From 3b22c01c46bb91ce2d39a0f8f7c5df8a6b1a7def Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 13 Apr 2023 13:37:00 -0400 Subject: [PATCH 1/3] adding easyconfigs: phyx-1.3-foss-2022a.eb, Armadillo-11.4.3-foss-2022a.eb and patches: phyx-1.3_link_flexiblas.patch --- .../Armadillo/Armadillo-11.4.3-foss-2022a.eb | 22 ++++++++ .../easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb | 51 +++++++++++++++++++ .../p/phyx/phyx-1.3_link_flexiblas.patch | 14 +++++ 3 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb new file mode 100644 index 000000000000..261ecca60bb2 --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb @@ -0,0 +1,22 @@ +name = 'Armadillo' +version = '11.4.3' + +homepage = 'https://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['87603263664988af41da2ca4f36205e36ea47a9281fa6cfd463115f3797a1da2'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Boost', '1.79.0'), + ('arpack-ng', '3.8.0'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb new file mode 100644 index 000000000000..1418ab60d05e --- /dev/null +++ b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'phyx' +version = '1.3' + +homepage = 'https://github.com/FePhyFoFum/%(name)s' +description = "phyx performs phylogenetics analyses on trees and sequences." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +github_account = 'FePhyFoFum' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_link_flexiblas.patch'] +checksums = [ + {'v1.3.tar.gz': 'b09677f98f997838b39cd2724463be06d0627ddc90a7e659dc90d4e02db624eb'}, + {'phyx-1.3_link_flexiblas.patch': 'e9dc98da0f3c5df8e5b8ac3e64c2b0f77358f61fc60a4aadce5ad790b636ebdd'}, +] + +builddependencies = [ + ('Autotools', '20220317', '', ('GCCcore', '11.3.0')), +] + +dependencies = [ + ('Armadillo', '11.4.3'), + ('NLopt', '2.7.1'), +] + +start_dir = 'src' + +#preconfigopts = 'autoconf && ' +preconfigopts = "autoreconf -f -i && " + + +preinstallopts = 'mkdir %(installdir)s/bin && ' + +sanity_check_paths = { + 'files': ['bin/' + _exec for _exec in ["pxaa2cdn", "pxbdfit", "pxbdsim", + "pxboot", "pxbp", "pxcat", "pxclsq", "pxcltr", "pxcolt", "pxconsq", + "pxcontrates", "pxfqfilt", "pxlog", "pxlssq", "pxlstr", "pxmrca", + "pxmrcacut", "pxmrcaname", "pxnw", "pxrecode", "pxrevcomp", + "pxrls", "pxrlt", "pxrmk", "pxrms", "pxrmt", "pxrr", "pxs2fa", "pxs2nex", + "pxs2phy", "pxseqgen", "pxssort", "pxsstat", "pxstrec", "pxsw", "pxt2new", + "pxt2nex", "pxtcol", "pxtcomb", "pxtlate", "pxtrt", "pxtscale", + "pxvcf2fa"]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch b/easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch new file mode 100644 index 000000000000..1b541919cf8d --- /dev/null +++ b/easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch @@ -0,0 +1,14 @@ +replace linking with lapack and blas by flexiblas +autor: Graham Derryberry +diff -Naur phyx-1.3.orig/src/Makefile.in phyx-1.3/src/Makefile.in +--- phyx-1.3.orig/src/Makefile.in 2023-04-12 22:44:14.000000000 -0400 ++++ phyx-1.3/src/Makefile.in 2023-04-13 09:57:34.000000000 -0400 +@@ -17,7 +17,7 @@ + HARM := @HARM@ + HOMP := @HOMP@ + +-CPP_LIBS = -llapack -lblas -lpthread -lm ++CPP_LIBS = -lflexiblas -lpthread -lm + ifeq "$(HNLOPT)" "Y" + CPP_LIBS += -lnlopt + endif From ad4a7024987d2c486de9e4edbbea0962b11df1d9 Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 13 Apr 2023 14:07:37 -0400 Subject: [PATCH 2/3] Fixing style error by removing commented out dead code --- easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb index 1418ab60d05e..8eb989c720dd 100644 --- a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb +++ b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb @@ -30,10 +30,8 @@ dependencies = [ start_dir = 'src' -#preconfigopts = 'autoconf && ' preconfigopts = "autoreconf -f -i && " - preinstallopts = 'mkdir %(installdir)s/bin && ' sanity_check_paths = { From 92b4203a7392059ecbc156ec966e19171bda0047 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 14 Apr 2023 19:52:36 +0200 Subject: [PATCH 3/3] Update easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb --- easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb index 8eb989c720dd..ba5ddd695731 100644 --- a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb +++ b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb @@ -20,7 +20,7 @@ checksums = [ ] builddependencies = [ - ('Autotools', '20220317', '', ('GCCcore', '11.3.0')), + ('Autotools', '20220317'), ] dependencies = [