Phenix: Difference between revisions

75 bytes added ,  19 March 2015
(Installation from source, and of Rosetta interface)
Line 917: Line 917:
== Installation from source, and of Rosetta interface ==
== Installation from source, and of Rosetta interface ==


Phenix can be installed from a ''binary'' installer. Despite this designation it has enough source files for re-compilation. Re-compilation is normally not required, and requires to specify the --source option to the ./install command.
Phenix can be installed from a ''binary'' installer. Despite this designation, it has the source files for re-compilation. However, re-compilation is normally not required, and requires to specify the --source option to the ./install command.


[http://www.phenix-online.org/documentation/reference/rosetta_refine.html phenix.rosetta_refine] (and [http://www.phenix-online.org/documentation/reference/mr_rosetta.html phenix.mr_rosetta]) requires a working Rosetta installation. The easiest way is to download one of the weekly binary+source Rosetta bundles (to be found following this [https://www.rosettacommons.org/software/license-and-download link]). If I understand correctly, the tar-file only has to be unpacked; binaries and libraries are pre-compiled. Your .bashrc has to be modified to have e.g.
[http://www.phenix-online.org/documentation/reference/rosetta_refine.html phenix.rosetta_refine] (and [http://www.phenix-online.org/documentation/reference/mr_rosetta.html phenix.mr_rosetta]) requires a working Rosetta installation. The easiest way is to download one of the weekly binary+source Rosetta bundles (to be found following this [https://www.rosettacommons.org/software/license-and-download link]). The tar-file only has to be unpacked; binaries and libraries are pre-compiled. Your .bashrc has to be modified to have e.g.
  export PHENIX_ROSETTA_PATH=/usr/local/src/rosetta_bin_linux_2015.09.57646_bundle
  export PHENIX_ROSETTA_PATH=/usr/local/src/rosetta_bin_linux_2015.09.57646_bundle
  export ROSETTA3_DB=$PHENIX_ROSETTA_PATH/main/database
  export ROSETTA3_DB=$PHENIX_ROSETTA_PATH/main/database
(or similarly for .cshrc) and
(or similarly for .cshrc) and
  rosetta.build_phenix_interface
  rosetta.build_phenix_interface
needs to be run.  
needs to be run. (For MR_rosetta, installation is described at [http://www.phenix-online.org/documentation/reference/mr_rosetta.html#id17].)


For MR_rosetta, installation is described at [http://www.phenix-online.org/documentation/reference/mr_rosetta.html#id17] .
If this fails (for example, compiler error messages), then one must re-compile Phenix and/or Rosetta. Try to re-compile only Phenix first (and after that, try rosetta.build_phenix_interface again); Rosetta re-compilation may take hours. There are several issues associated with re-compilation:
 
If this fails (for example, compiler error messages), then one must re-compile Phenix and/or Rosetta. Try to re-compile only Phenix first; Rosetta re-compilation may take hours. There are several issues associated with this:
* if the Phenix binary installer is not used: the Phenix source installer requires (on Fedora and RHEL) the openssl-devel and libXt-devel to be installed on the system
* if the Phenix binary installer is not used: the Phenix source installer requires (on Fedora and RHEL) the openssl-devel and libXt-devel to be installed on the system
* to re-compile Rosetta: go to the main/source directory and issue:  
* to re-compile Rosetta: go to the main/source directory and issue:  
  ./scons.py -j8 mode=release bin
  ./scons.py -j8 mode=release bin
if your machine has 8 or more cores. I was able to re-compile Rosetta on CentOS7 whereas re-compilation stopped with an error on Ubuntu 12.04 LTS.
(The -j8 should be used if your machine has 8 or more cores.) I was able to re-compile Rosetta on CentOS7 whereas re-compilation stopped with an error on Ubuntu 12.04.5 LTS.


== See also ==
== See also ==
1,330

edits