From 51d82f2d09923f8179857588b942769536c80ec4 Mon Sep 17 00:00:00 2001
From: Greta Assmann <greta.assmann@psi.ch>
Date: Wed, 24 Jul 2024 10:46:42 +0200
Subject: [PATCH] add rosetta

---
 Rosetta/README.md         | 18 ++++++++++++++++++
 Rosetta/build             | 21 +++++++++++++++++++++
 Rosetta/files/config.yaml | 11 +++++++++++
 Rosetta/modulefile        | 25 +++++++++++++++++++++++++
 4 files changed, 75 insertions(+)
 create mode 100644 Rosetta/README.md
 create mode 100755 Rosetta/build
 create mode 100644 Rosetta/files/config.yaml
 create mode 100644 Rosetta/modulefile

diff --git a/Rosetta/README.md b/Rosetta/README.md
new file mode 100644
index 0000000..307ad55
--- /dev/null
+++ b/Rosetta/README.md
@@ -0,0 +1,18 @@
+### Rosetta installation remarks: 
+
+As of July 2024, phenix 1.21 exists, and also Rosetta 3.14. These do not work together , as phenix/1.21.1 misses a file called command_line.py , which is existent in phenix 1.20  and is required for Rosetta. Also the compilation of phenix+Rosetta fails on RH7, so def needs to be done on RH8 nodes (Ra) and Rosetta 3.14 fails during compilation.  --> check  for new phenix releases if the compatabilty with Rosetta latest release was tested etc .
+ 
+As a result, phenix/1.20 plus Rosetta 3.13 is used. (July 2024)
+ 
+The installation of Rosetta +phenix requires a fully functional new phenix installation. A phenix command is run after the installation of Rosetta that builds the interface between the two:
+ - Install phenix ( see phenix ) 
+ - Install Rosetta as usual (see Pmodules MX Rosetta build script)
+ - copy the site.settings file into the correct folder as described in "NOTE: On linux, if you are using GCC 5.1 or later (Ubuntu 16.04 or later), there is an ABI change that requires an additional flag to allow linking between our CentOS 6 binary build and Rosetta. To apply this flag, copy this site.settings file to ${PHENIX_ROSETTA_PATH}/main/source/tools/build/site.settings before running this final step" "(https://phenix-online.org/documentation/reference/rosetta_install.html)
+ - then run the command
+ 
+ rosetta.build_phenix_interface nproc=10
+ 
+ - run rosetta.run_tests to test it.
+ 
+ IMPORTANT, both phenix and rosetta need to have the same file permisssions /owner as described in the phenix readme. In both cases the recommendation is to do it as -adm account on /afs/psi.ch/group/HPCE/user/xxx  and then run the installation from there (RH8 needed, RA therefore )
+
diff --git a/Rosetta/build b/Rosetta/build
new file mode 100755
index 0000000..b724eea
--- /dev/null
+++ b/Rosetta/build
@@ -0,0 +1,21 @@
+#!/usr/bin/env modbuild
+
+pbuild::prep(){
+    :
+}
+
+pbuild::configure(){
+    :
+}
+
+pbuild::compile() {
+    :
+}
+
+pbuild::install() {
+    mkdir "$PREFIX"
+    cd "$PREFIX"
+    tar -xf "${PMODULES_DISTFILESDIR}/Rosetta-${V}.tgz" --strip-components=1
+}
+
+
diff --git a/Rosetta/files/config.yaml b/Rosetta/files/config.yaml
new file mode 100644
index 0000000..29c46a9
--- /dev/null
+++ b/Rosetta/files/config.yaml
@@ -0,0 +1,11 @@
+format: 1
+Rosetta:
+  defaults:
+    group: MX
+    overlay: base
+    relstage: unstable
+    urls:
+      - url: https://www.rosettacommons.org/downloads/academic/3.13/rosetta_bin_linux_3.13_bundle.tgz
+        name: Rosetta-${V}.tgz
+  versions:
+    3.13:
diff --git a/Rosetta/modulefile b/Rosetta/modulefile
new file mode 100644
index 0000000..f886883
--- /dev/null
+++ b/Rosetta/modulefile
@@ -0,0 +1,25 @@
+#%Module1.0
+
+module-whatis	        "Rosetta™ is a molecular modeling software package for understanding protein structures, protein design, protein docking, protein-DNA and protein-protein interactions."
+module-url		         "https://www.rosettacommons.org/home"
+module-license	        "Academic License"
+module-maintainer       "greta.assmann@psi.ch>"
+
+module-help	"
+The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes
+.
+
+Rosetta development began in the laboratory of Dr. David Baker at the University of Washington as a structure prediction tool but since then has been adapted to solve common computational macromolecular problems.
+
+Development of Rosetta has moved beyond the University of Washington into the members of RosettaCommons, which include government laboratories, institutes, research centers, and partner corporations.
+
+The Rosetta community has many goals for the software, such as:
+
+    Understanding macromolecular interactions
+    Designing custom molecules
+    Developing efficient ways to search conformation and sequence space
+    Finding a broadly useful energy functions for various biomolecular representations
+"
+
+prepend-path   PHENIX_ROSETTA_PATH     $PREFIX
+