New, cleaner package repository structure.

Package repositories now look like this:

    top-level-dir/
        repo.yaml
        packages/
            libelf/
                package.py
            mpich/
                package.py
            ...

This leaves room at the top level for additional metadata, source,
per-repo configs, indexes, etc., and it makes it easy to see that
something is a spack repo (just look for repo.yaml and packages).

var/spack/repos/builtin/packages/samtools/package.py

@@ -0,0 +1,18 @@
+from spack import *
+
+class Samtools(Package):
+    """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")
+
+    depends_on("zlib")
+    depends_on("mpc")
+    parallel=False
+    patch("samtools1.2.patch",level=0)
+
+    def install(self, spec, prefix):
+        make("prefix=%s" % prefix, "install")
+

var/spack/repos/builtin/packages/samtools/samtools1.2.patch

@@ -0,0 +1,20 @@
+--- 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)