adding easyconfigs: AUGUSTUS-3.5.0-foss-2023b.eb and patches: AUGUSTU…

…S-3.5.0_include-cstdint.patch

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

@@ -0,0 +1,77 @@
+# Updated by: Pavel Grochal (INUITS)
+# License: GPLv2
+
+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': '2023b'}
+
+github_account = 'Gaius-Augustus'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-3.5.0_include-cstdint.patch']
+checksums = [
+    {'v3.5.0.tar.gz': '5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686'},
+    {'AUGUSTUS-3.5.0_include-cstdint.patch': '1f4ec090b83b0d67caab37dc7e96a81c2bcc7d803e5455348794538e0a43c319'},
+]
+
+builddependencies = [
+    ('Python', '3.11.5'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('Boost', '1.83.0'),
+    ('GSL', '2.7'),
+    ('SAMtools', '1.19.2'),
+    ('HTSlib', '1.19.1'),  # also provides tabix
+    ('BCFtools', '1.19'),
+    ('lpsolve', '5.5.2.11'),
+    ('SuiteSparse', '7.7.0', '-METIS-5.1.0'),
+    ('BamTools', '2.5.2'),
+    ('SQLite', '3.43.1'),
+]
+
+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/a/AUGUSTUS/AUGUSTUS-3.5.0_include-cstdint.patch

@@ -0,0 +1,28 @@
+Author: Jasper Grimm <[email protected]>
+Add cstdint includes to fix builds with gcc >= 13
+Based on patch from Kuoi <[email protected]>
+---
+diff --git a/auxprogs/homGeneMapping/include/sqliteDB.hh b/auxprogs/homGeneMapping/include/sqliteDB.hh
+index e842bcf9..67338bef 100644
+--- a/auxprogs/homGeneMapping/include/sqliteDB.hh
++++ b/auxprogs/homGeneMapping/include/sqliteDB.hh
+@@ -13,6 +13,7 @@
+ #include <string>
+ #include <vector>
+ #include <sqlite3.h>
++#include <cstdint>
+
+ using namespace std;
+
+diff --git a/include/sqliteDB.hh b/include/sqliteDB.hh
+index e66374b9..67a37826 100644
+--- a/include/sqliteDB.hh
++++ b/include/sqliteDB.hh
+@@ -11,6 +11,7 @@
+ #include <string>
+ #include <vector>
+ #include <sqlite3.h>
++#include <cstdint>
+
+ using namespace std;
+