Merge branch 'easybuilders:develop' into 20240916172022_new_pr_giflib522

easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch

@@ -0,0 +1,28 @@
+Fix incorrect version number in the 0.9.0 tar file.
+
+Åke Sandgren, 2024-09-16
+diff --git a/Cargo.lock b/Cargo.lock
+index 3e8f1fe..53fa5da 100644
+--- a/Cargo.lock
++++ b/Cargo.lock
+@@ -236,7 +236,7 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
+
+ [[package]]
+ name = "chopper"
+-version = "0.8.0"
++version = "0.9.0"
+ dependencies = [
+ "approx",
+ "atty",
+diff --git a/Cargo.toml b/Cargo.toml
+index f268dce..7f7277a 100644
+--- a/Cargo.toml
++++ b/Cargo.toml
+@@ -1,6 +1,6 @@
+ [package]
+ name = "chopper"
+-version = "0.8.0"
++version = "0.9.0"
+ authors = ["wdecoster <decosterwouter@gmail.com>"]
+ edition = "2021"
+

easybuild/easyconfigs/j/joypy/joypy-0.2.6-foss-2023a.eb

@@ -0,0 +1,28 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+# Update: Petr Král (INUITS)
+
+easyblock = 'PythonPackage'
+
+name = 'joypy'
+version = '0.2.6'
+
+homepage = 'https://github.com/sbebo/joypy'
+description = "Joyplots in Python with matplotlib & pandas"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCE_WHL]
+checksums = ['fffe882e8281e56e08b374a3148436cb448562ba39e4d566204c7e8ee2caddab']
+
+dependencies = [
+ ('Python', '3.11.3'),
+ ('SciPy-bundle', '2023.07'),
+ ('matplotlib', '3.7.2'),
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+moduleclass = 'math'

easybuild/easyconfigs/n/NanoComp/NanoComp-1.24.0-foss-2023a.eb

@@ -0,0 +1,42 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+# Update: Petr Král (INUITS)
+
+easyblock = 'PythonPackage'
+
+name = 'NanoComp'
+version = '1.24.0'
+
+homepage = 'https://github.com/wdecoster/NanoComp'
+description = "Comparing runs of Oxford Nanopore sequencing data and alignments"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['2ce02bb38c76137ee00ebcc68b6b2654a4a459993e901aebde436c4d54287b09']
+
+dependencies = [
+ ('Python', '3.11.3'),
+ ('SciPy-bundle', '2023.07'),
+ ('Pysam', '0.22.0'),
+ ('nanomath', '1.4.0'),
+ ('nanoget', '1.19.3'),
+ ('NanoPlot', '1.43.0'),
+ ('plotly.py', '5.16.0'),
+ ('plotly-orca', '1.3.1'),
+ ('joypy', '0.2.6'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_check_paths = {
+ 'files': ['bin/NanoComp'],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["NanoComp --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2023a.eb

@@ -0,0 +1,26 @@
+easyblock = 'PythonPackage'
+
+name = 'NanoFilt'
+version = '2.8.0'
+
+homepage = 'https://github.com/wdecoster/nanofilt'
+description = """Filtering and trimming of long read sequencing data."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['47f4f4f8be834f011570a8d76d07cc12abe0686c8917607316a8ccfb3e20758c']
+
+dependencies = [
+ ('Python', '3.11.3'),
+ ('Biopython', '1.83'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_check_commands = ["NanoFilt --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2023a.eb

@@ -0,0 +1,48 @@
+##
+# This is a contribution from SIB Swiss Institute of Bioinformatics
+# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it
+#
+# Authors:: Sebastien Moretti <sebastien.moretti@sib.swiss>
+#
+# Update: Petr Král (INUITS)
+##
+
+easyblock = 'PythonBundle'
+
+name = 'NanoLyse'
+version = '1.2.1'
+
+homepage = 'https://github.com/wdecoster/nanolyse'
+description = """Remove reads mapping to the lambda phage genome from a fastq file."""
+software_license = 'LicenseGPLv3'
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+dependencies = [
+ ('Python', '3.11.3'),
+ ('Biopython', '1.83'),
+ ('minimap2', '2.26'),
+]
+
+use_pip = True
+
+# Fetch the tar.gz, not the whl files!
+exts_list = [
+ ('mappy', '2.28', {
+ 'checksums': ['0ebf7a5d62bd668f5456028215e26176e180ca68161ac18d4f7b48045484cebb'],
+ }),
+ (name, version, {
+ 'checksums': ['933ee668da805fc9ec9fa86c9fca81a073438d45b5f64e23cf606c01e715b1d5'],
+ }),
+]
+
+sanity_check_paths = {
+ 'files': ['bin/NanoLyse'],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["NanoLyse --version"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.43.0-foss-2023a.eb

@@ -0,0 +1,43 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+# Update: Petr Král (INUITS)
+
+easyblock = 'PythonPackage'
+
+name = 'NanoPlot'
+version = '1.43.0'
+
+homepage = 'https://github.com/wdecoster/NanoPlot'
+description = "Plotting suite for long read sequencing data and alignments"
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['0f94096d689b552c32fd7246ad87cb6d5e5e2499dad5acc551091e0ff67f48df']
+
+dependencies = [
+ ('Python', '3.11.3'),
+ ('SciPy-bundle', '2023.07'),
+ ('Biopython', '1.83'),
+ ('Pysam', '0.22.0'),
+ ('nanomath', '1.4.0'),
+ ('nanoget', '1.19.3'),
+ ('plotly.py', '5.16.0'),
+ ('statsmodels', '0.14.1'),
+ ('Arrow', '14.0.1'), # for pyarrow
+ ('Kaleido', '0.2.1'),
+]
+
+download_dep_fail = True
+use_pip = True
+
+sanity_check_paths = {
+ 'files': ['bin/NanoPlot'],
+ 'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["NanoPlot --help"]
+
+sanity_pip_check = True
+
+moduleclass = 'bio'

easybuild/easyconfigs/p/PLINK/PLINK-1.90-beta-7.4-x86_64.eb

@@ -0,0 +1,22 @@
+easyblock = 'PackedBinary'
+
+name = 'PLINK'
+version = '1.90-beta-7.4-x86_64'
+
+homepage = 'https://www.cog-genomics.org/plink/1.9/'
+description = 'plink-1.9-x86_64: Whole-genome association analysis toolset'
+
+toolchain = SYSTEM
+
+source_urls = ['https://s3.amazonaws.com/plink1-assets/']
+sources = ['plink_linux_x86_64_20240818.zip']
+checksums = ['0ac294ffcd5d82f5b0d2d7f579ac85a87017f6fc46485b21793f5aff9c719e3d']
+
+sanity_check_paths = {
+ 'files': ['plink', 'prettify', 'toy.map', 'toy.ped'],
+ 'dirs': [],
+}
+
+sanity_check_commands = ["plink --help"]
+
+moduleclass = 'bio'