spaceranger: new manual download package @2.1.1 (#42391)

* spaceranger: new manual download package @2.1.1
* Adding license url

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>

1 files changed, 38 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/spaceranger/package.py b/var/spack/repos/builtin/packages/spaceranger/package.py
new file mode 100644
index 0000000000..9b02fc0942
--- /dev/null
+++ b/var/spack/repos/builtin/packages/spaceranger/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2024 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)
+
+import os
+
+from spack.package import *
+
+
+class Spaceranger(Package):
+    """Space Ranger is a set of analysis pipelines that process Visium data with brightfield
+    and fluorescence microscope images. Space Ranger allows users to map the whole
+    transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen (FF) tissues.
+
+    This package requires the user to accept a license and to download the tarball manually.
+    Once downloaded, the file should be placed within a manual mirror or within the current
+    directory. For instructions on making a manual mirror, see
+    https://spack.readthedocs.io/en/latest/mirrors.html"""
+
+    homepage = "https://www.10xgenomics.com/support/software/space-ranger/latest"
+    manual_download = True
+    license_url = "support.10xgenomics.com/license"
+
+    version("2.1.1", sha256="e3c2982ae91afc4031f7b29e4b27ea012243e1c61ca8fa246b8c1f6ef7c7c241")
+
+    # spaceranger is distributed as precompiled binaries that are not compatible with
+    # processors without the avx instruction set ...
+    # https://www.10xgenomics.com/support/software/space-ranger/downloads/space-ranger-system-requirements
+    conflicts("target=:k10")  # last AMD processor not to support avx
+    conflicts("target=:westmere")  # last Intel processor not to support avx
+    conflicts("target=:x86_64_v2")  # last generic architecture not to support avx
+
+    def url_for_version(self, version):
+        return "file://{0}/spaceranger-{1}.tar.gz".format(os.getcwd(), version)
+
+    def install(self, spec, prefix):
+        install_tree(".", prefix)