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| author | George Hartzell <hartzell@alerce.com> | 2017-03-28 19:35:46 -0700 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2017-03-28 21:35:46 -0500 |
| commit | 9385659aa1d692f2fce9b38d90156e332b2bf48f (patch) | |
| tree | b4fd3c58d69eb27001a81c49fcfbc98f7a71028c /var | |
| parent | d6cbae81c7c4dad025307c72141ce78d8d21b253 (diff) | |
| download | spack-9385659aa1d692f2fce9b38d90156e332b2bf48f.tar.gz spack-9385659aa1d692f2fce9b38d90156e332b2bf48f.tar.bz2 spack-9385659aa1d692f2fce9b38d90156e332b2bf48f.tar.xz spack-9385659aa1d692f2fce9b38d90156e332b2bf48f.zip | |
bowtie2: add support for version 2.3.1 (#3599)
* Add support for 2.3.1
Updated digest and added a dependency on tbb.
* Cleanup patch name and add description
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/bowtie2/bowtie2-2.2.5.patch (renamed from var/spack/repos/builtin/packages/bowtie2/bowtie2-2.5.patch) | 0 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/bowtie2/bowtie2-2.3.1.patch | 16 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/bowtie2/package.py | 16 |
3 files changed, 28 insertions, 4 deletions
diff --git a/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.5.patch b/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.2.5.patch index 290be39c73..290be39c73 100644 --- a/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.5.patch +++ b/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.2.5.patch diff --git a/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.3.1.patch b/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.3.1.patch new file mode 100644 index 0000000000..0f4a15b1a1 --- /dev/null +++ b/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.3.1.patch @@ -0,0 +1,16 @@ +--- Makefile.orig 2017-03-24 20:43:00.304532976 -0700 ++++ Makefile 2017-03-24 20:48:59.644532037 -0700 +@@ -26,10 +26,10 @@ + + INC = + LIBS = -lreadline -ltermcap -lz +-GCC_PREFIX = $(shell dirname `which gcc`) ++GCC_PREFIX = + GCC_SUFFIX = +-CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX) +-CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX) ++CC = cc ++CPP = c++ + CXX ?= $(CPP) + HEADERS = $(wildcard *.h) + BOWTIE_MM = 1 diff --git a/var/spack/repos/builtin/packages/bowtie2/package.py b/var/spack/repos/builtin/packages/bowtie2/package.py index a8a1a34ed4..6dbcea8dd0 100644 --- a/var/spack/repos/builtin/packages/bowtie2/package.py +++ b/var/spack/repos/builtin/packages/bowtie2/package.py @@ -27,12 +27,20 @@ from glob import glob class Bowtie2(Package): - """Description""" + """Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences""" homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml" - version('2.2.5', '51fa97a862d248d7ee660efc1147c75f', - url="http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip") + version('2.3.1', 'b4efa22612e98e0c23de3d2c9f2f2478') + version('2.2.5', '51fa97a862d248d7ee660efc1147c75f') - patch('bowtie2-2.5.patch', when='@2.2.5', level=0) + depends_on('tbb', when='@2.3.1') + + patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0) + patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0) + + def url_for_version(self, version): + url="http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/{0}/bowtie2-{0}-source.zip" + return url.format(version) def install(self, spec, prefix): make() |