From 599d6240f1a08413a8e66fba022ffb7a6eca4670 Mon Sep 17 00:00:00 2001
From: Greta Assmann <greta.assmann@psi.ch>
Date: Thu, 18 Jul 2024 16:06:34 +0200
Subject: [PATCH] add phenix

---
 phenix/README.md         | 26 ++++++++++++++++++++++++++
 phenix/build             | 26 ++++++++++++++++++++++++++
 phenix/files/config.yaml | 16 ++++++++++++++++
 phenix/modulefile        | 13 +++++++++++++
 4 files changed, 81 insertions(+)
 create mode 100644 phenix/README.md
 create mode 100755 phenix/build
 create mode 100644 phenix/files/config.yaml
 create mode 100644 phenix/modulefile

diff --git a/phenix/README.md b/phenix/README.md
new file mode 100644
index 0000000..8db5c37
--- /dev/null
+++ b/phenix/README.md
@@ -0,0 +1,26 @@
+### Installation
+
+- src files can only be retrieved with phenix login credentials. They are only valid for a month roughly - as a result new credentials need to be requested for academic purpose.
+- The build script will therefore expect the un-tared downloaded phenix folder in the BUILD_DIR folder
+- the default $PMODULES_TMPDIR is too small for phenix and needs another place. export PMODULES_TMPDIR=/w/y/w/  in the terminal (not in build script, does not work), I used /afs/psi.ch/groups/HPCE/user/assman_g/.. 
+- the installation of Phenix requires the owner of the files in the BUILDBLOCK_DIR to be the same as the owner of the PREFIX DIR. in a nutshell : files need to be owned by adm account in the BUILDBLOCK_DIR . ( which is why AFS is a good place to put this, as I can write as assman_g and assman_g-adm there, and files need to be owned by assman_g-adm for the install ) 
+- phenix needs sourcing of a shell script when loading the module: Problem- when unloading, the variables stay defined. ...TODO: find a way to unset these variables as well. 
+
+### Installation with Rosetta 
+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 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 ${PHENIX_ROSETTA_PATH}/main/source/tools/build/site.settings before running this final step" "(https://phenix-online.org/documentation/reference/rosetta_install.html)
+- the run the command
+
+rosetta.build_phenix_interface nproc=10 
+
+- run rosetta.run_tests to test it. 
+
+
+### Additional Remarks
+
+the phenix help pages (BB archive) does not work. 
diff --git a/phenix/build b/phenix/build
new file mode 100755
index 0000000..ab9dd31
--- /dev/null
+++ b/phenix/build
@@ -0,0 +1,26 @@
+#!/usr/bin/env modbuild
+
+
+pbuild::prep(){
+    :
+}
+
+pbuild::pre_configure() {
+
+    echo "${PMODULES_TMPDIR}"
+    echo "${SRC_DIR}"
+
+    # copy code from BUILD Dir into SRCDIR . wget does not work , because login credentials required for download (wget --user did not work)
+    cp -r "${BUILDBLOCK_DIR}/phenix-installer-${V}-intel-linux-2.6-x86_64-centos6/"*  "${SRC_DIR}"
+
+}
+pbuild::compile() {
+    :
+}
+
+pbuild::install() {
+    cd "${SRC_DIR}"
+    ./install --prefix="${PREFIX}"
+}
+
+
diff --git a/phenix/files/config.yaml b/phenix/files/config.yaml
new file mode 100644
index 0000000..e4fe4bb
--- /dev/null
+++ b/phenix/files/config.yaml
@@ -0,0 +1,16 @@
+---
+format: 1
+phenix:
+  defaults:
+    group: MX
+    overlay: base
+    relstage: stable
+  versions:
+    1.21.1-5286:
+      config:
+        relstage: unstable
+    1.20.1-4487:
+      config:
+        relstage: unstable
+
+
diff --git a/phenix/modulefile b/phenix/modulefile
new file mode 100644
index 0000000..fb9628b
--- /dev/null
+++ b/phenix/modulefile
@@ -0,0 +1,13 @@
+#%Module1.0
+
+module-whatis	        "Python-based Hierarchical ENvironment for Integrated Xtallography"
+module-url		         "http://www.phenix-online.org/"
+module-license	        "NON-COMMERCIAL END USER SOURCE  CODE  LICENSE"
+module-maintainer       "greta.assmann@psi.ch"
+
+module-help	"
+PHENIX is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
+Citing PHENIX:
+PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010).
+"
+puts stdout "source /opt/psi/MX/phenix/${V}/${P}-${V}/phenix_env.sh"