Coot: Difference between revisions

6,859 bytes added ,  11 February 2012
(Installing Coot on Mandriva)
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This is the recommended way for those who do not want to delve into the mysteries of compiling and linking a great but complex piece of software. Read the (somewhat outdated, it seems) [http://www.ysbl.york.ac.uk/%7Eemsley/coot/coot-faq.html Coot FAQ] to find "Additional Notes" for your operating system.
This is the recommended way for those who do not want to delve into the mysteries of compiling and linking a great but complex piece of software. Read the (somewhat outdated, it seems) [http://www.ysbl.york.ac.uk/%7Eemsley/coot/coot-faq.html Coot FAQ] to find "Additional Notes" for your operating system.


In short, just go to http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ and pick a suitable binary, e.g.
In short, just go to http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ (a mirror is at ftp://turn5.biologie.uni-konstanz.de/coot/software/binaries/nightlies/pre-release/ ) and pick a suitable binary, e.g.
coot-0.5-pre-1-revision-1003-binary-Linux-i386-fedora-5.tar.gz for a Red Hat Enterprise Linux 5 or CentOS-5 system (Fedora 6 corresponds to RHEL5, thus Fedora 5 binaries are OK). If you prefer a "stable" binary, these are at http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable/.
coot-0.5-pre-1-revision-1003-binary-Linux-i386-fedora-5.tar.gz for a Red Hat Enterprise Linux 5 or CentOS-5 system (Fedora 6 corresponds to RHEL5, thus Fedora 5 binaries are OK). If you prefer a "stable" binary, these are at http://www.ysbl.york.ac.uk/~emsley/software/binaries/stable/.


