mixcr: Added a new package for MiXCR. (#9864)

* mixcr: Added a new package for MiXCR.

* mixcr: Fixed spack license string.

1 files changed, 29 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/mixcr/package.py b/var/spack/repos/builtin/packages/mixcr/package.py
new file mode 100644
index 0000000000..3fef5fdb55
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mixcr/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 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 import *
+
+
+class Mixcr(Package):
+    """MiXCR is a universal framework that processes big immunome data from
+    raw sequences to quantitated clonotypes. MiXCR efficiently handles
+    paired- and single-end reads, considers sequence quality, corrects PCR
+    errors and identifies germline hypermutations. The software supports
+    both partial- and full-length profiling and employs all available RNA or
+    DNA information, including sequences upstream of V and downstream of J
+    gene segments."""
+
+    homepage = "https://mixcr.readthedocs.io/en/master/index.html"
+    url      = "https://github.com/milaboratory/mixcr/releases/download/v3.0.2/mixcr-3.0.2.zip"
+
+    version('3.0.2', sha256='b4dcad985053438d5f5590555f399edfbd8cb514e1b9717620ee0ad0b5eb6b33')
+
+    depends_on('java@8:')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix)