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| author | Mario Melara <mamelara@genepool1.nersc.gov> | 2015-09-23 16:30:44 -0700 |
|---|---|---|
| committer | Mario Melara <mamelara@genepool1.nersc.gov> | 2015-09-23 16:30:44 -0700 |
| commit | 521632b3dc30c81fe4230ef010b972e65d80c47a (patch) | |
| tree | 2fa3543060e358ccf28c21fb4a247163c7cc7173 | |
| parent | 6d4eed38457444d9b2b2b29b43d4c38c2fbb11d6 (diff) | |
| download | spack-521632b3dc30c81fe4230ef010b972e65d80c47a.tar.gz spack-521632b3dc30c81fe4230ef010b972e65d80c47a.tar.bz2 spack-521632b3dc30c81fe4230ef010b972e65d80c47a.tar.xz spack-521632b3dc30c81fe4230ef010b972e65d80c47a.zip | |
Added samtools bioinformatics software
| -rw-r--r-- | var/spack/packages/samtools/package.py | 18 | ||||
| -rw-r--r-- | var/spack/packages/samtools/samtools1.2.patch | 20 |
2 files changed, 38 insertions, 0 deletions
diff --git a/var/spack/packages/samtools/package.py b/var/spack/packages/samtools/package.py new file mode 100644 index 0000000000..72900398d8 --- /dev/null +++ b/var/spack/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") + diff --git a/var/spack/packages/samtools/samtools1.2.patch b/var/spack/packages/samtools/samtools1.2.patch new file mode 100644 index 0000000000..ead3ab4e2c --- /dev/null +++ b/var/spack/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) |