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[bowtie] added version 1.3.0. Patch fixed for new version (#17744)

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Jen Herting 2020-08-04 17:52:51 -04:00 committed by GitHub
parent f9ee76a817
commit 118948cb0a
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2 changed files with 14 additions and 1 deletions
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11
var/spack/repos/builtin/packages/bowtie/fix_narrowing_err_1.3.0.patch Normal file
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@ -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

4
var/spack/repos/builtin/packages/bowtie/package.py
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@ -13,6 +13,7 @@ class Bowtie(MakefilePackage):
homepage = "https://sourceforge.net/projects/bowtie-bio/" homepage = "https://sourceforge.net/projects/bowtie-bio/"
url = "https://github.com/BenLangmead/bowtie/archive/v1.2.0.tar.gz" url = "https://github.com/BenLangmead/bowtie/archive/v1.2.0.tar.gz"
version('1.3.0', sha256='d7c2d982a67884909f284a0ff150b56b20127cd7a1ced461c3c4c03e6a6374c5')
version('1.2.3', sha256='86402114caeacbb3a3030509cb59f0b7e96361c7b3ee2dd50e2cd68200898823') version('1.2.3', sha256='86402114caeacbb3a3030509cb59f0b7e96361c7b3ee2dd50e2cd68200898823')
# The bowtie project git tagged and GitHub released a v1.2.2, # 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 # 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:') patch('for_aarch64.patch', when='target=aarch64:')
# measures for narrowing error # 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): def edit(self, spec, prefix):
makefile = FileFilter('Makefile') makefile = FileFilter('Makefile')