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authorsnehring <snehring@users.noreply.github.com>2020-02-20 11:45:57 -0600
committerGitHub <noreply@github.com>2020-02-20 11:45:57 -0600
commitf5b5036ad55bf6e56cd5e1013d4eaacd6c56db7b (patch)
tree3f90b34aa1493a039c91f36e21ac0ddde90b3450
parent40410102d25e48c034cb5ef068f4ca5ab93243e9 (diff)
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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
-rw-r--r--var/spack/repos/builtin/packages/igv/package.py36
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)