Added STAR-Fusion (#4380)

* added perl-star-fusion and perl-intervaltree

* added perl-star-fusion and all dependencies

* changes

* made changes as requested to perl-star-fusion dependencies

* changed perl-intervaltree dependency

* changes to star fusion

* now using perl properly

4 files changed, 176 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/perl-dbfile/package.py b/var/spack/repos/builtin/packages/perl-dbfile/package.py
new file mode 100644
index 0000000000..7445d6e63a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-dbfile/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class PerlDbfile(PerlPackage):
+    """DB_File is a module which allows Perl programs to make use of the
+    facilities provided by Berkeley DB version 1.x (if you have a newer version
+    of DB, see "Using DB_File with Berkeley DB version 2 or greater").
+    It is assumed that you have a copy of the Berkeley DB manual pages at hand
+    when reading this documentation. The interface defined here mirrors the
+    Berkeley DB interface closely."""
+
+    homepage = "https://metacpan.org/pod/DB_File"
+    url      = "https://cpan.metacpan.org/authors/id/P/PM/PMQS/DB_File-1.840.tar.gz"
+
+    version('1.840', '8a2e98d457a216840ac893913c24141e')
+
+    depends_on('perl-extutils-makemaker', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-intervaltree/package.py b/var/spack/repos/builtin/packages/perl-intervaltree/package.py
new file mode 100644
index 0000000000..bcf1204c53
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-intervaltree/package.py
@@ -0,0 +1,37 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class PerlIntervaltree(PerlPackage):
+    """Set::IntervalTree uses Interval Trees to store and efficiently look up
+    ranges using a range-based lookup."""
+
+    homepage = "https://metacpan.org/release/Set-IntervalTree"
+    url      = "https://cpan.metacpan.org/authors/id/B/BE/BENBOOTH/Set-IntervalTree-0.10.tar.gz"
+
+    version('0.10', '42efe9369f1b30e7fd04e10c07226b06')
+
+    depends_on('perl-extutils-makemaker', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-star-fusion/package.py b/var/spack/repos/builtin/packages/perl-star-fusion/package.py
new file mode 100644
index 0000000000..65d673bf3b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-star-fusion/package.py
@@ -0,0 +1,59 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+from glob import glob
+
+
+class PerlStarFusion(Package):
+    """STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis
+    Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate
+    fusion transcripts supported by Illumina reads. STAR-Fusion further
+    processes the output generated by the STAR aligner to map junction reads
+    and spanning reads to a reference annotation set."""
+
+    homepage = "https://github.com/STAR-Fusion/STAR-Fusion"
+    url      = "https://github.com/STAR-Fusion/STAR-Fusion.git"
+
+    version('master', git='https://github.com/STAR-Fusion/STAR-Fusion.git', commit='a16a0a8')
+
+    extends('perl')
+
+    depends_on('star', type=('build', 'run'))
+    depends_on('perl', type=('build', 'run'))
+    depends_on('perl-intervaltree', type=('build', 'run'))
+    depends_on('perl-dbi', type=('build', 'run'))
+    depends_on('perl-dbfile', type=('build', 'run'))
+    depends_on('perl-uri-escape', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('STAR-Fusion', prefix.bin)
+        mkdirp(perl_lib_dir)
+        with working_dir('PerlLib'):
+            for pm in glob("*.pm"):
+                install(pm, perl_lib_dir)
+        with working_dir('util'):
+            for files in glob("*"):
+                install(files, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/perl-uri-escape/package.py b/var/spack/repos/builtin/packages/perl-uri-escape/package.py
new file mode 100644
index 0000000000..ffeb06f979
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-uri-escape/package.py
@@ -0,0 +1,39 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class PerlUriEscape(PerlPackage):
+    """This module provides functions to percent-encode and percent-decode URI
+    strings as defined by RFC 3986. Percent-encoding URI's is informally called
+    "URI escaping". This is the terminology used by this module, which predates
+    the formalization of the terms by the RFC by several years."""
+
+    homepage = "https://metacpan.org/pod/URI::Escape"
+    url      = "https://cpan.metacpan.org/authors/id/E/ET/ETHER/URI-1.71.tar.gz"
+
+    version('1.71', '247c3da29a794f72730e01aa5a715daf')
+
+    depends_on('perl-extutils-makemaker', type='build')