diff --git a/Release-Notes.md b/Release-Notes.md index 6d16db729..064f1ed1e 100644 --- a/Release-Notes.md +++ b/Release-Notes.md @@ -785,7 +785,7 @@ A new Job Distributor, JD3, is ready for use. This is mostly invisible to end u Although most improvements were in Rosetta3.7, we continue to improve the fraction of unmodified PDBs Rosetta can handle. (Don't worry - we've always been able to handle canonical protein well - but we are doing an ever-improving job with strange stuff like the GFP fluorophore, chemically concatenated ligands, glycans, RNA, etc). ###Cxx11 builds -Rosetta turned on Cxx11 features in its C++. This deprecates the compatibility of a lot of older compilers. See for more information. +Rosetta turned on Cxx11 features in its C++. This deprecates the compatibility of a lot of older compilers. See for more information. ###Executable naming We've tweaked the build system such that the built executables are named a little more simply. The tripartite names (rosetta_scripts.default.linuxgccrelease) will work as before, but now the two-part names rosetta_scripts.linuxgccrelease) will always point towards the default build, instead of the most recent build. @@ -951,7 +951,7 @@ Enzyme specificity re-design (using coupled_moves) ([http://www.ncbi.nlm.nih.gov * Multiple refactorings in the chemistry layers, allowing: * Poses with carbohydrates * Better support for ribonucleoprotein - * Support for all ligands in the PDB’s chemical dictionary (note you must [install that dictionary separately](build_documentation/Build-Documentation#setting-up-rosetta-3_obtaining-additional-files_pdb-chemical-components-dictionary)) + * Support for all ligands in the PDB’s chemical dictionary (note you must [install that dictionary separately](Building_Rosetta/Building-Rosetta#setting-up-rosetta-3_obtaining-additional-files_pdb-chemical-components-dictionary)) * Support for runtime manipulation of chemistry (adding/removing atoms) * Support for rotamer libraries with arbitrary numbers of backbone torsion dependencies * Automatic setup of bonds to [metal ions](rosetta_basics/non_protein_residues/Metals). diff --git a/_Sidebar.md b/_Sidebar.md index a789ae551..c46b4d2a3 100644 --- a/_Sidebar.md +++ b/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Tutorials| https://www.rosettacommons.org/demos/latest/Home#tutorials ]] diff --git a/application_documentation/RosettaNMR-with-Paramagnetic-Restraints.md b/application_documentation/RosettaNMR-with-Paramagnetic-Restraints.md index d8e6263fb..b4b65a863 100644 --- a/application_documentation/RosettaNMR-with-Paramagnetic-Restraints.md +++ b/application_documentation/RosettaNMR-with-Paramagnetic-Restraints.md @@ -8,7 +8,7 @@ The protocol capture is also available in the demos repository under `Rosetta/de This document is a protocol capture to the manuscript "Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints" by Kuenze G. et al. For following the steps in this protocol capture, it is recommended that the user downloads the weekly release version **v2019.02-dev60579** , which is available at [https://www.rosettacommons.org/software/license-and-download](https://www.rosettacommons.org/software/license-and-download). -Instructions on how to install Rosetta, information on software dependencies and install times, and how to get started with the program can be found on the Rosetta Commons documentation webpages: [https://www.rosettacommons.org/docs/latest/build\_documentation/Build-Documentation](https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation) and [https://www.rosettacommons.org/docs/latest/getting\_started/Getting-Started](https://www.rosettacommons.org/docs/latest/getting_started/Getting-Started). +Instructions on how to install Rosetta, information on software dependencies and install times, and how to get started with the program can be found on the Rosetta Commons documentation webpages: [https://www.rosettacommons.org/docs/latest/build\_documentation/Building-Rosetta](https://www.rosettacommons.org/docs/latest/Building_Rosetta/Building-Rosetta) and [https://www.rosettacommons.org/docs/latest/getting\_started/Getting-Started](https://www.rosettacommons.org/docs/latest/getting_started/Getting-Started). This protocol capture contains instructions for applying paramagnetic restraints in the RosettaNMR framework to four different modeling tasks: protein _de no_ structure prediction (_protocol 1_), modeling of symmetric proteins (_protocol 2_), protein-ligand docking (_protocol 3_) and protein-protein docking (_protocol 4_). All required input files for running those RosettaNMR calculations can be found in the directory accompanying this protocol capture. Copy the file **protocol\_capture\_rosettanmr\_inputfiles.tar.gz** to your desired location and extract and unpack the input file directory by running the command: diff --git a/application_documentation/_Sidebar.md b/application_documentation/_Sidebar.md index 279f997bd..5f0a4ae3b 100644 --- a/application_documentation/_Sidebar.md +++ b/application_documentation/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Tutorials| https://www.rosettacommons.org/demos/latest/Home#tutorials ]] diff --git a/application_documentation/rna/auto-drrafter.md b/application_documentation/rna/auto-drrafter.md index 714536d11..8879b8533 100644 --- a/application_documentation/rna/auto-drrafter.md +++ b/application_documentation/rna/auto-drrafter.md @@ -29,7 +29,7 @@ A demo of auto-DRRAFTER is available in `ROSETTA_HOME/main/demos/public/drrafter ##Setting up auto-DRRAFTER 1. Download Rosetta here . You will need to get a license before downloading Rosetta (free for academic users). auto-DRRAFTER will be available starting in Rosetta weekly releases *after* 2019.47. **auto-DRRAFTER is NOT available in Rosetta 3.11 (it will be available in 3.12)**. -2. If you're not using the precompiled binaries (these are available for Mac and Linux and you can access them by downloading source+binaries in Step 1), install Rosetta following the instructions available [here] (https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation). +2. If you're not using the precompiled binaries (these are available for Mac and Linux and you can access them by downloading source+binaries in Step 1), install Rosetta following the instructions available [here] (https://www.rosettacommons.org/docs/latest/Building_Rosetta/Building-Rosetta). 3. Make sure you have python installed and install networkx and mrcfile. For example, type: `pip install networkx mrcfile` 4. Install EMAN2 version 2.22 (https://blake.bcm.edu/emanwiki/EMAN2/Install). Confirm that `e2proc3d.py` and `e2segment3d.py` are installed by typing: ``` diff --git a/application_documentation/rna/drrafter.md b/application_documentation/rna/drrafter.md index b99243be0..814c01f4a 100644 --- a/application_documentation/rna/drrafter.md +++ b/application_documentation/rna/drrafter.md @@ -20,7 +20,7 @@ A demo of DRRAFTER is available in `ROSETTA_HOME/demos/public/drrafter/`. Instru ## Installing DRRAFTER 1. Download Rosetta [here](https://www.rosettacommons.org/software/license-and-download). You will need to get a license before downloading Rosetta (free for academic users). DRRAFTER is available in the Rosetta weekly releases starting with 2018.12. **DRRAFTER is NOT available in Rosetta 3.9.** -2. If you're not using the precompiled binaries (these are available for Mac and Linux and you can access them by downloading source+binaries in Step 1), install Rosetta following the instructions available [here](https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation). +2. If you're not using the precompiled binaries (these are available for Mac and Linux and you can access them by downloading source+binaries in Step 1), install Rosetta following the instructions available [here](https://www.rosettacommons.org/docs/latest/Building_Rosetta/Building-Rosetta). 3. Make sure that you have python (v2.7) installed. 4. Install Rosetta RNA tools. See instructions and documentation [here] (https://www.rosettacommons.org/docs/latest/application_documentation/rna/RNA-tools). 5. Check that the ROSETTA environmental variable is set (you should have set this up during RNA tools installation). Type `echo $ROSETTA`. This should return the path to your Rosetta directory. If it does not return anything, go back to step 4 and make sure that you follow the steps for RNA tools setup. diff --git a/application_documentation/tools/Tools.md b/application_documentation/tools/Tools.md index 28a9b8843..ba6365d41 100644 --- a/application_documentation/tools/Tools.md +++ b/application_documentation/tools/Tools.md @@ -1525,9 +1525,9 @@ tools/analysis/apps/sequence_tolerance.R ## Build scripts -* See [[Build Documentation]] for more information. +* See [[Building Rosetta]] for more information. -main/source/[[scons.py|Build Documentation]] +main/source/[[scons.py|Building Rosetta]]   - Main script for Rosetta compilation. main/source/ninja_build.py diff --git a/build_documentation/Build-Documentation.md b/build_documentation/Building-Rosetta.md similarity index 100% rename from build_documentation/Build-Documentation.md rename to build_documentation/Building-Rosetta.md diff --git a/build_documentation/Scons-Overview-and-Specifics.md b/build_documentation/Scons-Overview-and-Specifics.md index 1a567d8fe..f0ddf9f77 100644 --- a/build_documentation/Scons-Overview-and-Specifics.md +++ b/build_documentation/Scons-Overview-and-Specifics.md @@ -59,7 +59,7 @@ Platforms are initially setup by functions in the main/source/tools/build/ ##See Also -* [[Build Documentation]]: Information on setting up Rosetta +* [[Building Rosetta]]: Information on setting up Rosetta * [[Getting Started]]: A page for people new to Rosetta. New users start here. * [[TACC]]: Information for running Rosetta on the TACC/Stampede cluster. * [[Commands collection]]: A list of example command lines for running Rosetta executable files diff --git a/build_documentation/_Sidebar.md b/build_documentation/_Sidebar.md index feb9d9620..8f9658211 100644 --- a/build_documentation/_Sidebar.md +++ b/build_documentation/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] * [[Supported platforms|platforms]] diff --git a/build_documentation/platforms.md b/build_documentation/platforms.md index 333712689..cfc70a3b1 100644 --- a/build_documentation/platforms.md +++ b/build_documentation/platforms.md @@ -86,14 +86,14 @@ To assist in checking for compatibility, we have put together a small Python tes downloadable from Note: Even if the default compiler is a version without support, often there will be an updated compiler available on the system. -Talk to your system administrator for more details, and see [the build documentation](Build-Documentation#setting-up-rosetta-3_alternative-setup-for-individual-workstations_scons-mac-linux) +Talk to your system administrator for more details, and see [the Building