Update bioconductor packages (#41227)

Signed-off-by: Pablo <pablo.aledo@seqera.io>

8 files changed, 135 insertions, 4 deletions

diff --git a/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py b/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py
index d92d43d277..905eb44d64 100644
--- a/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py
+++ b/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py
@@ -15,7 +15,11 @@ class BioconductorDupradar(RPackage):
 
     bioc = "dupradar"
 
-    version("1.30.0", sha256="a299d7a4578047dfc19237e34255b0f50f70ce41d29762ef9f5a7741ba35aa3d")
+    version(
+        "1.30.0",
+        sha256="a299d7a4578047dfc19237e34255b0f50f70ce41d29762ef9f5a7741ba35aa3d",
+        deprecated=True,
+    )
 
     depends_on("r-kernsmooth")
     depends_on("subread")
diff --git a/var/spack/repos/builtin/packages/bioconductor-ebseq/package.py b/var/spack/repos/builtin/packages/bioconductor-ebseq/package.py
index 9a14a95c92..2893d6bfdc 100644
--- a/var/spack/repos/builtin/packages/bioconductor-ebseq/package.py
+++ b/var/spack/repos/builtin/packages/bioconductor-ebseq/package.py
@@ -23,7 +23,11 @@ class BioconductorEbseq(RPackage):
 
     bioc = "ebseq"
 
-    version("1.40.0", sha256="a5d3a88743d61062c6d68a426b19c53a4afd2fa216abc884d42c187780994378")
+    version(
+        "1.40.0",
+        sha256="a5d3a88743d61062c6d68a426b19c53a4afd2fa216abc884d42c187780994378",
+        deprecated=True,
+    )
 
     depends_on("r-blockmodeling")
     depends_on("r-gplots")
diff --git a/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py b/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py
index 657473676a..8785ae0835 100644
--- a/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py
+++ b/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py
@@ -17,4 +17,8 @@ class BioconductorRsubread(RPackage):
     depends_on("r-matrix")
     depends_on("zlib-api")
 
-    version("2.14.2", sha256="ac8be0fad0eb2743443e3a60a9a94eec78c746638aaccca70e7166d034dcebb5")
+    version(
+        "2.14.2",
+        sha256="ac8be0fad0eb2743443e3a60a9a94eec78c746638aaccca70e7166d034dcebb5",
+        deprecated=True,
+    )
diff --git a/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py b/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py
index fd1206a2c0..01900bb5ab 100644
--- a/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py
+++ b/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py
@@ -19,7 +19,11 @@ class BioconductorTximeta(RPackage):
 
     bioc = "tximeta"
 
-    version("1.18.1", sha256="ee486fc4b2352e2998a3c0c2064449ebcf09b5815f982597ea58311dc8064408")
+    version(
+        "1.18.1",
+        sha256="ee486fc4b2352e2998a3c0c2064449ebcf09b5815f982597ea58311dc8064408",
+        deprecated=True,
+    )
 
