1 files changed, 51 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/pindel/package.py b/var/spack/repos/builtin/packages/pindel/package.py
new file mode 100644
index 0000000000..7755fdd8aa
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+++ b/var/spack/repos/builtin/packages/pindel/package.py
@@ -0,0 +1,51 @@
+# 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 Pindel(MakefilePackage):
+    """Pindel can detect breakpoints from next-gen sequence data."""
+
+    homepage = "http://gmt.genome.wustl.edu/packages/pindel/"
+    url      = "https://github.com/genome/pindel/archive/v0.2.5.tar.gz"
+
+    version('0.2.5b8', 'e6de2ffb38ba1cb89351cdccabe78cde')
+    version('0.2.5b6', 'dc2febb18c203f0ef1ba02b7b882e94b')
+    version('0.2.5b5', '73e964bc19de9ab9e6e8a316353e3184')
+    version('0.2.5b4', 'b4aefd538d9f62578f46440c4bce497e')
+    version('0.2.5b1', 'a8e53e8919aa29093db13fad5ede93a5')
+    version('0.2.5a7', '5fb2bac6108547b5d60c38fc66abdfc4')
+    version('0.2.5',   'd4568cbb83ec25ef9f9f6f058b30053e')
+
+    depends_on('htslib@1.7:')
+    #
+    # This Makefile2 stuff is due to the original installer,
+    # The author wants to run make twice, the first
+    # time generates a Makefile.local then returns "false"
+    # User is then suppose to run make again and the
+    # package will compile. This is an attempt to
+    # stay as close to the original installer as possible
+    #
+
+    def edit(self, spec, prefix):
+        copy('Makefile', 'Makefile2')
+        myedit = FileFilter('Makefile2')
+        myedit.filter('-include Makefile.local', '#removed include')
+        myedit.filter('@false', '#removed autofailure')
+
+    def build(self, spec, prefix):
+        make("Makefile.local", "-f",
+             "Makefile2",
+             "HTSLIB=%s" % spec['htslib'].prefix)
+        make("HTSLIB=%s" % spec['htslib'].prefix)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('src/pindel', prefix.bin)
+        install('src/pindel2vcf', prefix.bin)
+        install('src/sam2pindel', prefix.bin)
+        install('src/pindel2vcf4tcga', prefix.bin)
+        install_tree('demo', prefix.doc)