Merge pull request #1452 from hartzell/feature/add-package-for-samtools

Add package for samtools

4 files changed, 101 insertions, 29 deletions

diff --git a/var/spack/repos/builtin/packages/bcftools/package.py b/var/spack/repos/builtin/packages/bcftools/package.py
new file mode 100644
index 0000000000..a1b4a06dbb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bcftools/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# 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 Bcftools(Package):
+    """BCFtools is a set of utilities that manipulate variant calls in the
+       Variant Call Format (VCF) and its binary counterpart BCF. All
+       commands work transparently with both VCFs and BCFs, both
+       uncompressed and BGZF-compressed."""
+
+    homepage = "http://samtools.github.io/bcftools/"
+    url      = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2"
+
+    version('1.3.1', '575001e9fca37cab0c7a7287ad4b1cdb')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        make("prefix=%s" % prefix, "all")
+        make("prefix=%s" % prefix, "install")
diff --git a/var/spack/repos/builtin/packages/htslib/package.py b/var/spack/repos/builtin/packages/htslib/package.py
new file mode 100644
index 0000000000..1a8b8fd2f5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/htslib/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 Htslib(Package):
+    """C library for high-throughput sequencing data formats."""
+
+    homepage = "https://github.com/samtools/htslib"
+    url      = "https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2"
+
+    version('1.3.1', '16d78f90b72f29971b042e8da8be6843')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py
index f5c7f4431f..6b0b224785 100644
--- a/var/spack/repos/builtin/packages/samtools/package.py
+++ b/var/spack/repos/builtin/packages/samtools/package.py
@@ -24,19 +24,27 @@
 ##############################################################################
 from spack import *
 
+
 class Samtools(Package):
-    """SAM Tools provide various utilities for manipulating alignments in the SAM format, 
-       including sorting, merging, indexing and generating
+    """SAM Tools provide various utilities for manipulating alignments in
+       the SAM format, including sorting, merging, indexing and generating
        alignments in a per-position format"""
 
     homepage = "www.htslib.org"
-    version('1.2','988ec4c3058a6ceda36503eebecd4122',url = "https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2")
+    url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2"
 
-    depends_on("zlib")
-    depends_on("mpc")
-    parallel=False
-    patch("samtools1.2.patch",level=0)
+    version('1.3.1', 'a7471aa5a1eb7fc9cc4c6491d73c2d88')
+    version('1.2', '988ec4c3058a6ceda36503eebecd4122')
 
-    def install(self, spec, prefix):
-        make("prefix=%s" % prefix, "install")
+    depends_on("ncurses")
+    depends_on("htslib", when='@1.3.1:')  # htslib became standalone
+    depends_on('zlib', when='@1.2')       # needed for builtin htslib
 
+    def install(self, spec, prefix):
+        if self.spec.version >= Version('1.3.1'):
+            configure('--prefix={0}'.format(prefix), '--with-ncurses')
+            make()
+            make('install')
+        else:
+            make("prefix=%s" % prefix)
+            make("prefix=%s" % prefix, "install")
diff --git a/var/spack/repos/builtin/packages/samtools/samtools1.2.patch b/var/spack/repos/builtin/packages/samtools/samtools1.2.patch
deleted file mode 100644
index ead3ab4e2c..0000000000
--- a/var/spack/repos/builtin/packages/samtools/samtools1.2.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- Makefile	2015-02-03 08:27:34.000000000 -0800
-+++ Makefile.new	2015-07-21 10:38:27.881406892 -0700
-@@ -26,7 +26,7 @@
- CFLAGS   = -g -Wall -O2
- LDFLAGS  =
- LDLIBS   =
--DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
-+DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0
- LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
-             sam_header.o bam_plbuf.o
- AOBJS=      bam_index.o bam_plcmd.o sam_view.o \
-@@ -37,7 +37,7 @@
-             faidx.o stats.o stats_isize.o bam_flags.o bam_split.o \
-             bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o
- INCLUDES=   -I. -I$(HTSDIR)
--LIBCURSES=  -lcurses # -lXCurses
-+#LIBCURSES=  -lcurses # -lXCurses
- 
- prefix      = /usr/local
- exec_prefix = $(prefix)