     depends_on("r", type=("build", "run"))
     depends_on("r-annotationdbi")
diff --git a/var/spack/repos/builtin/packages/r-dupradar/package.py b/var/spack/repos/builtin/packages/r-dupradar/package.py
new file mode 100644
index 0000000000..b86c04c021
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dupradar/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RDupradar(RPackage):
+    """Assessment of duplication rates in RNA-Seq datasets"""
+
+    maintainers("pabloaledo")
+
+    bioc = "dupRadar"
+
+    version("1.32.0", commit="7e07fc3a3901f8cae0203759fc24dd7df430a07f")
+    version("1.30.3", commit="19e3b13a148c47e69686cd1e872182c564fd4dcd")
+    version("1.30.0", commit="3d53d2d2e0c404a25845d78b8df8fee3f6b34eb5")
+
+    depends_on("r@3.2:", type=("build", "run"))
+    depends_on("r-kernsmooth", type=("build", "run"))
+    depends_on("r-rsubread", type=("build", "run"))
+    depends_on("subread", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-ebseq/package.py b/var/spack/repos/builtin/packages/r-ebseq/package.py
new file mode 100644
index 0000000000..3fd13c18b7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ebseq/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class REbseq(RPackage):
+    """An R package for gene and isoform differential expression analysis of RNA-seq data.
+
+    R/EBSeq is an R package for identifying genes and isoforms differentially
+    expressed (DE) across two or more biological conditions in an RNA-seq
+    experiment. Details can be found in Leng et al., 2013. It provides the syntax
+    required for identifying DE genes and isoforms in a two-group RNA-seq
+    experiment as well for identifying DE genes across more than two conditions
+    (the commands for identifying DE isoforms across more than two conditions
+    are the same as those required for gene-level analysis)."""
+
+    maintainers("pabloaledo")
+
+    bioc = "EBSeq"
+
+    version("2.0.0", commit="f1d4e4419988ab98540739c9349559fd437cb59f")
+    version("1.40.0", commit="7d1d2a2b4ea0df8cddfb5e57d6431f3948c5c4ca")
+
+    depends_on("r@3.0:", type=("build", "run"))
+    depends_on("r-bh", type=("build", "run"))
+    depends_on("r-blockmodeling", type=("build", "run"))
+    depends_on("r-gplots", type=("build", "run"))
+    depends_on("r-rcppeigen@0.3.2.9.0:", type=("build", "run"))
+    depends_on("r-rcpp@0.12.11:", type=("build", "run"))
+    depends_on("r-testthat", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-rsubread/package.py b/var/spack/repos/builtin/packages/r-rsubread/package.py
new file mode 100644
index 0000000000..1def92a934
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rsubread/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RRsubread(RPackage):
+    """Mapping, quantification and variant analysis of sequencing data"""
+
+    bioc = "Rsubread"
+
+    version("2.16.0", commit="62b92c9ed3fc2be89ed9f29e3db1809d1e115dbc")
+    version("2.14.2", commit="863bd98c6523b888da59335a6acb516d2676d412")
+
+    depends_on("r", type=("build", "run"))
+    depends_on("r-matrix", type=("build", "run"))
+    depends_on("r-r-utils", type=("build", "run"))
+    depends_on("zlib-api", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-tximeta/package.py b/var/spack/repos/builtin/packages/r-tximeta/package.py
new file mode 100644
index 0000000000..ee12ed3f9a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tximeta/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class RTximeta(RPackage):
+    """Transcript Quantification Import with Automatic Metadata
+
+    Transcript quantification import from Salmon and alevin with automatic
+    attachment of transcript ranges and release information, and other associated
+    metadata. De novo transcriptomes can be linked to the appropriate sources with
+    linkedTxomes and shared for computational reproducibility."""
+
+    bioc = "tximeta"
+
+    version("1.20.0", commit="c9cf6d6a80ca5129b91d723867aca0aec12e8299")
+    version("1.18.3", commit="3caed00397476cfe9c379f4bc5a361023fdd6ffa")
+    version("1.18.0", commit="8f87d53bbd6f2d97821dd8f7fdd54624928f862d")
+
+    depends_on("r", type=("build", "run"))
+    depends_on("r-annotationdbi", type=("build", "run"))
+    depends_on("r-annotationhub", type=("build", "run"))
+    depends_on("r-biocfilecache", type=("build", "run"))
+    depends_on("r-biostrings", type=("build", "run"))
+    depends_on("r-ensembldb", type=("build", "run"))
+    depends_on("r-genomeinfodb", type=("build", "run"))
+    depends_on("r-genomicfeatures", type=("build", "run"))
+    depends_on("r-genomicranges", type=("build", "run"))
+    depends_on("r-iranges", type=("build", "run"))
+    depends_on("r-jsonlite", type=("build", "run"))
+    depends_on("r-matrix", type=("build", "run"))
+    depends_on("r-r-utils", type=("build", "run"))
+    depends_on("r-s4vectors", type=("build", "run"))
+    depends_on("r-summarizedexperiment", type=("build", "run"))
+    depends_on("r-tibble", type=("build", "run"))
+    depends_on("r-tximport", type=("build", "run"))