Rosetta](Building-Rosetta#setting-up-rosetta-3_alternative-setup-for-individual-workstations_scons-mac-linux) for compiling with a non-default compiler. In worse-case scenarios, the weekly releases of Rosetta 2015.39 and before may be compatible with older compilers. ##See Also * [[Getting Started]]: A page for people new to Rosetta -* [[Build Documentation]]: Instructions for building Rosetta +* [[Building Rosetta]]: Instructions for building Rosetta * [[Scons Overview and Specifics]]: Advanced details on the Scons build system * [[TACC]]: Information for running Rosetta on the TACC/Stampede cluster. * [[Rosetta Servers]]: Web-based servers for Rosetta applications diff --git a/development_documentation/Common-Errors.md b/development_documentation/Common-Errors.md index f4070239f..48565e9c6 100644 --- a/development_documentation/Common-Errors.md +++ b/development_documentation/Common-Errors.md @@ -97,6 +97,6 @@ PhenixInterface::setAlgorithm( ##See Also * [[Development Documentation]] -* [[Build Documentation]] +* [[Building Rosetta]] * [[Scons Overview and Specifics]]: Detailed information on the Scons compiling system * [[FAQ]] \ No newline at end of file diff --git a/development_documentation/Development-Documentation.md b/development_documentation/Development-Documentation.md index b343cd091..d90a650d6 100644 --- a/development_documentation/Development-Documentation.md +++ b/development_documentation/Development-Documentation.md @@ -109,5 +109,5 @@ For RosettaCommons developers, we have a version of the Doxygen documentation wh * [[PyRosetta]]: Wiki page for PyRosetta, the independent Python interface to Rosetta * [[Rosetta Timeline]]: History of Rosetta * [[Getting Started]]: A page for people new to Rosetta -* [[Build Documentation]]: Information on building Rosetta +* [[Building Rosetta]]: Information on building Rosetta * [[Running Rosetta with options]]: Instructions for running Rosetta executables diff --git a/development_documentation/_Sidebar.md b/development_documentation/_Sidebar.md index c27f99c71..edc192868 100644 --- a/development_documentation/_Sidebar.md +++ b/development_documentation/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Tutorials| https://www.rosettacommons.org/demos/latest/Home#tutorials ]] diff --git a/development_documentation/code_structure/rosetta-library-structure.md b/development_documentation/code_structure/rosetta-library-structure.md index 8453ce43b..89a465292 100644 --- a/development_documentation/code_structure/rosetta-library-structure.md +++ b/development_documentation/code_structure/rosetta-library-structure.md @@ -4,11 +4,11 @@ The `rosetta/main/source` directory contains eight top level directories of whic - `src/` The src directory contains all the source files for the rosetta library. See [[An overview page for the src directory of the Rosetta|src-index-page]] for more information. - `test/` The test directory contains source files for rosetta's unit tests. The integration, and scientific tests now live in rosetta/main/tests. Together, these two sets of tests are used to verify that the rosetta library is functioning correctly. See [[A Guide to Running and Writing Tests for Rosetta|rosetta-tests]] for more information on Rosetta Tests. -- `bin/` The bin directory contains soft links to all the rosetta applications. Currently separate softlinks are stored for each combination of operating system (linux, macos), compiler(gcc, icc), and build mode (debug, release, release_debug). See the [[build documentation]] page for further information of the build system. -- `build/` The build directory is where all the object files and shared libraries for build configuration are stored. The directory structure is automatically created by the scons build system. See the [[build documentation]] page for further information of the build system. +- `bin/` The bin directory contains soft links to all the rosetta applications. Currently separate softlinks are stored for each combination of operating system (linux, macos), compiler(gcc, icc), and build mode (debug, release, release_debug). See the [[Building Rosetta]] page for further information of the build system. +- `build/` The build directory is where all the object files and shared libraries for build configuration are stored. The directory structure is automatically created by the scons build system. See the [[Building Rosetta]] page for further information of the build system. - `scripts/` The scripts directory is the recommended location for all RosettaScripts XML files (in the rosetta_scripts subdirectory) and Python scripts for scientific purposes (in the python subdirectory). Private PyRosetta applications are also placed in this directory. - `doc/` The doc directory [[once contained|History-of-Rosetta-documentation]] all the stand alone doxygen pages. Those pages are now this wiki (the documentation repository). It still holds an autogenerated page of option system information. -- `tools/` The tools directory contains the files for the custom SCons Builder for the rosetta library. See the [[build documentation]] page for further information of the build system. +- `tools/` The tools directory contains the files for the custom SCons Builder for the rosetta library. See the [[Building Rosetta]] page for further information of the build system. - `demo/` The demo directory once contained demos (now the demos repository). ##See Also diff --git a/development_documentation/test/Running-Tests-on-the-Test-Server.md