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authorGeorge Hartzell <hartzell@alerce.com>2016-07-27 13:20:49 -0400
committerGeorge Hartzell <hartzell@alerce.com>2016-08-04 14:18:03 -0400
commitba0577dc96597d35aaa75472e8ce014c307a03da (patch)
tree288ac40cffe81c29683f1506020549456e9af135 /var
parentef1369c365cb6d8ebaba2dd6b4ebc2f06acdf0ba (diff)
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Update samtools to support v1.3.1
Update the samtools package to support v1.3.1, which - now uses configure script; and - now depends on external htslib package. The dependency on mpc seems to have been bogus, it's never linked in, nor is it mentioned in the source tree. I *do* have a version in /usr/lib64, but ldd does not sure it being linked in either.... By depending on 'ncurses' I can do away with the need for the patch.
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/samtools/package.py25
-rw-r--r--var/spack/repos/builtin/packages/samtools/samtools1.2.patch20
2 files changed, 16 insertions, 29 deletions
diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py
index f5c7f4431f..7df3f5bcf8 100644
--- a/var/spack/repos/builtin/packages/samtools/package.py
+++ b/var/spack/repos/builtin/packages/samtools/package.py
@@ -25,18 +25,25 @@
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)