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bowtie: new versions and %gcc@8.0.0: fix (#10232)

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* bowtie: new versions and %gcc@8.0.0: fix

Bowtie development shifted from Sourceforge to GitHub.

This commit adds several versions from GitHub, using the archive
tarballs.  Note that the URL for 1.2.2 tarball is actually an '_p1'
tag....

It leaves the old 1.2 release download info in place.

Versions 1.2.0 and newer come from GitHub (I'm unsure if the 1.2 and
1.2.0 are equivalent).

Include a fix that enables %gcc@8.0.0: from:

  https://github.com/BenLangmead/bowtie/issues/87

But, v1.2.2 has trouble with "newer" gcc's, so it only adds v1.2.2 for
%gcc@6.0.0:.

Feel free to tighten this.  I know that:

- 1.2 -> 1.2.2 work with %gcc@5.5.0;
- 1.2 -> 1.2.1.1 work with %gcc@8.2.0; and
- 1.2.2 fails with %gcc@8.2.0

* Tighten to `conflicts('%gcc@8:', when='@1.2.2')`

* Point 1.2.2 and 1.2.2_p1 at the 1.2.2_p1 tarball
This commit is contained in:
George Hartzell 2019-01-07 09:30:59 -08:00 committed by Adam J. Stewart
parent 3b59f70751
commit b984adb386
2 changed files with 49 additions and 2 deletions
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22
var/spack/repos/builtin/packages/bowtie/issue-87.patch Normal file
View File

@ -0,0 +1,22 @@
From 58c6ac97b1938909881877ef83167f5eff0e8ab1 Mon Sep 17 00:00:00 2001
From: Rone Charles <rone_charles@fastmail.com>
Date: Tue, 4 Sep 2018 21:06:39 -0400
Subject: [PATCH] Fix isa return type
---
ebwt.h | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/ebwt.h b/ebwt.h
index fe6300cc..8f886b8d 100644
--- a/ebwt.h
+++ b/ebwt.h
@@ -862,7 +862,7 @@ class Ebwt {
TIndexOffU* ftab() const { return _ftab; }
TIndexOffU* eftab() const { return _eftab; }
TIndexOffU* offs() const { return _offs; }
- uint32_t* isa() const { return _isa; } /* check */
+ TIndexOffU* isa() const { return _isa; } /* check */
TIndexOffU* plen() const { return _plen; }
TIndexOffU* rstarts() const { return _rstarts; }
uint8_t* ebwt() const { return _ebwt; }

29
var/spack/repos/builtin/packages/bowtie/package.py
View File

@ -11,14 +11,39 @@ class Bowtie(MakefilePackage):
for short DNA sequences (reads) from next-gen sequencers."""
homepage = "https://sourceforge.net/projects/bowtie-bio/"
url = "https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.0/bowtie-1.2-source.zip"
url = "https://github.com/BenLangmead/bowtie/archive/v1.2.0.tar.gz"
version('1.2', '6d97f0ea1a65af11d17cc270cfac4af9')
# The bowtie project git tagged and GitHub released a v1.2.2,
# discovered/fixed a bug, git tagged a v1.2.2_p1 and moved the
# 1.2.2 release to use it rather than making a new `1.2.2_p1`
# release.
#
# We point both of the Spack versions at the same tarball so they
# build the binaries that are on the release page as v1.2.2
version('1.2.2_p1', sha256='e1b02b2e77a0d44a3dd411209fa1f44f0c4ee304ef5cc83f098275085740d5a1')
version('1.2.2', sha256='e1b02b2e77a0d44a3dd411209fa1f44f0c4ee304ef5cc83f098275085740d5a1', url="https://github.com/BenLangmead/bowtie/archive/v1.2.2_p1.tar.gz")
version('1.2.1.1', sha256='1b38408b88f61d18d7ff28b2470a8cfeefccb3fc59fd46e4cc62e23874e52c20')
version('1.2.1', sha256='b2a7c8c879cb08f00a82665bee43e1d4861de44a87912c54d168e44c90869728')
version('1.2.0', sha256='dc4e7951b8eca56ce7714c47fd4e84f72badd5312ee9546c912af1963570f894')
# Keeping the old 1.2 version around for reproducibility, it's not
# clearly identical to 1.2.0.
version('1.2', md5='6d97f0ea1a65af11d17cc270cfac4af9', url='https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.0/bowtie-1.2-source.zip')
# Feel free to tighten this. I know that v1.2.2 (aka v1.2.2_p1)
# builds with %gcc@5.5.5 and fails to build with %gcc@8.2.0. I'm
# not sure whether or not it works with other versions in the
# interval.
conflicts('%gcc@8:', when='@1.2.2:')
variant('tbb', default=False, description='Use Intel thread building block')
depends_on('tbb', when='+tbb')
# See: https://github.com/BenLangmead/bowtie/issues/87, a
# different fix is in the FreeBSD ports/package tree
# https://svnweb.freebsd.org/ports?view=revision&revision=483954
patch('issue-87.patch', when='%gcc@8.0.0:')
def edit(self, spec, prefix):
makefile = FileFilter('Makefile')
makefile.filter('CC = .*', 'CC = ' + env['CC'])