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| author | Mario Melara <mamelara@genepool1.nersc.gov> | 2015-09-24 11:21:54 -0700 |
|---|---|---|
| committer | Mario Melara <mamelara@genepool1.nersc.gov> | 2015-09-24 11:21:54 -0700 |
| commit | 13eb461ec31520c75d6d604038e455468d061a61 (patch) | |
| tree | 4ec67709fee0e5b05777562a5742b5100f89889e /var | |
| parent | 521632b3dc30c81fe4230ef010b972e65d80c47a (diff) | |
| download | spack-13eb461ec31520c75d6d604038e455468d061a61.tar.gz spack-13eb461ec31520c75d6d604038e455468d061a61.tar.bz2 spack-13eb461ec31520c75d6d604038e455468d061a61.tar.xz spack-13eb461ec31520c75d6d604038e455468d061a61.zip | |
Adding bowtie2 package along with patch
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/packages/bowtie2/bowtie2-2.5.patch | 16 | ||||
| -rw-r--r-- | var/spack/packages/bowtie2/package.py | 24 |
2 files changed, 40 insertions, 0 deletions
diff --git a/var/spack/packages/bowtie2/bowtie2-2.5.patch b/var/spack/packages/bowtie2/bowtie2-2.5.patch new file mode 100644 index 0000000000..290be39c73 --- /dev/null +++ b/var/spack/packages/bowtie2/bowtie2-2.5.patch @@ -0,0 +1,16 @@ +--- Makefile 2015-02-26 10:50:00.000000000 -0800 ++++ Makefile.new 2015-07-29 18:03:59.891357399 -0700 +@@ -22,10 +22,10 @@ + # + + 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/packages/bowtie2/package.py b/var/spack/packages/bowtie2/package.py new file mode 100644 index 0000000000..339aab6598 --- /dev/null +++ b/var/spack/packages/bowtie2/package.py @@ -0,0 +1,24 @@ +from spack import * +from glob import glob +class Bowtie2(Package): + """Description""" + 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") + + patch('bowtie2-2.5.patch',when='@2.2.5', level=0) + + def install(self, spec, prefix): + make() + mkdirp(prefix.bin) + for bow in glob("bowtie2*"): + install(bow, prefix.bin) + # install('bowtie2',prefix.bin) + # install('bowtie2-align-l',prefix.bin) + # install('bowtie2-align-s',prefix.bin) + # install('bowtie2-build',prefix.bin) + # install('bowtie2-build-l',prefix.bin) + # install('bowtie2-build-s',prefix.bin) + # install('bowtie2-inspect',prefix.bin) + # install('bowtie2-inspect-l',prefix.bin) + # install('bowtie2-inspect-s',prefix.bin) + |