{tools}[foss/2024a] snakemake v8.27.0

easybuild/easyconfigs/c/Cbc/Cbc-2.10.12-foss-2024a.eb

@@ -0,0 +1,53 @@
+easyblock = 'ConfigureMake'
+
+name = 'Cbc'
+version = '2.10.12'
+
+homepage = 'https://github.com/coin-or/Cbc'
+description = """Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming
+solver written in C++. It can be used as a callable library or using a
+stand-alone executable."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases']
+sources = ['%(version)s.tar.gz']
+checksums = ['9ed71e4b61668462fc3794c102e26b4bb01a047efbbbcbd69ae7bde1f04f46a8']
+
+builddependencies = [
+    ('Autotools', '20231222'),
+    ('Doxygen', '1.11.0'),
+    ('pkgconf', '2.2.0'),
+]
+dependencies = [
+    ('METIS', '5.1.0'),
+    ('MUMPS', '5.7.2', '-metis'),
+    ('CoinUtils', '2.11.12'),
+    ('Osi', '0.108.11'),
+    ('Clp', '1.17.10'),
+    ('Cgl', '0.60.8'),
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.3.1'),
+]
+
+# Use BLAS/LAPACK from toolchain
+configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" --with-metis-lib="-lmetis" '
+configopts += ' --with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord"  '
+configopts += ' --without-glpk --with-coinutils-lib="-lCoinUtils"  '
+configopts += ' --with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data  '
+configopts += ' --with-clp-lib="-lOsiClp -lClpSolver -lClp" --with-clp-datadir=$EBROOTCLP/share/coin/Data  '
+configopts += ' --with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi"  '
+configopts += ' --with-osi-datadir=$EBROOTOSI/share/coin/Data --with-cgl-lib="-lCgl"  '
+configopts += ' --with-cgl-datadir=$EBROOTCGL/share/coin/Data '
+
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s', 'lib/libCbc.so', 'lib/libCbcSolver.so', 'lib/libOsiCbc.so'],
+    'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'],
+}
+
+# other coin-or projects expect <header.hpp> instead of <coin/header.hpp>
+modextrapaths = {'CPATH': 'include/coin'}
+
+moduleclass = 'math'

easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2024a.eb

@@ -0,0 +1,48 @@
+easyblock = 'ConfigureMake'
+
+name = 'Cgl'
+version = '0.60.8'
+
+homepage = 'https://github.com/coin-or/Cgl'
+description = """The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that
+can be used with other COIN-OR packages that make use of cuts, such as, among
+others, the linear solver Clp or the mixed integer linear programming solvers
+Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or
+communicate with a solver. It does not directly call a solver."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases/']
+sources = ['%(version)s.tar.gz']
+checksums = ['1482ba38afb783d124df8d5392337f79fdd507716e9f1fb6b98fc090acd1ad96']
+
+builddependencies = [
+    ('Autotools', '20231222'),
+    ('Doxygen', '1.11.0'),
+    ('pkgconf', '2.2.0'),
+]
+dependencies = [
+    ('CoinUtils', '2.11.12'),
+    ('Osi', '0.108.11'),
+    ('Clp', '1.17.10'),
+]
+
+# Use CoinUtils from EB
+configopts = '--with-coinutils-lib="-lCoinUtils" '
+configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data '
+configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" '
+configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data '
+configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" '
+configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data '
+
+
+sanity_check_paths = {
+    'files': ['lib/libCgl.so'],
+    'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'],
+}
+
+# other coin-or projects expect <header.hpp> instead of <coin/header.hpp>
+modextrapaths = {'CPATH': 'include/coin'}
+
+moduleclass = 'math'

easybuild/easyconfigs/c/Clp/Clp-1.17.10-foss-2024a.eb

@@ -0,0 +1,51 @@
+easyblock = 'ConfigureMake'
+
+name = 'Clp'
+version = '1.17.10'
+
+homepage = 'https://github.com/coin-or/Clp'
+description = """Clp (Coin-or linear programming) is an open-source linear programming solver.
+It is primarily meant to be used as a callable library, but a basic,
+stand-alone executable version is also available."""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases/']
+sources = ['%(version)s.tar.gz']
+checksums = ['0d79ece896cdaa4a3855c37f1c28e6c26285f74d45f635046ca0b6d68a509885']
+
+builddependencies = [
+    ('Autotools', '20231222'),
+    ('Doxygen', '1.11.0'),
+    ('pkgconf', '2.2.0'),
+]
+dependencies = [
+    ('METIS', '5.1.0'),
+    ('MUMPS', '5.7.2', '-metis'),
+    ('CoinUtils', '2.11.12'),
+    ('Osi', '0.108.11'),
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.3.1'),
+]
+
+# Use BLAS/LAPACK from toolchain
+configopts = '--with-blas="$LIBBLAS" '
+configopts += '--with-lapack="$LIBLAPACK" '
+configopts += '--with-metis-lib="-lmetis" '
+configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord '
+configopts += '-lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" '
+configopts += '--without-glpk --with-coinutils-lib="-lCoinUtils" '
+configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data '
+configopts += '--with-osi-lib="-lOsi" --with-osi-datadir=$EBROOTOSI/share/coin/Data '
+
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s', 'lib/libClp.so', 'lib/libClpSolver.so', 'lib/libOsiClp.so'],
+    'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'],
+}
+
+# other coin-or projects expect <header.hpp> instead of <coin/header.hpp>
+modextrapaths = {'CPATH': 'include/coin'}
+
+moduleclass = 'math'

easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.12-GCC-13.3.0.eb

@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'CoinUtils'
+version = '2.11.12'
+
+homepage = 'https://github.com/coin-or/CoinUtils'
+description = """CoinUtils (Coin-OR Utilities) is an open-source collection of classes and
+functions that are generally useful to more than one COIN-OR project."""
+
+# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases/']
+sources = ['%(version)s.tar.gz']
+checksums = ['eef1785d78639b228ae2de26b334129fe6a7d399c4ac6f8fc5bb9054ba00de64']
+
+builddependencies = [
+    ('Autotools', '20231222'),
+    ('Doxygen', '1.11.0'),
+    ('pkgconf', '2.2.0'),
+]
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.3.1'),
+]
+
+
+sanity_check_paths = {
+    'files': ['lib/libCoinUtils.so'],
+    'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'],
+}
+
+# other coin-or projects expect <header.hpp> instead of <coin/header.hpp>
+modextrapaths = {'CPATH': 'include/coin'}
+
+moduleclass = 'math'

easybuild/easyconfigs/m/MUMPS/MUMPS-5.7.2-foss-2024a-metis.eb

@@ -0,0 +1,27 @@
+name = 'MUMPS'
+version = '5.7.2'
+versionsuffix = '-metis'
+
+homepage = 'https://graal.ens-lyon.fr/MUMPS/'
+description = "A parallel sparse direct solver"
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['http://mumps-solver.org/']
+sources = ['%(name)s_%(version)s.tar.gz']
+checksums = ['1362d377ce7422fc886c55212b4a4d2c381918b5ca4478f682a22d0627a8fbf8']
+
+dependencies = [
+    ('SCOTCH', '7.0.6'),
+    ('METIS', '5.1.0'),
+]
+
+parallel = 1
+
+# fix 'Type mismatch between actual argument' errors with GCC 10.x
+prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && '
+
+buildopts = 'all SONAME_VERSION="%(version)s"'
+
+moduleclass = 'math'

easybuild/easyconfigs/o/Osi/Osi-0.108.11-GCC-13.3.0.eb

@@ -0,0 +1,46 @@
+easyblock = 'ConfigureMake'
+
+name = 'Osi'
+version = '0.108.11'
+
+homepage = 'https://github.com/coin-or/Osi'
+description = """Osi (Open Solver Interface) provides an abstract base class to a generic linear
+programming (LP) solver, along with derived classes for specific solvers. Many
+applications may be able to use the Osi to insulate themselves from a specific
+LP solver. That is, programs written to the OSI standard may be linked to any
+solver with an OSI interface and should produce correct results. The OSI has
+been significantly extended compared to its first incarnation. Currently, the
+OSI supports linear programming solvers and has rudimentary support for integer
+programming."""
+
+toolchain = {'name': 'GCC', 'version': '13.3.0'}
+
+source_urls = ['https://github.com/coin-or/%(name)s/archive/refs/tags/releases/']
+sources = ['%(version)s.tar.gz']
+checksums = ['1063b6a057e80222e2ede3ef0c73c0c54697e0fee1d913e2bef530310c13a670']
+
+builddependencies = [
+    ('Autotools', '20231222'),
+    ('Doxygen', '1.11.0'),
+    ('pkgconf', '2.2.0'),
+]
+dependencies = [
+    ('CoinUtils', '2.11.12'),
+    ('bzip2', '1.0.8'),
+    ('zlib', '1.3.1'),
+]
+
+# Disable GLPK because Osi requires GLPK<=4.48
+configopts = '--without-glpk --with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin '
+configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data'
+
+
+sanity_check_paths = {
+    'files': ['lib/libOsi.so', 'lib/libOsiCommonTests.so'],
+    'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'],
+}
+
+# other coin-or projects expect <header.hpp> instead of <coin/header.hpp>
+modextrapaths = {'CPATH': 'include/coin'}
+
+moduleclass = 'math'

easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2024a.eb

@@ -0,0 +1,35 @@
+# Contribution by
+# DeepThought, Flinders University
+# R.QIAO <[email protected]>
+# Updated: Petr Král (INUITS)
+
+easyblock = 'PythonPackage'
+
+name = 'PuLP'
+version = '2.8.0'
+
+homepage = 'https://github.com/coin-or/pulp'
+description = """
+PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and
+call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to
+solve linear problems.
+"""
+
+toolchain = {'name': 'foss', 'version': '2024a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['4903bf96110bbab8ed2c68533f90565ebb76aa367d9e4df38e51bf727927c125']
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('GLPK', '5.0'),
+    ('Cbc', '2.10.12'),
+    # Gurobi requires a seperate license
+    # ('Gurobi', '9.5.0'),
+]
+
+download_dep_fail = True
+sanity_pip_check = True
+use_pip = True
+
+moduleclass = 'tools'

easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.6-gompi-2024a.eb

@@ -0,0 +1,25 @@
+name = 'SCOTCH'
+version = '7.0.6'
+
+homepage = 'https://www.labri.fr/perso/pelegrin/scotch/'
+description = """Software package and libraries for sequential and parallel graph partitioning,
+static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning."""
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://gitlab.inria.fr/%(namelower)s/%(namelower)s/-/archive/v%(version)s/']
+sources = ['%(namelower)s-v%(version)s.tar.gz']
+checksums = ['b44acd0d2f53de4b578fa3a88944cccc45c4d2961cd8cefa9b9a1d5431de8e2b']
+
+builddependencies = [
+    ('Bison', '3.8.2'),
+    ('flex', '2.6.4'),
+]
+dependencies = [
+    ('zlib', '1.3.1'),
+]
+
+threadedmpi = False
+
+moduleclass = 'math'