From c981797762bf33a0c9b08685c68efa19dbacb9d0 Mon Sep 17 00:00:00 2001
From: Jakub Kropacek <jakub.kropacek@vsb.cz>
Date: Tue, 19 Oct 2021 18:33:53 +0200
Subject: [PATCH] 	new file:  
 g/GATK/GATK-4.1.9.0-GCCcore-10.2.0-Java-11.eb 	new file:  
 p/picard/picard-2.23.8-Java-11.eb

---
 g/GATK/GATK-4.1.9.0-GCCcore-10.2.0-Java-11.eb | 53 +++++++++++++++++++
 p/picard/picard-2.23.8-Java-11.eb             | 53 +++++++++++++++++++
 2 files changed, 106 insertions(+)
 create mode 100644 g/GATK/GATK-4.1.9.0-GCCcore-10.2.0-Java-11.eb
 create mode 100644 p/picard/picard-2.23.8-Java-11.eb

diff --git a/g/GATK/GATK-4.1.9.0-GCCcore-10.2.0-Java-11.eb b/g/GATK/GATK-4.1.9.0-GCCcore-10.2.0-Java-11.eb
new file mode 100644
index 00000000..c81c3875
--- /dev/null
+++ b/g/GATK/GATK-4.1.9.0-GCCcore-10.2.0-Java-11.eb
@@ -0,0 +1,53 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB
+# Authors::   George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis.georgatos@uni.lu>,
+#             Kenneth Hoste (UGent)
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+# Modified by: Adam Huffman, Jonas Demeulemeester
+# The Francis Crick Institute
+# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen
+##
+
+easyblock = 'Tarball'
+
+name = 'GATK'
+version = '4.1.9.0'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://www.broadinstitute.org/gatk/'
+description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute
+ to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,
+ with a primary focus on variant discovery and genotyping as well as strong emphasis on
+ data quality assurance. Its robust architecture, powerful processing engine and
+ high-performance computing features make it capable of taking on projects of any size."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/']
+sources = ['gatk-%(version)s.zip']
+
+dependencies = [
+    ('Java', '11', '', True),
+    ('Python', '3.8.6'),
+]
+
+modextrapaths = {'PATH': ''}
+
+sanity_check_paths = {
+    'files': ['gatk'],
+    'dirs': [],
+}
+sanity_check_commands = [
+    "gatk --help",
+    "gatk --list",
+]
+
+# modloadmsg = "WARNING: GATK v%(version)s support for Java 11 is in beta state. Use at your own risk.\n"
+
+moduleclass = 'bio'
diff --git a/p/picard/picard-2.23.8-Java-11.eb b/p/picard/picard-2.23.8-Java-11.eb
new file mode 100644
index 00000000..69d41920
--- /dev/null
+++ b/p/picard/picard-2.23.8-Java-11.eb
@@ -0,0 +1,53 @@
+##
+# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild
+#
+# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia
+# Homepage: https://www.adelaide.edu.au/phoenix/
+#
+# Copyright::   adelaide.edu.au/phoenix
+# Authors::	Robert Qiao <robert.qiao@adelaide.edu.au>, Exe Escobedo <exequiel.sepulvedaescobedo@adelaide.edu.au>
+# License::	MIT
+#
+# 2.10.1:
+# Adam Huffman
+# The Francis Crick Institute
+# 2.18.11:
+# Jonas Demeulemeester
+# The Francis Crick Institute
+# 2.21.1
+# Pavel Grochal (INUITS)
+# 2.25.1
+# J. Sassmannshausen (GSTT)
+# 2.25.5
+# Erica Bianco (HPCNow!)
+##
+
+easyblock = 'JAR'
+
+name = 'picard'
+version = '2.23.8'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://broadinstitute.github.io/picard/'
+description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s']
+sources = [{
+    'filename': '%(name)s-%(version)s.jar',
+    'download_filename': '%(name)s.jar',
+}]
+
+postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"]
+
+dependencies = [('Java', '11')]
+
+sanity_check_paths = {
+    'files': ['picard.jar'],
+    'dirs': [],
+}
+
+modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar"
+
+moduleclass = 'bio'