From 6a2efe4114becc7aa02f6f95a9610375f3292d91 Mon Sep 17 00:00:00 2001
From: Adam Huffman <bloch@verdurin.com>
Date: Thu, 31 Aug 2023 11:52:07 +0000
Subject: [PATCH] adding easyconfigs: inferCNV-1.14.2-foss-2022b-R-4.2.2.eb,
 rjags-4-13-foss-2022b-R-4.2.2.eb

---
 .../inferCNV-1.14.2-foss-2022b-R-4.2.2.eb     | 54 +++++++++++++++++++
 .../r/rjags/rjags-4-13-foss-2022b-R-4.2.2.eb  | 29 ++++++++++
 2 files changed, 83 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/inferCNV/inferCNV-1.14.2-foss-2022b-R-4.2.2.eb
 create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-13-foss-2022b-R-4.2.2.eb

diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.14.2-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.14.2-foss-2022b-R-4.2.2.eb
new file mode 100644
index 00000000000..06120b55395
--- /dev/null
+++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.14.2-foss-2022b-R-4.2.2.eb
@@ -0,0 +1,54 @@
+easyblock = 'Bundle'
+
+name = 'inferCNV'
+version = '1.14.2'
+versionsuffix = '-R-%(rver)s'
+local_biocver = '3.16'
+
+homepage = 'https://github.com/broadinstitute/inferCNV/wiki'
+description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence
+ for somatic large-scale chromosomal copy number alterations, such as gains or
+ deletions of entire chromosomes or large segments of chromosomes."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+dependencies = [
+    ('Python', '3.10.8'),
+    ('R', '4.2.2'),
+    ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'),
+    ('rjags', '4-13', '-R-%(rver)s'),
+]
+
+exts_default_options = {
+    'source_urls': [
+        'https://bioconductor.org/packages/release/bioc/src/contrib/',  # current version of packages
+        'https://bioconductor.org/packages/%s/bioc/src/contrib/' % local_biocver,
+        'https://bioconductor.org/packages/%s/bioc/src/contrib/Archive/%%(name)s' % local_biocver,
+        'https://bioconductor.org/packages/%s/data/annotation/src/contrib/' % local_biocver,
+        'https://bioconductor.org/packages/%s/data/experiment/src/contrib/' % local_biocver,
+        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
+        'https://cran.r-project.org/src/contrib/',  # current version of packages
+        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+    ],
+    'source_tmpl': '%(name)s_%(version)s.tar.gz'
+}
+
+exts_defaultclass = 'RPackage'
+
+exts_list = [
+    ('phyclust', '0.1-33', {
+        'checksums': ['38786608193bcad6aeb5517f2d5f836c9773bdd09fc484b4bd40b06a71f5a413'],
+    }),
+    ('infercnv', version, {
+        'checksums': ['7705f9d2796303f55034e026578a5877caf80b8dc929a15918b242a89a0ca512'],
+    }),
+]
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['infercnv'],
+}
+
+moduleclass = 'bio'
diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-13-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/rjags/rjags-4-13-foss-2022b-R-4.2.2.eb
new file mode 100644
index 00000000000..77fe842ea5d
--- /dev/null
+++ b/easybuild/easyconfigs/r/rjags/rjags-4-13-foss-2022b-R-4.2.2.eb
@@ -0,0 +1,29 @@
+easyblock = 'RPackage'
+
+name = 'rjags'
+version = '4-13'
+versionsuffix = '-R-%(rver)s'
+
+homepage = 'https://cran.r-project.org/web/packages/rjags'
+description = """The rjags package is an interface to the JAGS library."""
+
+toolchain = {'name': 'foss', 'version': '2022b'}
+
+source_urls = [
+    'https://cran.r-project.org/src/contrib/',
+    'https://cran.r-project.org/src/contrib/Archive/rjags/',
+]
+sources = ['%(name)s_%(version)s.tar.gz']
+checksums = ['f85cc34c5127b828d8a3fa3613ef29f147c868bdaf55eb0f7406c10abbf92b32']
+
+dependencies = [
+    ('R', '4.2.2'),
+    ('JAGS', '4.3.2'),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['rjags'],
+}
+
+moduleclass = 'math'