{bio}[foss/2022a,system/system] NanoCaller v3.4.1, RTG-Tools v3.12.1 w/ Java 11

easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.4.1-foss-2022a.eb

@@ -0,0 +1,45 @@
+easyblock = 'Tarball'
+
+name = 'NanoCaller'
+version = '3.4.1'
+
+homepage = 'https://github.com/WGLab/NanoCaller'
+description = """NanoCaller is a computational method that integrates long reads in deep
+ convolutional neural network for the detection of SNPs/indels from long-read sequencing data."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ['https://github.com/WGLab/%(name)s/archive/']
+sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}]
+
+checksums = ['b90970c9e0491f454a5fbd7ab998111e69c5a0b90bad6388bfbe636b73368bf8']
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('BCFtools', '1.15.1'),
+    ('python-parasail', '1.3.3'),
+    ('MUSCLE', '5.1.0'),
+    ('Pysam', '0.19.1'),
+    ('SAMtools', '1.16.1'),
+    ('TensorFlow', '2.11.0'),
+    ('WhatsHap', '1.7'),
+    ('vcflib', '1.0.9', '-R-4.2.1'),
+    ('intervaltree-python', '3.1.0'),
+    ('tqdm', '4.64.0'),
+    ('RTG-Tools', '3.12.1', '-Java-11', SYSTEM),
+]
+
+modextrapaths = {
+    'PATH': '',
+    'PYTHONPATH': '',
+}
+
+sanity_check_paths = {
+    'files': ['NanoCaller'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["NanoCaller --help"]
+
+moduleclass = 'bio'

easybuild/easyconfigs/r/RTG-Tools/RTG-Tools-3.12.1-Java-11.eb

@@ -0,0 +1,42 @@
+easyblock = 'CmdCp'
+
+name = 'RTG-Tools'
+version = '3.12.1'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://www.realtimegenomics.com/products/rtg-tools'
+description = """ RTG Tools contains utilities to easily manipulate and accurately compare multiple VCF files,
+ as well as utilities for processing other common NGS data formats. """
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/RealTimeGenomics/rtg-tools/archive']
+sources = ['%(version)s.tar.gz']
+checksums = ['6ee0ffe1bba7b5497aa09b147a7525b77b1808e6a71368aad440cbd64658085c']
+
+builddependencies = [('ant', '1.10.12', versionsuffix)]
+dependencies = [('Java', '11')]
+
+local_comp_cmd = "export RTG_MEM=1G && "
+# NOTE Tests of RTG-Tools reserve 60% machine's memory.
+# That causes them to fail on debug clusters and work on full nodes only.
+# therefore this easyconfig has been tested on a full node and `ant runalltests` was removed from the easyconfig.
+# local_comp_cmd += 'ant runalltests && '
+local_comp_cmd += 'ant zip-nojre && '
+local_comp_cmd += 'unzip %(builddir)s/rtg-tools-%(version)s/dist/rtg-tools-%(version)s-unknown-nojre.zip'
+
+cmds_map = [('.*', local_comp_cmd)]
+
+files_to_copy = ['rtg-tools-%(version)s-unknown/*']
+
+# add default configuration: no crash reporting, no usage logging
+postinstallcmds = ["echo 'RTG_TALKBACK=false\nRTG_USAGE=' > %(installdir)s/rtg.cfg"]
+
+modextrapaths = {'PATH': ['']}
+
+sanity_check_paths = {
+    'files': ['rtg', 'rtg.cfg', 'RTG.jar'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'