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

* 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

2 files changed, 50 insertions, 3 deletions

diff --git a/var/spack/repos/builtin/packages/bowtie/issue-87.patch b/var/spack/repos/builtin/packages/bowtie/issue-87.patch
new file mode 100644
index 0000000000..de19e42a84
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bowtie/issue-87.patch
@@ -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; }
diff --git a/var/spack/repos/builtin/packages/bowtie/package.py b/var/spack/repos/builtin/packages/bowtie/package.py
index a7f547ce24..021b50c477 100644
--- a/var/spack/repos/builtin/packages/bowtie/package.py
+++ b/var/spack/repos/builtin/packages/bowtie/package.py
@@ -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"
-
-    version('1.2', '6d97f0ea1a65af11d17cc270cfac4af9')
+    url      = "https://github.com/BenLangmead/bowtie/archive/v1.2.0.tar.gz"
+
+    # 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'])