From 3e7beb23a0b29bbbdf4832b303bae44bd9ffba8b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 13 Sep 2023 18:11:55 +0200
Subject: [PATCH] adding easyconfigs: nanopolish-0.14.0-foss-2022a.eb,
 VBZ-Compression-1.0.3-gompi-2022a.eb

---
 .../nanopolish-0.14.0-foss-2022a.eb           | 61 +++++++++++++++++++
 .../VBZ-Compression-1.0.3-gompi-2022a.eb      | 43 +++++++++++++
 2 files changed, 104 insertions(+)
 create mode 100644 easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2022a.eb
 create mode 100644 easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2022a.eb

diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2022a.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2022a.eb
new file mode 100644
index 00000000000..2ca012c73d5
--- /dev/null
+++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2022a.eb
@@ -0,0 +1,61 @@
+easyblock = 'MakeCp'
+
+name = 'nanopolish'
+version = '0.14.0'
+
+homepage = 'https://github.com/jts/nanopolish'
+description = "Software package for signal-level analysis of Oxford Nanopore sequencing data."
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = [
+    'https://github.com/jts/nanopolish/archive/',
+    'https://github.com/mateidavid/fast5/archive/',
+]
+sources = [
+    {
+        'source_urls': ['https://github.com/jts/nanopolish/archive/'],
+        'download_filename': 'v%(version)s.tar.gz',
+        'filename': SOURCE_TAR_GZ,
+    },
+    {
+        'source_urls': ['https://github.com/hasindu2008/slow5lib/archive/'],
+        'download_filename': 'v1.1.0.tar.gz',
+        'filename': 'slow5lib-v1.1.0.tar.gz',
+    },
+]
+checksums = [
+    {'nanopolish-0.14.0.tar.gz': 'bcc1a7e2d23941592d817da3af9165b3843ae52b11a3ca5983d6417f1614ef78'},
+    {'slow5lib-v1.1.0.tar.gz': 'f13f08b85a9a11086b5d9378251093d1858d0dc29d8e727eabacfa57a73f4277'},
+]
+
+builddependencies = [('Eigen', '3.4.0')]
+
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('Python', '3.10.4'),
+    ('Biopython', '1.79'),
+    ('Pysam', '0.19.1'),
+    ('HDF5', '1.12.2'),
+    ('HTSlib', '1.15.1'),
+    ('minimap2', '2.24'),
+    ('VBZ-Compression', '1.0.3'),
+]
+
+prebuildopts = "rmdir slow5lib && ln -s %(builddir)s/slow5lib-*/ slow5lib && "
+buildopts = "HDF5=noinstall EIGEN=noinstall HTS=noinstall MINIMAP2=noinstall"
+
+runtest = 'test ' + buildopts
+
+files_to_copy = [(['nanopolish'], 'bin'), 'scripts']
+
+postinstallcmds = ["chmod a+rx %(installdir)s/scripts/*"]
+
+sanity_check_paths = {
+    'files': ['bin/nanopolish'],
+    'dirs': ['scripts'],
+}
+
+modextrapaths = {'PATH': 'scripts'}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2022a.eb b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2022a.eb
new file mode 100644
index 00000000000..d6e8caabfdb
--- /dev/null
+++ b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2022a.eb
@@ -0,0 +1,43 @@
+easyblock = 'CMakeMake'
+
+name = 'VBZ-Compression'
+version = '1.0.3'
+
+homepage = 'https://github.com/nanoporetech/vbz_compression'
+description = "VBZ compression HDF5 plugin for nanopolish"
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+
+source_urls = [
+    'https://github.com/nanoporetech/vbz_compression/archive',
+    'https://github.com/lemire/streamvbyte/archive',
+]
+sources = [
+    {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ},
+    {'download_filename': 'v0.4.1.tar.gz', 'filename': 'streamvbyte-v0.4.1.tar.gz'},
+]
+checksums = [
+    {'VBZ-Compression-1.0.3.tar.gz': 'a7450e076db628681bbc0e2b3f941c6c21cc2981a7e1c78628807ffdf1b34f31'},
+    {'streamvbyte-v0.4.1.tar.gz': '4c4e53134a60b0b06816d3faa7dcde28c3e5e8a656dd415d16d80ae6e3d39fcc'},
+]
+
+builddependencies = [('CMake', '3.24.3')]
+
+dependencies = [
+    ('HDF5', '1.12.2'),
+    ('zstd', '1.5.2'),
+]
+
+preconfigopts = "rmdir %(builddir)s/vbz_compression*/third_party/streamvbyte && "
+preconfigopts += "mv %(builddir)s/streamvbyte-* %(builddir)s/streamvbyte && "
+preconfigopts += "mv %(builddir)s/streamvbyte %(builddir)s/vbz_compression*/third_party/. && "
+configopts = "-DENABLE_CONAN=OFF -DENABLE_PERF_TESTING=OFF -DENABLE_PYTHON=OFF "
+
+sanity_check_paths = {
+    'files': ['hdf5/lib/plugin/libvbz_hdf_plugin.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+modextrapaths = {'HDF5_PLUGIN_PATH': 'hdf5/lib/plugin/'}
+
+moduleclass = 'lib'