From f7a10c1213920e079ad3c3d86dde85e37ac1542d Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Mon, 18 Nov 2024 14:21:03 +0100
Subject: [PATCH] adding easyconfigs: snpEff-5.2c-GCCcore-12.3.0-Java-11.eb

---
 .../snpEff-5.2c-GCCcore-12.3.0-Java-11.eb     | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb

diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb
new file mode 100644
index 00000000000..c9f29979a1d
--- /dev/null
+++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb
@@ -0,0 +1,37 @@
+easyblock = 'Tarball'
+
+name = 'snpEff'
+version = '5.2c'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://pcingola.github.io/SnpEff/'
+description = """SnpEff is a variant annotation and effect prediction tool.
+ It annotates and predicts the effects of genetic variants (such as amino acid changes)."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+source_urls = ['https://snpeff.blob.core.windows.net/versions/']
+sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')]
+checksums = ['9926f600662707e85478940abc283ef120a909f1d41c32a036f01d958cd51232']
+
+dependencies = [
+    # ignore website claim that Java 12+ is required, nothing is compiled for
+    # anything newer than Java 11
+    ('Java', '11', '', SYSTEM),
+    ('Python', '3.11.3'),
+    ('Perl', '5.36.1'),
+]
+
+fix_perl_shebang_for = ['scripts/*.pl']
+fix_python_shebang_for = ['scripts/*.py']
+
+sanity_check_paths = {
+    'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["%(name)s -version"]
+
+modextrapaths = {'PATH': 'scripts'}
+
+moduleclass = 'bio'