From e26bc12c9da9007c763d73726a20c795b331b701 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Mon, 9 Dec 2024 16:16:24 +0100
Subject: [PATCH 1/2] adding easyconfigs: purge_dups-1.2.6-foss-2023b.eb

---
 .../purge_dups/purge_dups-1.2.6-foss-2023b.eb | 85 +++++++++++++++++++
 1 file changed, 85 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb

diff --git a/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb
new file mode 100644
index 00000000000..6848c4131d1
--- /dev/null
+++ b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb
@@ -0,0 +1,85 @@
+easyblock = 'PythonBundle'
+
+name = 'purge_dups'
+version = '1.2.6'
+
+homepage = 'https://github.com/dfguan/purge_dups'
+description = "purge haplotigs and overlaps in an assembly based on read depth"
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+builddependencies = [
+    ('pybind11', '2.11.1'),
+]
+
+dependencies = [
+    ('zlib', '1.2.13'),
+    ('bzip2', '1.0.8'),
+    ('Python', '3.11.5'),
+    ('matplotlib', '3.8.2'),
+    ('minimap2', '2.28'),
+]
+
+use_pip = True
+
+default_easyblock = 'MakeCp'
+
+components = [
+    (name, version, {
+        'source_urls': ['https://github.com/dfguan/purge_dups/archive'],
+        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'checksums': ['75b20df834d28410858ccd4e2d65b6c70849f3cbe5fc05959f38bfc2d041c704'],
+        'start_dir': 'purge_dups-%(version)s',
+        'prebuildopts': "cd src && ",
+        'buildopts': 'CC="$CC" CFLAGS="$CFLAGS"',
+        'files_to_copy': ['bin', 'scripts'],
+    }),
+    ('KMC', '20190629', {
+        'source_urls': ['https://github.com/dfguan/KMC/archive'],
+        'sources': [{'download_filename': 'c05a5f9.tar.gz', 'filename': SOURCE_TAR_GZ}],
+        'patches': [{
+            'name': 'KMC_use_EB_pybind11_and_libs.patch',
+            'sourcepath': 'KMC-c05a5f9fd94683248ebe04484a60f86792cf328f',
+        }],
+        'checksums': [
+            '7251941f4b1913bfdd68759d9292b419d95fe7c63815056e15ecb097a12a0bc4',
+            '2f54971aae26787777d0e4b638a9682bd4bc22cbf3fda170c7baf4c610808ac9',
+        ],
+        'prebuildopts': 'cd KMC-* && ',
+        'buildopts': 'CC="$CXX"',
+        'files_to_copy': [(['KMC-*/bin/*kmc*'], 'bin'), 'KMC-*/spectra.py'],
+    }),
+]
+
+exts_list = [
+    ('runner', '20191220', {
+        'preinstallopts': "sed -i 's/0.0.0/%(version)s/g' setup.py && ",
+        'sources': [{
+            'git_config': {
+                'url': 'https://github.com/dfguan/',
+                'repo_name': 'runner',
+                'commit': '73a4d11',
+            },
+            'filename': 'runner-%(version)s.tar.gz',
+        }],
+        'checksums': [None],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/kmc', 'bin/purge_dups'],
+    'dirs': ['scripts'],
+}
+
+sanity_check_commands = [
+    "purge_dups -h 2>&1 | grep 'Program: purge_dups'",
+    "kmc --help",
+    "run_purge_dups.py -h",
+    "hist_plot.py -h",
+]
+
+sanity_pip_check = True
+
+modextrapaths = {'PATH': 'scripts'}
+
+moduleclass = 'bio'

From 7b618299a721907a13fe315099a5343b8676b8ed Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Mon, 9 Dec 2024 16:19:15 +0100
Subject: [PATCH 2/2] purge_dups: Add KMC patch to use EB pybind11 and libs

---
 .../KMC_use_EB_pybind11_and_libs.patch        | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/purge_dups/KMC_use_EB_pybind11_and_libs.patch

diff --git a/easybuild/easyconfigs/p/purge_dups/KMC_use_EB_pybind11_and_libs.patch b/easybuild/easyconfigs/p/purge_dups/KMC_use_EB_pybind11_and_libs.patch
new file mode 100644
index 00000000000..465979ce64b
--- /dev/null
+++ b/easybuild/easyconfigs/p/purge_dups/KMC_use_EB_pybind11_and_libs.patch
@@ -0,0 +1,39 @@
+Use pybind11 from EasyBuild install
+Required to use Python != 3.10
+Also use zlib and bzip2 from EB install
+
+Åke Sandgren, 2024-12-09
+diff --git a/makefile b/makefile
+index 09f4de3..918dcae 100644
+--- a/makefile
++++ b/makefile
+@@ -36,9 +36,7 @@ $(KMC_MAIN_DIR)/raduls_sse41.o \
+ $(KMC_MAIN_DIR)/raduls_avx2.o \
+ $(KMC_MAIN_DIR)/raduls_avx.o
+ 
+-KMC_LIBS = \
+-$(KMC_MAIN_DIR)/libs/libz.a \
+-$(KMC_MAIN_DIR)/libs/libbz2.a
++KMC_LIBS = -lz -lbz2
+ 
+ KMC_DUMP_OBJS = \
+ $(KMC_DUMP_DIR)/nc_utils.o \
+@@ -64,9 +62,7 @@ $(KMC_TOOLS_DIR)/fastq_reader.o \
+ $(KMC_TOOLS_DIR)/fastq_writer.o \
+ $(KMC_TOOLS_DIR)/percent_progress.o
+ 
+-KMC_TOOLS_LIBS = \
+-$(KMC_TOOLS_DIR)/libs/libz.a \
+-$(KMC_TOOLS_DIR)/libs/libbz2.a
++KMC_TOOLS_LIBS = -lz -lbz2
+ 
+ $(KMC_OBJS) $(KMC_DUMP_OBJS) $(KMC_API_OBJS): %.o: %.cpp
+ 	$(CC) $(CFLAGS) -c $< -o $@
+@@ -102,7 +98,6 @@ py_kmc_api: $(PY_KMC_API_OBJS) $(PY_KMC_API_OBJS)
+ 	-mkdir -p $(KMC_BIN_DIR)
+ 	$(CC) -fPIC -Wall -shared -std=c++11 -O3 $(PY_KMC_API_DIR)/py_kmc_api.cpp $(PY_KMC_API_OBJS) \
+ 	-I $(KMC_API_DIR) \
+-	-I $(PY_KMC_API_DIR)/libs/pybind11/include \
+ 	-I `python3 -c "import sysconfig;print(sysconfig.get_paths()['include'])"` \
+ 	-o $(KMC_BIN_DIR)/$@`python3-config --extension-suffix`
+