b/development_documentation/test/Running-Tests-on-the-Test-Server.md index 991f06c2d..d736ee504 100644 --- a/development_documentation/test/Running-Tests-on-the-Test-Server.md +++ b/development_documentation/test/Running-Tests-on-the-Test-Server.md @@ -75,7 +75,7 @@ If you happen to work on a project for which this seems appropriate—for exampl * [[Testing server]]: Information on the testing server * [[Integration tests]]: General information on Rosetta's integration tests -* [[Build Documentation]]: Find instructions for building Rosetta mpi executables here +* [[Building Rosetta]]: Find instructions for building Rosetta mpi executables here * [[Testing server]]: Server that can be used to run Rosetta integration tests automatically * [[Running Tests on the Test Server]]: Instructions for using the testing server * [[Testing home page|rosetta-tests]] diff --git a/development_documentation/test/Writing-MPI-Integration-Tests.md b/development_documentation/test/Writing-MPI-Integration-Tests.md index de4a73b35..65ee4eb1b 100644 --- a/development_documentation/test/Writing-MPI-Integration-Tests.md +++ b/development_documentation/test/Writing-MPI-Integration-Tests.md @@ -26,7 +26,7 @@ Only those tests that have a `command.mpi` file will run in this mode. * [[Integration tests]]: General information on Rosetta's integration tests * [[Running Rosetta in MPI mode|running-rosetta-with-options#mpi]] -* [[Build Documentation]]: Find instructions for building Rosetta mpi executables here +* [[Building Rosetta]]: Find instructions for building Rosetta mpi executables here * [[Testing server]]: Server that can be used to run Rosetta integration tests automatically * [[Running Tests on the Test Server]]: Instructions for using the testing server * [[Testing home page|rosetta-tests]] diff --git a/development_documentation/tutorials/devel-tutorials.md b/development_documentation/tutorials/devel-tutorials.md index 319ff2c2b..78724934a 100644 --- a/development_documentation/tutorials/devel-tutorials.md +++ b/development_documentation/tutorials/devel-tutorials.md @@ -35,5 +35,5 @@ The following is a list of guides for using specific Rosetta features or perform * [[PyRosetta]]: Wiki page for PyRosetta, the independent Python interface to Rosetta * [[Rosetta Timeline]]: History of Rosetta * [[Getting Started]]: A page for people new to Rosetta -* [[Build Documentation]]: Information on building Rosetta +* [[Building Rosetta]]: Information on building Rosetta * [[Running Rosetta with options]]: Instructions for running Rosetta executables \ No newline at end of file diff --git a/development_documentation/tutorials/writing-an-app.md b/development_documentation/tutorials/writing-an-app.md index 21fbd2911..f07e2ca4e 100644 --- a/development_documentation/tutorials/writing-an-app.md +++ b/development_documentation/tutorials/writing-an-app.md @@ -23,5 +23,5 @@ This guide is under construction. Clearly a "Writing a 'Writing a Rosetta Appli * [[RosettaEncyclopedia]]: Detailed descriptions of concepts in Rosetta. * [[RosettaScripts]]: Instructions for writing RosettaScripts, the Rosetta XML interface * [[PyRosetta]]: Wiki page for PyRosetta, the independent Python interface to Rosetta -* [[Build Documentation]]: Information on building Rosetta +* [[Building Rosetta]]: Information on building Rosetta * [[Running Rosetta with options]]: Instructions for running Rosetta executables diff --git a/getting_started/FAQ.md b/getting_started/FAQ.md index caaf95d98..d8b1791f3 100644 --- a/getting_started/FAQ.md +++ b/getting_started/FAQ.md @@ -29,7 +29,7 @@ Most modern processors should be suitable. The one limitation you may run into i #### How do I compile Rosetta? -Please see the page [[Build Documentation]] or the [Installation tutorial](https://www.rosettacommons.org/demos/latest/tutorials/install_build/install_build) for instructions on how to compile and install Rosetta. +Please see the page [[Building Rosetta]] or the [Installation tutorial](https://www.rosettacommons.org/demos/latest/tutorials/install_build/install_build) for instructions on how to compile and install Rosetta. #### Where can I learn how to use Rosetta? diff --git a/getting_started/Getting-Started.md b/getting_started/Getting-Started.md index 7e48e9979..8988e710d 100644 --- a/getting_started/Getting-Started.md +++ b/getting_started/Getting-Started.md @@ -91,7 +91,7 @@ After downloading Rosetta, go through [these detailed tutorials](https://www.ros Local installation implies that one will be using Rosetta through a [[command line interface (or terminal)|http://en.wikipedia.org/wiki/Command-line_interface]]. For local users, you are unlikely to want to install Rosetta to the entire system. Rosetta is quite happy to be compiled and installed by regular users without administrative rights — this is how the developers use it. -You may need administrative rights to install [[dependencies|Build-Documentation#dependencies]]. +You may need administrative rights to install [[dependencies|Building-Rosetta#dependencies]]. * First untar/uncompress your downloaded copy of the code (`tar -xvzf Rosetta[releasenumber].tar.gz`). @@ -103,7 +103,7 @@ You may need administrative rights to install [[dependencies|Build-Documentation Replace with a number one processor fewer than your computer has. Expect compilation to take a while (hours on one processor). -See our extensive [[build documentation|Build-Documentation#compiling-rosetta-3]] for further instructions and troubleshooting. +See our extensive [[Building Rosetta|Building-Rosetta#compiling-rosetta-3]] for further instructions and troubleshooting. ###Windows Unfortunately, we are not currently able to support the whole of Rosetta on Windows. @@ -136,7 +136,7 @@ Developers can update these doc pages through our [interactive wiki](https://www * [Introductory Rosetta Tutorials](https://www.rosettacommons.org/demos/latest/Home#tutorials) * [[Resources for learning biophysics and computational modeling]] -* [[Build Documentation]]: Information on setting up Rosetta +* [[Building Rosetta]]: Information on setting up Rosetta * [[I want to do x]]: Guides to specific types of structural perturbations using RosettaScripts * [[Application Documentation]]: Links to documentation for a variety of Rosetta applications * [[Analyzing Results]]: Tips for analyzing results generated using Rosetta diff --git a/getting_started/_Sidebar.md b/getting_started/_Sidebar.md index 6d64974bb..0dc8d9737 100644 --- a/getting_started/_Sidebar.md +++ b/getting_started/_Sidebar.md @@ -14,7 +14,7 @@ * [[Rosetta canon]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Tutorials| https://www.rosettacommons.org/demos/latest/Home#tutorials ]] diff --git a/internal_documentation/GithubWorkflow.md b/internal_documentation/GithubWorkflow.md index ff487bffc..3bee7480a 100644 --- a/internal_documentation/GithubWorkflow.md +++ b/internal_documentation/GithubWorkflow.md @@ -48,7 +48,7 @@ Branching and merging is the preferred development pattern in git, and because t * You will need to pre-accept GitHub's RSA key fingerprint by following [[the last step of the SSH instructions|https://help.github.com/articles/generating-ssh-keys]]. * People contributing code will need to sign either the [developer agreement]() (for members of a RosettaCommons member lab) or the [Contributor Licensing Agreement](insert link) before their PRs can be accepted. * Members of RosettaCommons labs should consult the internal wiki for more details on getting set up as a RosettaCommons member. (Ask other lab members for the website and login info.) -* You will need some of the standard [[Rosetta external dependencies|Build-Documentation]] like a compiler, etc. +* You will need some of the standard [[Rosetta external dependencies|Building-Rosetta]] like a compiler, etc. ####Obtaining Rosetta. diff --git a/internal_documentation/_Sidebar.md b/internal_documentation/_Sidebar.md index 02ef7e6ef..677958188 100644 --- a/internal_documentation/_Sidebar.md +++ b/internal_documentation/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Tutorials| https://www.rosettacommons.org/demos/latest/Home#tutorials ]] diff --git a/internal_documentation/a-guide-to-developing-in-rosetta.md b/internal_documentation/a-guide-to-developing-in-rosetta.md index 7490f72d4..ea9675102 100644 --- a/internal_documentation/a-guide-to-developing-in-rosetta.md +++ b/internal_documentation/a-guide-to-developing-in-rosetta.md @@ -58,7 +58,7 @@ Rosetta uses Doxygen to produce documentation. [[Tips for writing doxygen docume Compiling the Rosetta library and application using SCons ========================================================= -[[A Guide to Using SCons to Build Rosetta|Build-Documentation]] demonstrates some simple features of the build system followed by a more detailed discussion of the build system structure and how it can be extended. Rosetta uses a custom SCons builder. The builder allows multiple build configurations. +[[A Guide to Using SCons to Build Rosetta|Building-Rosetta]] demonstrates some simple features of the build system followed by a more detailed discussion of the build system structure and how it can be extended. Rosetta uses a custom SCons builder. The builder allows multiple build configurations. Running and Writing Unit, Integration, Performance, and Scientific Tests ======================================================================== diff --git a/internal_documentation/how-to-write-documentation.md b/internal_documentation/how-to-write-documentation.md index bcf617609..d20e5de14 100644 --- a/internal_documentation/how-to-write-documentation.md +++ b/internal_documentation/how-to-write-documentation.md @@ -44,7 +44,7 @@ Organization and Navigation The directory structure of the documentation repository is given below with a brief description of what belongs in each directory/subdirectory. * **getting_started**: Pages geared toward people who are completely new to Rosetta. Most of these pages are fairly broad, tutorial-type pages intended to guide new users toward the documentation (or other resources) that is most relevant to their particular problem. -* **build_documentation**: Pages describing how to build Rosetta (but nothing related to actually using Rosetta). If you want to write about different platforms, compilers, etc., then this is the place to put that information. +* **Building_Rosetta**: Pages describing how to build Rosetta (but nothing related to actually using Rosetta). If you want to write about different platforms, compilers, etc., then this is the place to put that information. * **rosetta_basics**: Pages that are generally relevant to running Rosetta and/or understanding specific Rosetta concepts but that aren't specific to a given application. Some pages fit best in the top level of this directory, but there are several subdirectories that are a better fit for many pages: * **file_types**: Descriptions of particular input/output file formats (PDB, silent file, params file, etc.). If, for