From d6d24b7041a94abcd79ec091ec1fe188933e2b96 Mon Sep 17 00:00:00 2001
From: Lukas Krupcik <lukas.krupcik@vsb.cz>
Date: Mon, 25 Oct 2021 08:33:58 +0200
Subject: [PATCH] new file: b/BWA/BWA-0.7.17-intel-2020b.eb new
file: s/snpEff/snpEff-5.0-GCCcore-10.2.0-Java-11-Python-3.8.6.eb
---
b/BWA/BWA-0.7.17-intel-2020b.eb | 20 ++++++++++
...5.0-GCCcore-10.2.0-Java-11-Python-3.8.6.eb | 38 +++++++++++++++++++
2 files changed, 58 insertions(+)
create mode 100644 b/BWA/BWA-0.7.17-intel-2020b.eb
create mode 100644 s/snpEff/snpEff-5.0-GCCcore-10.2.0-Java-11-Python-3.8.6.eb
diff --git a/b/BWA/BWA-0.7.17-intel-2020b.eb b/b/BWA/BWA-0.7.17-intel-2020b.eb
new file mode 100644
index 00000000..95e6043a
--- /dev/null
+++ b/b/BWA/BWA-0.7.17-intel-2020b.eb
@@ -0,0 +1,20 @@
+# IT4Innovations
+# LK 2021
+
+name = 'BWA'
+version = '0.7.17'
+
+homepage = 'http://bio-bwa.sourceforge.net/'
+description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
+ relatively short nucleotide sequences against a long reference sequence such as the human genome."""
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/lh3/%(name)s/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd']
+
+dependencies = [('zlib', '1.2.11')]
+
+moduleclass = 'bio'
diff --git a/s/snpEff/snpEff-5.0-GCCcore-10.2.0-Java-11-Python-3.8.6.eb b/s/snpEff/snpEff-5.0-GCCcore-10.2.0-Java-11-Python-3.8.6.eb
new file mode 100644
index 00000000..16f11ded
--- /dev/null
+++ b/s/snpEff/snpEff-5.0-GCCcore-10.2.0-Java-11-Python-3.8.6.eb
@@ -0,0 +1,38 @@
+# IT4Innovations
+# LK 2021
+
+easyblock = 'Tarball'
+
+name = 'snpEff'
+version = '5.0'
+versionsuffix = '-Java-%(javaver)s-Python-%(pyver)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': '10.2.0'}
+
+source_urls = ['https://snpeff.blob.core.windows.net/versions/']
+sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')]
+checksums = ['2b177440eb4a2c3bbfc8f50d4adf9e405f3dcfc05a31a55c96f773f07832af34']
+
+dependencies = [
+ ('Java', '11', '', True),
+ ('Python', '3.8.6'),
+ ('Perl', '5.32.0'),
+]
+
+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'