adding package igv (#15096)

* igv: adding package igv

* removing some remaining initial boilerplate

* changing path construction to be more correct

* adding in type for java dep, also forgot about prefix.bin etc

1 files changed, 36 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/igv/package.py b/var/spack/repos/builtin/packages/igv/package.py
new file mode 100644
index 0000000000..990b5e1962
--- /dev/null
+++ b/var/spack/repos/builtin/packages/igv/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2020 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 Igv(Package):
+    """The Integrative Genomics Viewer (IGV) is a high-performance visualization
+    tool for interactive exploration of large, integrated genomic datasets.
+    It supports a wide variety of data types, including array-based and
+    next-generation sequence data, and genomic annotations."""
+
+    homepage = "https://software.broadinstitute.org/software/igv/home"
+    url      = "https://data.broadinstitute.org/igv/projects/downloads/2.8/IGV_Linux_2.8.0.zip"
+
+    maintainers = ['snehring']
+
+    version('2.8.0', sha256='897f683645b02c4da55424110b885071c2b9dd51bc180174e2a9b10788bf3257')
+
+    # They ship with 11, out of an abundance of caution I'm going to restrict
+    # it to just 11.
+
+    depends_on('java@11:11.99', type='run')
+
+    def install(self, spec, prefix):
+        # Binary dist, just copy what we need, which should be the lib
+        # directory, the two script, and the arg file
+        install_tree('lib', prefix.lib)
+        mkdirp(prefix.bin)
+        filter_file('^prefix=.*$', 'prefix=' + prefix,
+                    'igv.sh', 'igv_hidpi.sh')
+        install('igv.sh', prefix.bin)
+        install('igv_hidpi.sh', prefix.bin)
+        install('igv.args', prefix)