{bio}[foss/2022b] leafcutter v0.2.9 w/ R 4.2.2 + additional required extensions in R-bundle-Bioconductor v3.16

easybuild/easyconfigs/l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb

@@ -0,0 +1,39 @@
+easyblock = 'RPackage'
+
+name = 'leafcutter'
+version = '0.2.9'
+# there's no proper 0.2.9 release, so using commit that updated DESCRIPTION file 
+local_commit = 'd02bc35'
+versionsuffix = '-R-%(rver)s'
+
+homepage = "http://davidaknowles.github.io/leafcutter/index.html"
+description = """Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. 
+ The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) 
+ intron usage across samples. The advantages of this approach include: easy detection of novel introns, 
+ modeling of more complex splicing events than exonic PSI, avoiding the challenge of isoform abundance 
+ estimation, simple, computationally efficient algorithms scaling to 100s or even 1000s of samples.
+ For details please see our bioRxiv preprint and corresponding Nature Genetics publication.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = ['https://github.com/davidaknowles/leafcutter/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['defee98257b330200b86b1a158231b818025a1f30c019c254907c2669efdf9f7']
+
+dependencies = [
+    ('SAMtools', '1.17'),
+    ('RegTools', '1.0.0'),
+    ('Python', '3.10.8'),
+    ('R', '4.2.2'),
+    ('R-bundle-Bioconductor', '3.16', versionsuffix),
+]
+
+start_dir = 'leafcutter'
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': [name],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

@@ -1247,6 +1247,19 @@ exts_list = [
     ('UCell', '2.2.0', {
         'checksums': ['e3ca2b2d77a780a9450853e869bc10654c47485777d39a703203dc44d97df4bc'],
     }),
+    ('intervals', '0.15.4', {
+        'checksums': ['50c0e1e3aab3e7b72cc1f0a6559d96caa3a360e969c38538479907e6cbe39f8f'],
+    }),
+    ('oompaBase', '3.2.9', {
+        'checksums': ['14ca2b8e713a6a7ce13758f7f5c183dbc4fdfedc4f1244ca31bbdadf8a16bcb2'],
+    }),
+    ('oompaData', '3.1.3', {
+        'checksums': ['aeb932f75d3de2101d2e1b387fe76677f2d38d4819710320c0e3df07df3ab73d'],
+    }),
+    ('TailRank', '3.2.2', {
+        'checksums': ['21ed95ea47d21155f08ae2ad7bca9547f89f492000bc1defe1cc5ec172739d09'],
+    }),
+
 ]
 
 modextrapaths = {'R_LIBS_SITE': ''}