir/pymolMPEG.sh
+chmod u+x $prefix/pymolMPEG.sh
 ## Make a startup files, which is always executed on startup.
 t="'"
@@ Line 138: / Line 115: @@
 echo "pymol.plugins.preferences = {'instantsave': False, 'verbose': False}" >> $modules/pymol/pymol_path/run_on_startup.py
 echo "pymol.plugins.autoload = {'apbs_tools': False}" >> $modules/pymol/pymol_path/run_on_startup.py
-echo "pymol.plugins.set_startup_path( [$t$pymoldir/$pymolscriptrepo/plugins$t,$t$modules/pmg_tk/startup$t] )" >> $modules/pymol/pymol_path/run_on_startup.py
+echo "pymol.plugins.set_startup_path( [$t$prefix/$pymolscriptrepo/plugins$t,$t$modules/pmg_tk/startup$t] )" >> $modules/pymol/pymol_path/run_on_startup.py
 echo "pymol.plugins.preferences = {'instantsave': True, 'verbose': False}" >> $modules/pymol/pymol_path/run_on_startup.py
 === Change MPEG settings ===