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  yum whatprovides <thatlibrary>
  yum whatprovides <thatlibrary>
and install the library, again using yum (assuming yum is available in your distribution, otherwise use apt or whatever is there for this purpose).
and install the library, again using yum (assuming yum is available in your distribution, otherwise use apt or whatever is there for this purpose).
==== Example: installing coot-0.7-pre-1-revision-3999-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz on 64bit SL6.1 ====
First of all, SL (Scientific Linux) is a derivative of RHEL, as is CentOS. So all three OSs behave exactly the same.
The binaries with "x86_64" binaries are for 64bit systems; the "i386" binaries are for 32bit systems. Since my notebook is 64bits, I downloaded http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/coot-0.7-pre-1-revision-3999-binary-Linux-x86_64-centos-5-python-gtk2.tar.gz . As root, I did "cd /usr/local/src" and un-tarred. Then
[root@localhost src]# ldd coot-Linux-x86_64-centos-5-gtk2-python/bin/coot-real
linux-vdso.so.1 =>  (0x00007ffffc5dd000)
libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x0000003dccc00000)
libguilegtk-2.0.so.0 => not found
libgthread-2.0.so.0 => /lib64/libgthread-2.0.so.0 (0x0000003dcb400000)
libguile.so.17 => not found
libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x0000003dc8400000)
libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00007fc66033b000)
libltdl.so.3 => not found
libclipper-ccp4.so.2 => not found
libclipper-cif.so.2 => not found
libclipper-phs.so.2 => not found
libclipper-contrib.so.2 => not found
libclipper-minimol.so.2 => not found
libclipper-cns.so.2 => not found
libclipper-mmdb.so.2 => not found
libclipper-core.so.2 => not found
libccp4c.so.0 => not found
librfftw.so.2 => not found
libfftw.so.2 => not found
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fc66011b000)
libssm.so.0 => not found
libmmdb.so.0 => not found
libpython2.7.so.1.0 => not found
libutil.so.1 => /lib64/libutil.so.1 (0x00007fc65ff16000)
libgtkglext-x11-1.0.so.0 => not found
libgdkglext-x11-1.0.so.0 => not found
libXmu.so.6 => /usr/lib64/libXmu.so.6 (0x0000003dcd800000)
libXt.so.6 => /usr/lib64/libXt.so.6 (0x0000003dd8800000)
libSM.so.6 => /usr/lib64/libSM.so.6 (0x0000003dd5c00000)
libICE.so.6 => /usr/lib64/libICE.so.6 (0x0000003dd5800000)
libpangox-1.0.so.0 => /usr/lib64/libpangox-1.0.so.0 (0x0000003dc9c00000)
libglut.so.3 => not found
libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003dd3000000)
libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x00007fc65fcb5000)
libXext.so.6 => /usr/lib64/libXext.so.6 (0x0000003dcc400000)
libX11.so.6 => /usr/lib64/libX11.so.6 (0x0000003dcb000000)
libgnomecanvas-2.so.0 => /usr/lib64/libgnomecanvas-2.so.0 (0x0000003de0800000)
libart_lgpl_2.so.2 => /usr/lib64/libart_lgpl_2.so.2 (0x0000003ddfc00000)
libpangoft2-1.0.so.0 => /usr/lib64/libpangoft2-1.0.so.0 (0x0000003dd1000000)
libgsl.so.0 => not found
libgslcblas.so.0 => not found
libcurl.so.4 => /usr/lib64/libcurl.so.4 (0x00007fc65fa5f000)
libidn.so.11 => /lib64/libidn.so.11 (0x0000003dd2c00000)
librt.so.1 => /lib64/librt.so.1 (0x00007fc65f857000)
libssl.so.6 => not found
libcrypto.so.6 => not found
libz.so.1 => /lib64/libz.so.1 (0x0000003dc9800000)
libglade-2.0.so.0 => /usr/lib64/libglade-2.0.so.0 (0x0000003de0c00000)
libgtk-x11-2.0.so.0 => /usr/lib64/libgtk-x11-2.0.so.0 (0x0000003dd1800000)
libgdk-x11-2.0.so.0 => /usr/lib64/libgdk-x11-2.0.so.0 (0x0000003dd0800000)
libatk-1.0.so.0 => /usr/lib64/libatk-1.0.so.0 (0x0000003dd0c00000)
libgdk_pixbuf-2.0.so.0 => /usr/lib64/libgdk_pixbuf-2.0.so.0 (0x0000003dcf400000)
libpangocairo-1.0.so.0 => /usr/lib64/libpangocairo-1.0.so.0 (0x0000003dcf800000)
libpango-1.0.so.0 => /usr/lib64/libpango-1.0.so.0 (0x0000003dd2000000)
libcairo.so.2 => /usr/lib64/libcairo.so.2 (0x0000003dcfc00000)
libgobject-2.0.so.0 => /lib64/libgobject-2.0.so.0 (0x0000003dca800000)
libgmodule-2.0.so.0 => /lib64/libgmodule-2.0.so.0 (0x0000003dcac00000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fc65f64e000)
libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00007fc65f368000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003dd4800000)
libm.so.6 => /lib64/libm.so.6 (0x00007fc65f0e3000)
libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x0000003dca000000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003dd2800000)
libc.so.6 => /lib64/libc.so.6 (0x00007fc65ed41000)
libfreebl3.so => /lib64/libfreebl3.so (0x0000003dd5400000)
/lib64/ld-linux-x86-64.so.2 (0x00007fc66058c000)
libuuid.so.1 => /lib64/libuuid.so.1 (0x0000003dd3400000)
libXdamage.so.1 => /usr/lib64/libXdamage.so.1 (0x0000003dd1400000)
libXfixes.so.3 => /usr/lib64/libXfixes.so.3 (0x0000003dce800000)
libXxf86vm.so.1 => /usr/lib64/libXxf86vm.so.1 (0x0000003dd3800000)
libdrm.so.2 => /usr/lib64/libdrm.so.2 (0x0000003dd2400000)
libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x0000003dcbc00000)
libgailutil.so.18 => /usr/lib64/libgailutil.so.18 (0x0000003ddec00000)
libgio-2.0.so.0 => /lib64/libgio-2.0.so.0 (0x0000003dcc000000)
libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x0000003dcc800000)
libfontconfig.so.1 => /usr/lib64/libfontconfig.so.1 (0x0000003dcd400000)
libldap-2.4.so.2 => /lib64/libldap-2.4.so.2 (0x0000003ddc400000)
libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x0000003dd6800000)
libkrb5.so.3 => /lib64/libkrb5.so.3 (0x0000003dd6400000)
libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x0000003dd4c00000)
libcom_err.so.2 => /lib64/libcom_err.so.2 (0x00007fc65eb38000)
libssl3.so => /usr/lib64/libssl3.so (0x0000003dd9000000)
libsmime3.so => /usr/lib64/libsmime3.so (0x0000003dd8c00000)
libnss3.so => /usr/lib64/libnss3.so (0x0000003dd8400000)
libnssutil3.so => /usr/lib64/libnssutil3.so (0x0000003dd8000000)
libplds4.so => /lib64/libplds4.so (0x0000003dd7400000)
libplc4.so => /lib64/libplc4.so (0x0000003dd7c00000)
libnspr4.so => /lib64/libnspr4.so (0x0000003dd7000000)
libssh2.so.1 => /usr/lib64/libssh2.so.1 (0x0000003ddc800000)
libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x00007fc65e7e4000)
libXrender.so.1 => /usr/lib64/libXrender.so.1 (0x0000003dce000000)
libXinerama.so.1 => /usr/lib64/libXinerama.so.1 (0x0000003dcec00000)
libXi.so.6 => /usr/lib64/libXi.so.6 (0x0000003dcdc00000)
libXrandr.so.2 => /usr/lib64/libXrandr.so.2 (0x0000003dce400000)
libXcursor.so.1 => /usr/lib64/libXcursor.so.1 (0x0000003dcf000000)
libXcomposite.so.1 => /usr/lib64/libXcomposite.so.1 (0x0000003dd0000000)
libpixman-1.so.0 => /usr/lib64/libpixman-1.so.0 (0x0000003dd0400000)
libXau.so.6 => /usr/lib64/libXau.so.6 (0x0000003dcb800000)
libresolv.so.2 => /lib64/libresolv.so.2 (0x00007fc65e5c6000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00007fc65e3a7000)
libexpat.so.1 => /lib64/libexpat.so.1 (0x0000003dcd000000)
liblber-2.4.so.2 => /lib64/liblber-2.4.so.2 (0x0000003ddbc00000)
libsasl2.so.2 => /usr/lib64/libsasl2.so.2 (0x0000003dda400000)
libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x0000003dd6000000)
libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00007fc65e1a3000)
libssl.so.10 => /usr/lib64/libssl.so.10 (0x00007fc65df48000)
libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x00007fc65dbae000)


=== Installation on Debian/Ubuntu from debian archive files ===
=== Installation on Debian/Ubuntu from debian archive files ===
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