From 7fb68d5b42cd48f3e9e82db1ddb27ba1e06fa875 Mon Sep 17 00:00:00 2001
From: Josef Hrabal <josef.hrabal@vsb.cz>
Date: Fri, 11 Oct 2019 09:48:22 +0200
Subject: [PATCH] 	new file:   g/GATK/GATK-4.1.4.0-Java-1.8.0_202.eb 
 new file:   g/Go/Go-1.13.1.eb 	new file:   s/Singularity/Singularity-3.4.1.eb

---
 g/GATK/GATK-4.1.4.0-Java-1.8.0_202.eb | 43 ++++++++++++++++++++
 g/Go/Go-1.13.1.eb                     | 26 ++++++++++++
 s/Singularity/Singularity-3.4.1.eb    | 57 +++++++++++++++++++++++++++
 3 files changed, 126 insertions(+)
 create mode 100644 g/GATK/GATK-4.1.4.0-Java-1.8.0_202.eb
 create mode 100644 g/Go/Go-1.13.1.eb
 create mode 100644 s/Singularity/Singularity-3.4.1.eb

diff --git a/g/GATK/GATK-4.1.4.0-Java-1.8.0_202.eb b/g/GATK/GATK-4.1.4.0-Java-1.8.0_202.eb
new file mode 100644
index 00000000..eedc55f4
--- /dev/null
+++ b/g/GATK/GATK-4.1.4.0-Java-1.8.0_202.eb
@@ -0,0 +1,43 @@
+# IT4Innovations 2019
+
+easyblock = 'Tarball'
+
+name = 'GATK'
+version = '4.1.4.0'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'http://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': 'system', 'version': ''}
+
+# download manually from http://www.broadinstitute.org/gatk/download
+source_urls = [
+    ' https://github.com/broadinstitute/gatk/releases/download/%(version)s/']
+
+sources = ['gatk-%(version)s.zip']
+
+dependencies = [('Java', '1.8.0_202')]
+
+
+postinstallcmds = [
+    'mkdir %(installdir)s/bin',
+    'mv %(installdir)s/gatk %(installdir)s/bin',
+]
+
+modextravars = {
+    'export GATK_LOCAL_JAR': '%(installdir)s/gatk-package-%(version)s-local.jar'
+}
+
+sanity_check_paths = {
+    'files': [
+        'gatk-package-%(version)s-local.jar',
+        'gatk-package-%(version)s-spark.jar'],
+    'dirs': ['bin'],
+}
+
+moduleclass = 'bio'
diff --git a/g/Go/Go-1.13.1.eb b/g/Go/Go-1.13.1.eb
new file mode 100644
index 00000000..056ca8eb
--- /dev/null
+++ b/g/Go/Go-1.13.1.eb
@@ -0,0 +1,26 @@
+# It4Innovations 2019
+
+easyblock = 'Tarball'
+
+name = 'Go'
+version = '1.13.1'
+
+homepage = 'http://www.golang.org'
+description = """Go is an open source programming language that makes it easy to build
+ simple, reliable, and efficient software."""
+
+toolchain = {'name': 'system', 'version': ''}
+
+source_urls = ['https://dl.google.com/go/']
+sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz']
+
+checksums = ['b7df1f54d4d176a19bc416643c63738e']
+
+sanity_check_paths = {
+    'files': ['bin/go', 'bin/gofmt'],
+    'dirs': ['api', 'doc', 'lib', 'pkg'],
+}
+
+modextravars = {'GOROOT': '%(installdir)s'}
+
+moduleclass = 'compiler'
diff --git a/s/Singularity/Singularity-3.4.1.eb b/s/Singularity/Singularity-3.4.1.eb
new file mode 100644
index 00000000..3020080e
--- /dev/null
+++ b/s/Singularity/Singularity-3.4.1.eb
@@ -0,0 +1,57 @@
+# IT4Innovations 2019
+
+easyblock = 'ConfigureMake'
+
+name = 'Singularity'
+version = '3.4.1'
+
+homepage = 'https://github.com/sylabs/singularity'
+description = "Singularity is an open source container platform designed to be simple, fast, and secure. Singularity is optimized for EPC and HPC workloads, allowing untrusted users to run untrusted containers in a trusted way."
+
+toolchain = {'name': 'system', 'version': ''}
+
+source_urls = ['https://github.com/sylabs/singularity/releases/download/v%s/' % version]
+sources = ['singularity-%(version)s.tar.gz']
+checksums = ['27ea29349ba6f5f467a6d256580ea21f']
+
+builddependencies = [
+        ('Go', '1.13.1'),
+]
+
+dependencies = [
+        ('squashfs-tools', '4.3'),
+]
+
+osdependencies = [
+    ('openssl-devel', 'libssl-dev', 'libopenssl-devel'),
+]
+
+skipsteps = ['configure']
+#prebuildopts = 'export GOPATH=$(pwd):$GOPATH && '
+skipsteps = ['configure']
+prebuildopts = 'mkdir -p src/github.com/sylabs && '
+prebuildopts += 'ln -sf %(builddir)s/singularity src/github.com/sylabs/singularity && '
+prebuildopts += './mconfig -p %(installdir)s -b build && '
+prebuildopts += 'cd build && '
+preinstallopts = 'cd build && '
+
+
+postinstallcmds = [
+        'echo "mksquashfs path = /apps/all/squashfs-tools/4.3/bin" >> %(installdir)s/etc/singularity/singularity.conf',
+]
+
+# next steps after installation
+# INSTALLATION_PATH=your_installation_path
+# chown root:root $INSTALLATION_PATH/Singularity/*/etc/singularity/singularity.conf
+# chown root:root $INSTALLATION_PATH/Singularity/*/etc/singularity/capability.json
+# chown root:root $INSTALLATION_PATH/Singularity/*/etc/singularity/ecl.toml
+# chown root:root $INSTALLATION_PATH/Singularity/*/libexec/singularity/bin/*-suid
+# chmod 4755 $INSTALLATION_PATH/Singularity/*/libexec/singularity/bin/*-suid
+# chmod +s $INSTALLATION_PATH/Singularity/*/libexec/singularity/bin/*-suid
+
+sanity_check_paths = {
+    'files': ['bin/singularity'],
+    'dirs': ['bin', 'etc', 'libexec', 'var'],
+}
+
+moduleclass = 'tools'