diff options
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/bowtie2/bowtie2-2.3.0.patch | 16 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/bowtie2/package.py | 31 |
2 files changed, 44 insertions, 3 deletions
diff --git a/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.3.0.patch b/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.3.0.patch new file mode 100644 index 0000000000..58bcee6572 --- /dev/null +++ b/var/spack/repos/builtin/packages/bowtie2/bowtie2-2.3.0.patch @@ -0,0 +1,16 @@ +--- Makefile.orig 2017-10-19 16:22:27.589185696 -0700 ++++ Makefile 2017-10-19 16:23:26.094227199 -0700 +@@ -25,10 +25,10 @@ + bindir = $(prefix)/bin + + INC = +-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 bd6e956b80..067c6c52cc 100644 --- a/var/spack/repos/builtin/packages/bowtie2/package.py +++ b/var/spack/repos/builtin/packages/bowtie2/package.py @@ -34,18 +34,43 @@ class Bowtie2(Package): url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip" version('2.3.1', 'b4efa22612e98e0c23de3d2c9f2f2478') + version('2.3.0', '3ab33f30f00f3c30fec1355b4e569ea2') version('2.2.5', '51fa97a862d248d7ee660efc1147c75f') - depends_on('tbb', when='@2.3.1') - depends_on('readline') - depends_on('zlib') + depends_on('tbb', when='@2.3.0:') + depends_on('readline', when='@2.3.1:') + depends_on('perl', type='run') + depends_on('python', type='run') + depends_on('zlib', 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) + patch('bowtie2-2.3.0.patch', when='@2.3.0', level=0) # seems to have trouble with 6's -std=gnu++14 conflicts('%gcc@6:') + @run_before('install') + def filter_sbang(self): + """Run before install so that the standard Spack sbang install hook + can fix up the path to the perl|python binary. + """ + + with working_dir(self.stage.source_path): + kwargs = {'ignore_absent': True, 'backup': False, 'string': False} + + match = '^#!/usr/bin/env perl' + perl = self.spec['perl'].command + substitute = "#!{perl}".format(perl=perl) + files = ['bowtie2', ] + filter_file(match, substitute, *files, **kwargs) + + match = '^#!/usr/bin/env python' + python = self.spec['python'].command + substitute = "#!{python}".format(python=python) + files = ['bowtie2-build', 'bowtie2-inspect'] + filter_file(match, substitute, *files, **kwargs) + def install(self, spec, prefix): make() mkdirp(prefix.bin) |