example, someone wanted to write a brief page describing the format of a blueprint file, this is where it would go. * **Glossary**: This page currently only contains the Glossary (It's in its own subdirectory so it can have its own sidebar). The RosettaEncyclopedia could also probably go in here, but you probably won't want to add pages to this directory. diff --git a/rosetta_basics/Glossary/_Sidebar.md b/rosetta_basics/Glossary/_Sidebar.md index 814f08c6e..32bcd9fab 100644 --- a/rosetta_basics/Glossary/_Sidebar.md +++ b/rosetta_basics/Glossary/_Sidebar.md @@ -2,7 +2,7 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Basics|rosetta_basics/Rosetta-Basics]] diff --git a/rosetta_basics/MPI.md b/rosetta_basics/MPI.md index c75f09878..a8d6d8e86 100644 --- a/rosetta_basics/MPI.md +++ b/rosetta_basics/MPI.md @@ -9,7 +9,7 @@ Certain protocols (listed below) use MPI non-trivially. These protocols do use ( ## Building Rosetta with MPI -* See Also [[Build Documentation]] +* See Also [[Building Rosetta]] In order to enable MPI runs, you need to have Rosetta compiled with MPI support. @@ -60,5 +60,5 @@ TODO * [[JD2]]: The Job Distributor, commonly used when running MPI protocols * [[Running Rosetta with options]] -* [[Build Documentation]]: Information on building Rosetta +* [[Building Rosetta]]: Information on building Rosetta * [[Rosetta Basics]] \ No newline at end of file diff --git a/rosetta_basics/Rosetta-Basics.md b/rosetta_basics/Rosetta-Basics.md index 9252c6027..afbd9e069 100644 --- a/rosetta_basics/Rosetta-Basics.md +++ b/rosetta_basics/Rosetta-Basics.md @@ -120,7 +120,7 @@ * [[Glossary]]: Brief definitions of Rosetta terms * [[RosettaEncyclopedia]]: Detailed descriptions of additional concepts in Rosetta. * [[Rosetta overview]]: Overview of major concepts in Rosetta -* [[Build Documentation]]: Information on setting up Rosetta +* [[Building Rosetta]]: Information on setting up Rosetta * [[Rosetta on different scales]]: Guidelines for how to scale your Rosetta runs * [[TACC]]: Information for running Rosetta on the TACC/Stampede cluster. * [[Solving a Biological Problem]]: Guide to approaching biological problems using Rosetta diff --git a/rosetta_basics/_Sidebar.md b/rosetta_basics/_Sidebar.md index cb76c17bb..f18a1de8a 100644 --- a/rosetta_basics/_Sidebar.md +++ b/rosetta_basics/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Tutorials| https://www.rosettacommons.org/demos/latest/Home#tutorials ]] diff --git a/rosetta_basics/running-rosetta-with-options.md b/rosetta_basics/running-rosetta-with-options.md index d1f04bccb..a9ddb4b8f 100644 --- a/rosetta_basics/running-rosetta-with-options.md +++ b/rosetta_basics/running-rosetta-with-options.md @@ -29,7 +29,7 @@ path_to/some_rosetta_app.linuxgccrelease -database path/to/rosetta/Rosetta/main/ For a few examples, see the [[commands collection]] page. ##Location of Rosetta Executables -After Rosetta is [[compiled | build_documentation/Build-Documentation ]], links to binary executables are copied to the Rosetta/main/source/bin directory. (This is the bin/ directory off of the directory where you compiled the code.) **Full paths** to these executables need to be given when running Rosetta, _unless_ this directory is added to the **PATH** variable in your shell profile (~/.bashrc (linux), ~/.bash_profile (mac), etc). export PATH=$PATH:/path/to/rosetta/bin +After Rosetta is [[compiled | Building_Rosetta/Building-Rosetta ]], links to binary executables are copied to the Rosetta/main/source/bin directory. (This is the bin/ directory off of the directory where you compiled the code.) **Full paths** to these executables need to be given when running Rosetta, _unless_ this directory is added to the **PATH** variable in your shell profile (~/.bashrc (linux), ~/.bash_profile (mac), etc). export PATH=$PATH:/path/to/rosetta/bin ##[[Rosetta Database|database]] @@ -134,7 +134,7 @@ For developers, please see the page on the [[RosettaThreadManager]] for informat Running Rosetta via MPI ======================== -Where threads are a useful means of parallelizing the execution of blocks of code involving many small tasks that share memory, across a limited number of cores on a single node, process-level cross-communication can also be useful for job-level parallelism. Most Rosetta applications support job-level parallelism using MPI (the Message Passing Interface). MPI allows many processes to communicate with one another by passing messages. This is advantageous over entirely independent processes, since it allows load-balancing (processes that finish their work sooner can do the work that would otherwise be waiting in the queue of a slower process) and, in some cases, data reduction and analysis prior to output (see, for example, the [[simple_cycpep_predict]] application). If the Rosetta MPI executables were compiled (using the `extras=mpi` option with `scons`, for example), then in the executable directory there will be an extra set of executables specifically for MPI, for example fixbb.mpi.linuxgccrelease . If these have not yet been compiled, please refer to the [[Setting Up Rosetta 3| Build-Documentation#MPI]] page for more information. To run these executables, simply run them via mpiexec (or mpirun for older mpi implementations): +Where threads are a useful means of parallelizing the execution of blocks of code involving many small tasks that share memory, across a limited number of cores on a single node, process-level cross-communication