From 118948cb0abd78cfca59799a48454a4cd9525a78 Mon Sep 17 00:00:00 2001
From: Jen Herting <jen@herting.cc>
Date: Tue, 4 Aug 2020 17:52:51 -0400
Subject: [PATCH] [bowtie] added version 1.3.0. Patch fixed for new version
(#17744)
---
.../packages/bowtie/fix_narrowing_err_1.3.0.patch | 11 +++++++++++
var/spack/repos/builtin/packages/bowtie/package.py | 4 +++-
2 files changed, 14 insertions(+), 1 deletion(-)
create mode 100644 var/spack/repos/builtin/packages/bowtie/fix_narrowing_err_1.3.0.patch
diff --git a/var/spack/repos/builtin/packages/bowtie/fix_narrowing_err_1.3.0.patch b/var/spack/repos/builtin/packages/bowtie/fix_narrowing_err_1.3.0.patch
new file mode 100644
index 0000000000..0da7fe0de3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bowtie/fix_narrowing_err_1.3.0.patch
@@ -0,0 +1,11 @@
+--- a/alphabet.cpp 2020-07-28 15:02:56.137635525 -0400
++++ b/alphabet.cpp 2020-07-28 15:05:32.385589360 -0400
+@@ -274,7 +274,7 @@
+ const char *iupacs = "!ACMGRSVTWYHKDBN!acmgrsvtwyhkdbn";
+
+ signed char mask2iupac[16] = {
+- -1,
++ static_cast<char>(-1),
+ 'A', // 0001
+ 'C', // 0010
+ 'M', // 0011
diff --git a/var/spack/repos/builtin/packages/bowtie/package.py b/var/spack/repos/builtin/packages/bowtie/package.py
index ce7f8b03a0..737ae8c893 100644
--- a/var/spack/repos/builtin/packages/bowtie/package.py
+++ b/var/spack/repos/builtin/packages/bowtie/package.py
@@ -13,6 +13,7 @@ class Bowtie(MakefilePackage):
homepage = "https://sourceforge.net/projects/bowtie-bio/"
url = "https://github.com/BenLangmead/bowtie/archive/v1.2.0.tar.gz"
+ version('1.3.0', sha256='d7c2d982a67884909f284a0ff150b56b20127cd7a1ced461c3c4c03e6a6374c5')
version('1.2.3', sha256='86402114caeacbb3a3030509cb59f0b7e96361c7b3ee2dd50e2cd68200898823')
# 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
@@ -50,7 +51,8 @@ class Bowtie(MakefilePackage):
patch('for_aarch64.patch', when='target=aarch64:')
# measures for narrowing error
- patch('fix_narrowing_err.patch')
+ patch('fix_narrowing_err.patch', when='@:1.2.3')
+ patch('fix_narrowing_err_1.3.0.patch', when='@1.3.0:')
def edit(self, spec, prefix):
makefile = FileFilter('Makefile')
--
GitLab