From 31d10510306fe8f221a0f821661640b9d1260945 Mon Sep 17 00:00:00 2001
From: Alexandre Strube <a.strube@fz-juelich.de>
Date: Tue, 17 Jan 2023 18:05:00 +0100
Subject: [PATCH] Bedtools from upstream
---
.../b/BEDTools/BEDTools-2.30.0-GCC-11.3.0.eb | 45 +++++++++++++++++++
1 file changed, 45 insertions(+)
create mode 100644 Golden_Repo/b/BEDTools/BEDTools-2.30.0-GCC-11.3.0.eb
diff --git a/Golden_Repo/b/BEDTools/BEDTools-2.30.0-GCC-11.3.0.eb b/Golden_Repo/b/BEDTools/BEDTools-2.30.0-GCC-11.3.0.eb
new file mode 100644
index 000000000..3fe167c95
--- /dev/null
+++ b/Golden_Repo/b/BEDTools/BEDTools-2.30.0-GCC-11.3.0.eb
@@ -0,0 +1,45 @@
+# Author: Maxime Schmitt, University of Luxembourg
+# Author: Adam Huffman, The Francis Crick Institute
+#
+# Based on the work of: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics (SIB)
+# Biozentrum - University of Basel
+
+easyblock = 'MakeCp'
+
+name = 'BEDTools'
+version = '2.30.0'
+
+homepage = "https://bedtools.readthedocs.io/"
+description = """BEDTools: a powerful toolset for genome arithmetic.
+The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and
+computing coverage.
+The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8']
+
+builddependencies = [('Python', '3.10.4')]
+
+dependencies = [
+ ('XZ', '5.2.5'),
+ ('zlib', '1.2.12'),
+ ('bzip2', '1.0.8'),
+ ('BamTools', '2.5.2'),
+]
+
+buildopts = 'CXX="$CXX"'
+
+files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"]
+
+sanity_check_paths = {
+ 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']],
+ 'dirs': files_to_copy,
+}
+
+sanity_check_commands = ['bedtools --help']
+
+moduleclass = 'bio'
--
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