This easyconfig:
name = 'Rosetta'
version = '3.13'
homepage = 'https://www.rosettacommons.org'
description = """Rosetta is the premier software suite for modeling
macromolecular structures. As a flexible,
multi-purpose application, it includes tools for structure prediction, design,
and remodeling of proteins and
nucleic acids."""
toolchain = {'name': 'foss', 'version': '2019b'}
toolchainopts = {'usempi': True}
sources = ['%(namelower)s_src_%(version)s_bundle.tgz']
patches = ['no.libxml2.build.patch']
moduleclass = 'bio'
---------------------------------
This patch:
diff -urNb rosetta_src_2021.16.61629_bundle/main/source/projects.settings
rosetta_src_2021.16.61629_bundle_new/main/source/projects.settings
--- rosetta_src_2021.16.61629_bundle/main/source/projects.settings
2021-04-20 16:48:40.000000000 -0400
+++ rosetta_src_2021.16.61629_bundle_new/main/source/projects.settings
2022-02-03 14:59:11.546839000 -0500
@@ -57,7 +57,6 @@
"cppdb", # Must come before sqlite3 for static build
"sqlite3",
"cifparse",
- "libxml2",
"libzmq",
"rdkit",
]
diff -urNb
rosetta_src_2021.16.61629_bundle/main/source/tools/build/basic.settings
rosetta_src_2021.16.61629_bundle_new/main/source/tools/build/basic.settings
--- rosetta_src_2021.16.61629_bundle/main/source/tools/build/basic.settings
2021-04-20 16:58:07.000000000 -0400
+++ rosetta_src_2021.16.61629_bundle_new/main/source/tools/build/basic.settings
2022-02-03 16:41:20.569433000 -0500
@@ -153,7 +153,6 @@
"isystem external/",
"isystem external/include/",
"isystem external/dbio/",
- "isystem external/libxml2/include",
"isystem external/rdkit",
],
"cxx" : [
@@ -164,7 +163,6 @@
"isystem external/",
"isystem external/include/",
"isystem external/dbio/",
- "isystem external/libxml2/include",
"isystem external/rdkit",
#"fno-omit-frame-pointer", # -- useful for profiling on
linux using RotateRight's Zoom profiler
@@ -1373,7 +1371,6 @@
"isystem external/",
"isystem external/include/",
"isystem external/dbio/",
- "isystem external/libxml2/include",
"isystem external/rdkit",
],
"cxx" : [
@@ -1383,7 +1380,6 @@
"isystem external/",
"isystem external/include/",
"isystem external/dbio/",
- "isystem external/libxml2/include",
"isystem external/rdkit",
],
"warn" : [
@@ -2002,7 +1998,6 @@
"isystem external/",
"isystem external/include/",
"isystem external/dbio/",
- "isystem external/libxml2/include",
"isystem external/rdkit",
],
"cxx" : [
@@ -2012,7 +2007,6 @@
"isystem external/",
"isystem external/include/",
"isystem external/dbio/",
- "isystem external/libxml2/include",
"isystem external/rdkit",
],
"compile" : [
diff -urNb
rosetta_src_2021.16.61629_bundle/main/source/tools/build/site.settings
rosetta_src_2021.16.61629_bundle_new/main/source/tools/build/site.settings
--- rosetta_src_2021.16.61629_bundle/main/source/tools/build/site.settings
2021-04-20 16:58:07.000000000 -0400
+++ rosetta_src_2021.16.61629_bundle_new/main/source/tools/build/site.settings
2022-02-03 16:45:31.839408000 -0500
@@ -28,6 +28,9 @@
"include_path" : os.environ["INCLUDE"].split(":") if "INCLUDE" in
os.environ else [],
},
"appends" : {
+ "flags" : {
+ "link" : ["lxml2"],
+ },
},
"overrides" : {
## Uncomment the following line if your compiler need additional environment
variables to function (e.g. license key locations)
<https://www.njit.edu/> Glenn (Gedaliah) Wolosh, Ph.D.
Ass't Director Research Software and Cloud Computing
Acad & Research Computing Systems
[email protected] <mailto:[email protected]> • (973) 596-5437 <tel:(973) 596-5437>
A Top 100 National University
U.S. News & World Report
> On Feb 11, 2022, at 7:10 AM, Frédéric Wautelet <[email protected]>
> wrote:
>
> Hi,
>
> I also encountered this error. Could you please explain how you managed to
> disable libxml2?
>
> Thank you.
>
> With best regards,
> Frédéric Wautelet
>
>
>
> On 4/02/22 17:57, Glenn (Gedaliah) Wolosh wrote:
>> I was able to disable the internal libxml2. Problem resolved. Thanks
> --
> <Tv1z61Nf2bZCe6o6.png>
> Frédéric WAUTELET
> HPC Operations Engineer
> Faculty of Sciences
>
> T. +32(0)81725459
> [email protected] <mailto:[email protected]>
> http://www.ptci.unamur.be <http://www.ptci.unamur.be/>
> Université de Namur ASBL
> Rue de Bruxelles 61 - 5000 Namur
> Belgique
>
> Let’s respect the environment together.
> Only print this message if necessary!
>
