tximeta: add package (#39207)

* tximeta: add package
  Signed-off-by: Pablo <pablo.aledo@seqera.io>
* [@spackbot] updating style on behalf of pabloaledo

---------

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

1 files changed, 39 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py b/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py
new file mode 100644
index 0000000000..fd1206a2c0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bioconductor-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 BioconductorTximeta(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."""
+
+    homepage = "https://bioconductor.org/packages/release/bioc/html/tximeta.html"
+    url = "https://bioconductor.org/packages/release/bioc/src/contrib/tximeta_1.18.1.tar.gz"
+
+    bioc = "tximeta"
+
+    version("1.18.1", sha256="ee486fc4b2352e2998a3c0c2064449ebcf09b5815f982597ea58311dc8064408")
+
+    depends_on("r", type=("build", "run"))
+    depends_on("r-annotationdbi")
+    depends_on("r-annotationhub")
+    depends_on("r-biocfilecache")
+    depends_on("r-biostrings")
+    depends_on("r-ensembldb")
+    depends_on("r-genomeinfodb")
+    depends_on("r-genomicfeatures")
+    depends_on("r-genomicranges")
+    depends_on("r-iranges")
+    depends_on("r-s4vectors")
+    depends_on("r-summarizedexperiment")
+    depends_on("r-tximport")
+    depends_on("r-jsonlite")
+    depends_on("r-matrix")
+    depends_on("r-tibble")