From 7a2564a7b19badd827f523a45cb83984d0eabc25 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20Kr=C3=A1l?= <petr@inuits.eu>
Date: Fri, 12 Jan 2024 14:53:06 +0100
Subject: [PATCH] adding easyconfigs: PASA-2.5.3-foss-2022b.eb,
 pblat-2.5.1-foss-2022b.eb

---
 .../p/PASA/PASA-2.5.3-foss-2022b.eb           | 43 +++++++++++++++++++
 .../p/pblat/pblat-2.5.1-foss-2022b.eb         | 41 ++++++++++++++++++
 2 files changed, 84 insertions(+)
 create mode 100644 easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2022b.eb
 create mode 100644 easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2022b.eb

diff --git a/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2022b.eb b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2022b.eb
new file mode 100644
index 00000000000..3dad7ad19d0
--- /dev/null
+++ b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2022b.eb
@@ -0,0 +1,43 @@
+easyblock = 'ConfigureMake'
+
+name = 'PASA'
+version = '2.5.3'
+
+homepage = 'https://github.com/PASApipeline/PASApipeline'
+description = """PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'),
+ is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript
+ sequences to automatically model gene structures, and to maintain gene structure annotation consistent
+ with the most recently available experimental sequence data. PASA also identifies and classifies all
+ splicing variations supported by the transcript alignments."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['https://github.com/PASApipeline/PASApipeline/archive/']
+sources = ['%(namelower)s-v%(version)s.tar.gz']
+checksums = ['9b2f6a301b73fd8c713af0977cf6e97f3d928988d6b79715ebe81e19b51152eb']
+
+dependencies = [
+    ('SQLite', '3.39.4'),
+    ('GMAP-GSNAP', '2023-04-20'),
+    ('pblat', '2.5.1'),
+    ('minimap2', '2.26'),
+    ('FASTA', '36.3.8i'),
+]
+
+buildininstalldir = True
+
+skipsteps = ['configure', 'install']
+
+unpack_options = '--strip-components=1'
+
+local_bins = ['%(namelower)s', 'cdbfasta', 'cdbyank', 'cln2qual', 'mdust',
+    'psx', 'seqclean', 'seqclean.psx', 'slclust', 'trimpoly']
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in local_bins],
+    'dirs': []
+}
+
+sanity_check_commands = ['command -v %(namelower)s']
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2022b.eb b/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2022b.eb
new file mode 100644
index 00000000000..1fee4320100
--- /dev/null
+++ b/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2022b.eb
@@ -0,0 +1,41 @@
+easyblock = 'MakeCp'
+
+name = 'pblat'
+version = '2.5.1'
+
+homepage = 'https://github.com/icebert/pblat'
+description = """When the query file format is fasta, you can specify many threads to process it.
+ It can reduce run time linearly, and use almost equal memory as the original blat program.
+ This is useful when you blat a big query file to a huge reference like human whole genome sequence."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+github_account = 'icebert'
+source_urls = [GITHUB_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['e85a4d752b8e159502d529f0f9e47579851a6b466b6c2f1f4d49f598642bc615']
+
+dependencies = [
+    ('HTSlib', '1.17'),
+    ('zlib', '1.2.12'),
+    ('OpenSSL', '1.1', '', SYSTEM),
+]
+
+# use HTSlib dependency provided through EasyBuild
+prebuildopts = "sed -i '5s/.\/htslib/$\{EBROOTHTSLIB\}\/include\/htslib/' Makefile && "
+prebuildopts += "sed -i '40s/ htslib\/libhts.a//' Makefile && "
+prebuildopts += "sed -i '41s/htslib\/libhts.a/-lhts -lcurl/' Makefile && "
+prebuildopts += "sed -i -e '/htslib\/libhts.a:/,+2d' Makefile && "
+
+files_to_copy = [
+    (['%(name)s'], 'bin'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s'],
+    'dirs': []
+}
+
+sanity_check_commands = ["command -v %(name)s"]
+
+moduleclass = 'bio'