Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

…asyconfigs into 20240912170418_new_pr_Ghostscript10031

easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1-GCCcore-13.3.0.eb

@@ -0,0 +1,51 @@
+easyblock = 'MesonNinja'
+
+name = 'GObject-Introspection'
+version = '1.80.1'
+
+homepage = 'https://gi.readthedocs.io/en/latest/'
+description = """GObject introspection is a middleware layer between C libraries
+ (using GObject) and language bindings. The C library can be scanned at
+ compile time and generate a metadata file, in addition to the actual
+ native C library. Then at runtime, language bindings can read this
+ metadata and automatically provide bindings to call into the C library."""
+
+toolchain = {'name': 'GCCcore', 'version': '13.3.0'}
+
+source_urls = [FTPGNOME_SOURCE]
+sources = [SOURCELOWER_TAR_XZ]
+patches = ['GObject-Introspection-1.80.1_install-GLib-GIR-files.patch']
+checksums = [
+    {'gobject-introspection-1.80.1.tar.xz': 'a1df7c424e15bda1ab639c00e9051b9adf5cea1a9e512f8a603b53cd199bc6d8'},
+    {'GObject-Introspection-1.80.1_install-GLib-GIR-files.patch':
+     'c1909f1b7fd30784ae789ac0b5e45e0ca3dd2456890b864efa86a2f8c2e563aa'},
+]
+
+builddependencies = [
+    ('binutils', '2.42'),
+    ('pkgconf', '2.2.0'),
+    ('CMake', '3.29.3'),
+    ('Meson', '1.4.0'),
+    ('Ninja', '1.12.1'),
+    ('Python', '3.12.3'),
+    ('Bison', '3.8.2'),
+    ('cairo', '1.18.0'),
+    ('flex', '2.6.4'),
+]
+
+dependencies = [
+    ('GLib', '2.80.4'),
+    ('libffi', '3.4.5'),
+    ('util-linux', '2.40'),
+]
+
+preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true "
+configopts = "-Dcairo=enabled"
+
+sanity_check_paths = {
+    'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] +
+             ['lib/libgirepository-1.0.' + SHLIB_EXT],
+    'dirs': ['include', 'share']
+}
+
+moduleclass = 'devel'

easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.80.1_install-GLib-GIR-files.patch

@@ -0,0 +1,52 @@
+This reverts a commit from upstream
+>  build: Do not install generated GLib GIR files
+>
+> GLib 2.79 ships its own introspection data.
+
+However GObject-Introspection requires (optionally) Cairo, which requires GLib
+which requires GLib-Introspection for generating the introspection data.
+
+So there is a cyclic dependency, see https://gitlab.gnome.org/GNOME/gobject-introspection/-/issues/517
+
+Author: Alexander Grund (TU Dresden)
+
+diff --git a/gir/meson.build b/gir/meson.build
+index 3a016831..312aa886 100644
+--- a/gir/meson.build
++++ b/gir/meson.build
+@@ -241,6 +241,8 @@ glib_gir = custom_target('gir-glib',
+   output: 'GLib-2.0.gir',
+   depends: [gir_giscanner_pymod, glib_gir_dep, gdump],
+   depend_files: gir_giscanner_built_files,
++  install: true,
++  install_dir: girdir,
+   env: g_ir_scanner_env,
+   command: glib_command + [
+     '--cflags-begin'] + glib_includes + extra_giscanner_cflags + [
+@@ -308,6 +310,8 @@ gobject_gir = custom_target('gir-gobject',
+   output: 'GObject-2.0.gir',
+   depends: [glib_gir, gir_giscanner_pymod, gobject_gir_dep, gdump],
+   depend_files: gir_giscanner_built_files,
++  install: true,
++  install_dir: girdir,
+   env: g_ir_scanner_env,
+   command: gobject_command + [
+     '--include-uninstalled=' + glib_gir.full_path(),
+@@ -360,6 +364,8 @@ uninstalled_gir_files += custom_target('gir-gmodule',
+   output: 'GModule-2.0.gir',
+   depends: [glib_gir, gir_giscanner_pymod, gmodule_gir_dep, gdump],
+   depend_files: gir_giscanner_built_files,
++  install: true,
++  install_dir: girdir,
+   env: g_ir_scanner_env,
+   command: gmodule_command + [
+     '--include-uninstalled=' + glib_gir.full_path(),
+@@ -455,6 +461,8 @@ gio_gir = custom_target('gir-gio',
+   output: 'Gio-2.0.gir',
+   depends: [gobject_gir, gir_giscanner_pymod, gio_gir_dep, gdump],
+   depend_files: gir_giscanner_built_files,
++  install: true,
++  install_dir: girdir,
+   env: g_ir_scanner_env,
+   command: gio_command + [
+     '--include-uninstalled=' + gobject_gir.full_path(),

easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2023a.eb

@@ -0,0 +1,32 @@
+easyblock = 'PythonPackage'
+
+name = 'NanoStat'
+version = '1.6.0'
+
+homepage = 'https://github.com/wdecoster/nanostat'
+description = """Calculate various statistics from a long read sequencing dataset in fastq,
+ bam or albacore sequencing summary format."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['e45fa8d1ab49bdaed17596c26c0af148b44e4af46238391a8bb7a1b4cc940079']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('nanoget', '1.19.3'),
+    ('nanomath', '1.4.0'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+sanity_check_paths = {
+    'files': ['bin/NanoStat'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["NanoStat --help"]
+
+moduleclass = 'tools'

easybuild/easyconfigs/n/nanoQC/nanoQC-0.9.4-foss-2023a.eb

@@ -0,0 +1,31 @@
+easyblock = 'PythonPackage'
+
+name = 'nanoQC'
+version = '0.9.4'
+
+homepage = 'https://github.com/wdecoster/nanoQC'
+description = """Quality control tools for long read sequencing
+ data aiming to replicate some of the plots made by fastQC."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['05685656138cbaf099b18831d1ceeaca93faf3399881cc2efda44c04d3b316e3']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('Biopython', '1.83'),
+    ('SciPy-bundle', '2023.07'),
+    ('bokeh', '3.2.2'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+options = {'modulename': 'nanoQC'}
+
+sanity_check_commands = ["nanoQC --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/n/nanoget/nanoget-1.19.3-foss-2023a.eb

@@ -0,0 +1,30 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+# Update: Petr Král (INUITS)
+
+easyblock = 'PythonPackage'
+
+name = 'nanoget'
+version = '1.19.3'
+
+homepage = 'https://github.com/wdecoster/nanoget'
+description = "Functions to extract information from Oxford Nanopore sequencing data and alignments"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['da981810edb1cbe42cbbfbe5fcf753f29bf5555204cd51256b28a284a036a71b']
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+    ('Biopython', '1.83'),
+    ('Pysam', '0.22.0'),
+    ('nanomath', '1.4.0'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/n/nanomath/nanomath-1.4.0-foss-2023a.eb

@@ -0,0 +1,33 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+# Update: Petr Král (INUITS)
+
+easyblock = 'PythonBundle'
+
+name = 'nanomath'
+version = '1.4.0'
+
+homepage = 'https://github.com/wdecoster/nanomath'
+description = "A few simple math functions for other Oxford Nanopore processing scripts"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+    ('Python', '3.11.3'),
+    ('SciPy-bundle', '2023.07'),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('Python-Deprecated', '1.1.0', {
+        'modulename': 'deprecated',
+        'checksums': ['a242b3c1721f97912330b12cd5529abfa5b3876084a6c60a2c683a87d4b0dd6f'],
+    }),
+    (name, version, {
+        'checksums': ['ed7a38fbb156d9a68a95c2570fe3c2035321d0a3e234580496750afca4927ced'],
+    }),
+]
+
+moduleclass = 'math'