Merge pull request #21476 from PetrKralCZ/20240924153329_new_pr_AUGUS…

…TUS350

{bio,math}[GCC/12.3.0,foss/2023a] AUGUSTUS v3.5.0, lpsolve v5.5.2.11

easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2023a.eb

@@ -0,0 +1,74 @@
+# Updated by: Pavel Grochal (INUITS)
+# License: GPLv2
+# Update: Petr Král (INUITS)
+
+easyblock = 'ConfigureMake'
+
+name = 'AUGUSTUS'
+version = '3.5.0'
+
+homepage = 'https://bioinf.uni-greifswald.de/augustus/'
+description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+github_account = 'Gaius-Augustus'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+checksums = ['5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686']
+
+builddependencies = [
+    ('Python', '3.11.3'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('Boost', '1.82.0'),
+    ('GSL', '2.7'),
+    ('SAMtools', '1.18'),
+    ('HTSlib', '1.18'),  # also provides tabix
+    ('BCFtools', '1.18'),
+    ('lpsolve', '5.5.2.11'),
+    ('SuiteSparse', '7.1.0'),
+    ('BamTools', '2.5.2'),
+    ('SQLite', '3.42.0'),
+]
+
+skipsteps = ['configure']
+
+# run "make clean" to avoid using binaries included with the source tarball
+prebuildopts = "make clean && "
+
+_tmpl = 'INCLUDE_PATH_{dep}=-I{root}{incl} LIBRARY_PATH_{dep}="-L{root}{lib} -Wl,-rpath,{root}{lib}"'
+
+buildopts = ' '.join([
+    'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" ',
+    _tmpl.format(dep='ZLIB', root='$EBROOTZLIB', incl='/include', lib='/lib'),
+    _tmpl.format(dep='BOOST', root='$EBROOTBOOST', incl='/include', lib='/lib'),
+    _tmpl.format(dep='LPSOLVE', root='$EBROOTLPSOLVE', incl='/include', lib='/lib'),
+    _tmpl.format(dep='SUITESPARSE', root='$EBROOTSUITESPARSE', incl='/include', lib='/lib'),
+    _tmpl.format(dep='GSL', root='$EBROOTGSL', incl='/include', lib='/lib'),
+    _tmpl.format(dep='SQLITE', root='$EBROOTSQLITE', incl='/include', lib='/lib'),
+    _tmpl.format(dep='BAMTOOLS', root='$EBROOTBAMTOOLS', incl='/include/bamtools', lib='/lib'),
+    _tmpl.format(dep='HTSLIB', root='$EBROOTHTSLIB', incl='/include/htslib', lib='/lib'),
+])
+
+preinstallopts = "sed -i '/ln -sf/d' Makefile && "
+installopts = 'INSTALLDIR=%(installdir)s '
+
+sanity_check_paths = {
+    'files': ['bin/augustus', 'bin/bam2hints', 'bin/etraining', 'bin/fastBlockSearch',
+              'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes',
+              'bin/load2sqlitedb', 'bin/prepareAlign'],
+    'dirs': ['config', 'scripts'],
+}
+sanity_check_commands = ['augustus --help']
+
+modextrapaths = {'PATH': 'scripts'}
+modextravars = {
+    'AUGUSTUS_BIN_PATH': '%(installdir)s/bin',
+    'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config',
+    'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts',
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.3.0.eb

@@ -0,0 +1,33 @@
+easyblock = 'CmdCp'
+
+name = 'lpsolve'
+version = '5.5.2.11'
+
+homepage = 'https://sourceforge.net/projects/lpsolve/'
+description = "Mixed Integer Linear Programming (MILP) solver"
+
+toolchain = {'name': 'GCC', 'version': '12.3.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['lp_solve_%(version)s_source.tar.gz']
+checksums = ['6d4abff5cc6aaa933ae8e6c17a226df0fc0b671c438f69715d41d09fe81f902f']
+
+local_lpsolve_ver = '%(version_major)s%(version_minor)s'
+start_dir = 'lpsolve%s' % local_lpsolve_ver
+
+local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && '
+local_comp_cmd += "sh ccc"
+cmds_map = [('.*', local_comp_cmd)]
+
+local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver
+files_to_copy = [
+    (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'),
+    (['../lp*.h'], 'include'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)],
+    'dirs': ['include'],
+}
+
+moduleclass = 'math'