progress on #335 HOMER

335_HOMER/HOMER-4.11-foss-2023a-R-4.3.2.eb

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+easyblock = 'Binary'
+
+name = 'HOMER'
+version = '4.11'
+versionsuffix = '-R-%(rver)s'
+
+homepage = "http://homer.ucsd.edu/homer/"
+description = """HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and
+ next-gen sequencing analysis.  It is a collection of command line programs for unix-style operating systems written
+ in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding
+ 8-20 bp motifs in large scale genomics data.  HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq,
+ RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+
+source_urls = ['http://homer.ucsd.edu/homer']
+sources = ['configureHomer.pl']
+checksums = ['ccdaa3004a0e0df0882634671d4a1acc88364761e0e6c7ea329ebbf1eb729537']
+
+dependencies = [
+    ('Perl', '5.36.1'),
+    ('R', '4.3.0'),
+    ('SAMtools', '1.18'),
+    ('R-bundle-Bioconductor', '3.18', versionsuffix)
+]
+
+# Create _data_folder and, from a test install, copy in the data dir and config.txt and update.txt
+# Post install follow instructions in ${BB_APPS_DATA}/HOMER/README.md to install genomes
+_data_folder = '${BB_APPS_DATA}/HOMER/%(version)s-%(toolchain_name)s-%(toolchain_version)s'
+
+postinstallcmds = [
+    "cd %(installdir)s && mv configureHomer.pl-%(version)s configureHomer.pl",
+    "cd %(installdir)s && perl ./configureHomer.pl -keepScript -install homer -version v%(version)s",
+    "rm -rf %%(installdir)s/data && ln -fs %s/data %%(installdir)s/" % _data_folder,
+    "ln -fs %s/config.txt %%(installdir)s/config.txt" % _data_folder,
+    "ln -fs %s/update.txt %%(installdir)s/update.txt" % _data_folder,
+]
+
+sanity_check_paths = {
+    'files': ['bin/homer', 'bin/getGenomeTilingPeaks'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'