can also be useful for job-level parallelism. Most Rosetta applications support job-level parallelism using MPI (the Message Passing Interface). MPI allows many processes to communicate with one another by passing messages. This is advantageous over entirely independent processes, since it allows load-balancing (processes that finish their work sooner can do the work that would otherwise be waiting in the queue of a slower process) and, in some cases, data reduction and analysis prior to output (see, for example, the [[simple_cycpep_predict]] application). If the Rosetta MPI executables were compiled (using the `extras=mpi` option with `scons`, for example), then in the executable directory there will be an extra set of executables specifically for MPI, for example fixbb.mpi.linuxgccrelease . If these have not yet been compiled, please refer to the [[Setting Up Rosetta 3| Building-Rosetta#MPI]] page for more information. To run these executables, simply run them via mpiexec (or mpirun for older mpi implementations): mpiexec -np 16 fixbb.mpi.linuxgccrelease -database /path/to/database @ flags @@ -257,7 +257,7 @@ Rosetta is a highly versatile piece of software, and both its options system and * [[Fixing errors]]: Troubleshooting common errors in Rosetta * [[Getting Started]]: A page for people new to Rosetta. New users start here. -* [[Build Documentation]]: Information on setting up Rosetta +* [[Building Rosetta]]: Information on setting up Rosetta * [[Rosetta on different scales]]: Guidelines for how to scale your Rosetta runs * [[TACC]]: Information for running Rosetta on the TACC/Stampede cluster. * [[Solving a Biological Problem]]: Guide to approaching biological problems using Rosetta diff --git a/rosetta_basics/structural_concepts/_Sidebar.md b/rosetta_basics/structural_concepts/_Sidebar.md index e5fc39843..ffd20dfd4 100644 --- a/rosetta_basics/structural_concepts/_Sidebar.md +++ b/rosetta_basics/structural_concepts/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Basics|rosetta_basics/Rosetta-Basics]] diff --git a/scripting_documentation/PyRosetta/_Sidebar.md b/scripting_documentation/PyRosetta/_Sidebar.md index f4e97aa9e..a663b6818 100644 --- a/scripting_documentation/PyRosetta/_Sidebar.md +++ b/scripting_documentation/PyRosetta/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Basics|rosetta_basics/Rosetta-Basics]] diff --git a/scripting_documentation/RosettaScripts/FeaturesReporter/_Sidebar.md b/scripting_documentation/RosettaScripts/FeaturesReporter/_Sidebar.md index de27f22ed..8b8f4a4f7 100644 --- a/scripting_documentation/RosettaScripts/FeaturesReporter/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/FeaturesReporter/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Basics|rosetta_basics/Rosetta-Basics]] diff --git a/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/_Sidebar.md b/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/_Sidebar.md index 4faf9cccc..0df8b2e82 100644 --- a/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Basics|rosetta_basics/Rosetta-Basics]] diff --git a/scripting_documentation/RosettaScripts/FeaturesReporter/rscripts/_Sidebar.md b/scripting_documentation/RosettaScripts/FeaturesReporter/rscripts/_Sidebar.md index 94af5a392..dfd94cbc3 100644 --- a/scripting_documentation/RosettaScripts/FeaturesReporter/rscripts/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/FeaturesReporter/rscripts/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Basics|rosetta_basics/Rosetta-Basics]] diff --git a/scripting_documentation/RosettaScripts/FeaturesReporter/tutorials/FeaturesTutorialRunSciBench.md b/scripting_documentation/RosettaScripts/FeaturesReporter/tutorials/FeaturesTutorialRunSciBench.md index 120d4fb0a..0df6d1064 100644 --- a/scripting_documentation/RosettaScripts/FeaturesReporter/tutorials/FeaturesTutorialRunSciBench.md +++ b/scripting_documentation/RosettaScripts/FeaturesReporter/tutorials/FeaturesTutorialRunSciBench.md @@ -117,7 +117,7 @@ The Features Reporters can be run in parallel either through MPI or through a ba MPI --- -For MPI-based runs, make sure to [[ compile MPI-mode Rosetta | Build-Documentation#setting-up-rosetta-3_alternative-setup-for-individual-workstations_message-passing-interface-mpi ]]. +For MPI-based runs, make sure to [[ compile MPI-mode Rosetta | Building-Rosetta#setting-up-rosetta-3_alternative-setup-for-individual-workstations_message-passing-interface-mpi ]]. ### Sqlite3 diff --git a/scripting_documentation/RosettaScripts/FeaturesReporter/tutorials/_Sidebar.md b/scripting_documentation/RosettaScripts/FeaturesReporter/tutorials/_Sidebar.md index beda8593d..046684492 100644 --- a/scripting_documentation/RosettaScripts/FeaturesReporter/tutorials/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/FeaturesReporter/tutorials/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Basics|rosetta_basics/Rosetta-Basics]] diff --git a/scripting_documentation/RosettaScripts/Filters/_Sidebar.md b/scripting_documentation/RosettaScripts/Filters/_Sidebar.md index b37eb316e..ca1f9f0d0 100644 --- a/scripting_documentation/RosettaScripts/Filters/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/Filters/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Basics|rosetta_basics/Rosetta-Basics]] diff --git a/scripting_documentation/RosettaScripts/Movers/_Sidebar.md b/scripting_documentation/RosettaScripts/Movers/_Sidebar.md index b37eb316e..ca1f9f0d0 100644 --- a/scripting_documentation/RosettaScripts/Movers/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/Movers/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Basics|rosetta_basics/Rosetta-Basics]] diff --git a/scripting_documentation/RosettaScripts/SimpleMetrics/_Sidebar.md b/scripting_documentation/RosettaScripts/SimpleMetrics/_Sidebar.md index 19e142d78..fc0620124 100644 --- a/scripting_documentation/RosettaScripts/SimpleMetrics/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/SimpleMetrics/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Basics|rosetta_basics/Rosetta-Basics]] diff --git a/scripting_documentation/RosettaScripts/TaskOperations/_Sidebar.md b/scripting_documentation/RosettaScripts/TaskOperations/_Sidebar.md index f41e9d5c9..97856434a 100644 --- a/scripting_documentation/RosettaScripts/TaskOperations/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/TaskOperations/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Basics|rosetta_basics/Rosetta-Basics]] diff --git a/scripting_documentation/RosettaScripts/Using-RosettaScripts-with-VSCode.md b/scripting_documentation/RosettaScripts/Using-RosettaScripts-with-VSCode.md index 7d53d8277..195309a53 100644 --- a/scripting_documentation/RosettaScripts/Using-RosettaScripts-with-VSCode.md +++ b/scripting_documentation/RosettaScripts/Using-RosettaScripts-with-VSCode.md @@ -23,7 +23,7 @@ Follow the following five steps: ``` /Rosetta/main/source/bin/rosetta_scripts.default.linuxgccrelease -output_schema rosettascripts.xsd ``` -Replace `` with your Rostta path, and `.default.linuxgccrelease` with your build, operating system, compiler, and mode (_e.g._ `.cxx11thread.maxcosclangrelease` for the threaded build on MacOS). This command will run the RosettaScripts application, which will write out an XSD file and then exit. Place this XSD file someplace convenient. (Note that Rosetta [[must be compiled first|Build-Documentation]].) +Replace `` with your Rostta path, and `.default.linuxgccrelease` with your build, operating system, compiler, and mode (_e.g._ `.cxx11thread.maxcosclangrelease` for the threaded build on MacOS). This command will run the RosettaScripts application, which will write out an XSD file and then exit. Place this XSD file someplace convenient. (Note that Rosetta [[must be compiled first|Building-Rosetta]].) 5. Open a RosettaScripts XML file in VSCode. (You can create a new, empty RosettaScripts XML file by running the RosettaScripts application with no options and cutting-and-pasting from the output into VSCode.) Add the following lines to the top of your XML file: @@ -47,4 +47,4 @@ When using VSCode: ## See also * [[RosettaScripts]] -* [[Compiling Rosetta|Build-Documentation]]. \ No newline at end of file +* [[Compiling Rosetta|Building-Rosetta]]. \ No newline at end of file diff --git a/scripting_documentation/RosettaScripts/_Sidebar.md b/scripting_documentation/RosettaScripts/_Sidebar.md index b217aad09..4d454c9d5 100644 --- a/scripting_documentation/RosettaScripts/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Tutorials| https://www.rosettacommons.org/demos/latest/Home#tutorials ]] diff --git a/scripting_documentation/RosettaScripts/composite_protocols/_Sidebar.md b/scripting_documentation/RosettaScripts/composite_protocols/_Sidebar.md index 33d6bcd71..1004ce874 100644 --- a/scripting_documentation/RosettaScripts/composite_protocols/_Sidebar.md +++ b/scripting_documentation/RosettaScripts/composite_protocols/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Basics|rosetta_basics/Rosetta-Basics]] diff --git a/scripting_documentation/TopologyBroker/_Sidebar.md b/scripting_documentation/TopologyBroker/_Sidebar.md index 303beaa55..2543c1afe 100644 --- a/scripting_documentation/TopologyBroker/_Sidebar.md +++ b/scripting_documentation/TopologyBroker/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Basics|rosetta_basics/Rosetta-Basics]] diff --git a/scripting_documentation/_Sidebar.md b/scripting_documentation/_Sidebar.md index aeb526f25..0a7fb5a9e 100644 --- a/scripting_documentation/_Sidebar.md +++ b/scripting_documentation/_Sidebar.md @@ -1,6 +1,6 @@ [[Getting Started]] -[[Build Documentation|build_documentation/Build-Documentation]] +[[Building Rosetta|Building_Rosetta/Building-Rosetta]] [[Rosetta Tutorials| https://www.rosettacommons.org/demos/latest/Home#tutorials ]] diff --git a/structure_prediction/simple_cycpep_predict.md b/structure_prediction/simple_cycpep_predict.md index 0ee905982..a8fe4015f 100644 --- a/structure_prediction/simple_cycpep_predict.md +++ b/structure_prediction/simple_cycpep_predict.md @@ -37,7 +37,7 @@ The application is also available in MPI form for sampling large numbers of conf mpirun -np 25 /my_rosetta_path/main/source/bin/simple_cycpep_predict.mpi.linuxgccrelease -cyclic_peptide:MPI_processes_by_level 1 24 -cyclic_peptide:MPI_batchsize_by_level 10 -cyclic_peptide:MPI_output_fraction 0.1 -nstruct 2500 -cyclic_peptide:sequence_file inputs/seq.txt -cyclic_peptide:genkic_closure_attempts 1000 -cyclic_peptide:min_genkic_hbonds 2 -mute all -unmute protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_summary -in:file:native inputs/native.pdb -out:file:silent output.silent ``` -See the [[Build Documentation]] for details on the MPI (Message Passing Interface) build, and the MPI section below for more information about the MPI-specific options. +See the [[Building Rosetta]] for details on the MPI (Message Passing Interface) build, and the MPI section below for more information about the MPI-specific options. # Full inputs