Michael R. Crusoe pushed to branch master at Debian Med / jellyfish
Commits: 8cac4aa0 by Michael R. Crusoe at 2018-03-12T05:22:40-07:00 Add the missing small_mers.sh file, courtesy upstream. - - - - - 3952220c by Michael R. Crusoe at 2018-03-12T05:31:14-07:00 add fix from upstream for arm/ppc - - - - - 6 changed files: - debian/changelog - debian/copyright - + debian/patches/6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch - + debian/patches/add_small_mers.sh.patch - debian/patches/series - − debian/patches/skip_small_mers.sh Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +jellyfish (2.2.8-2) unstable; urgency=medium + + * Add the missing small_mers.sh file, courtesy upstream. + * Fix arm/powerpc build, patch courtesy upstream (Closes: #890137) + + -- Michael R. Crusoe <[email protected]> Mon, 12 Mar 2018 05:31:00 -0700 + jellyfish (2.2.8-1) unstable; urgency=medium * New upstream version ===================================== debian/copyright ===================================== --- a/debian/copyright +++ b/debian/copyright @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: JELLYFISH Upstream-Contact: Guillaume Marçais <[email protected]> Source: http://www.cbcb.umd.edu/software/jellyfish/ @@ -7,7 +7,6 @@ Files: * Copyright: Copyright 2011-2014 Guillaume Marçais1, Carl Kingsford License: GPL-3+ - Files: jellyfish/randomc.h Copyright: Copyright 2008 Agner Fog License: GPL ===================================== debian/patches/6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch ===================================== --- /dev/null +++ b/debian/patches/6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch @@ -0,0 +1,22 @@ +From 6dfc57b516249454dc0a708ceb4833623cbf0ffd Mon Sep 17 00:00:00 2001 +From: Guillaume Marcais <[email protected]> +Date: Wed, 14 Feb 2018 07:29:54 -0500 +Subject: [PATCH] Fix testing on arm64. + +--- + jellyfish/fastq2sam.cc | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/jellyfish/fastq2sam.cc b/jellyfish/fastq2sam.cc +index e152ccf..b0b6b0d 100644 +--- a/jellyfish/fastq2sam.cc ++++ b/jellyfish/fastq2sam.cc +@@ -25,7 +25,7 @@ int main(int argc, char* argv[]) { + // os << "@PG\tID:fastq2sam\tPN:fastq2sam\n"; + + std::string name, seq, quals; +- char c = is.get(); ++ int c = is.get(); + while(c == '@') { + std::getline(is, name); + std::getline(is, seq); ===================================== debian/patches/add_small_mers.sh.patch ===================================== --- /dev/null +++ b/debian/patches/add_small_mers.sh.patch @@ -0,0 +1,27 @@ +From 0adb7ea223a6718bad4e82fc9813ae7708b59ee2 Mon Sep 17 00:00:00 2001 +From: Guillaume Marcais <[email protected]> +Date: Mon, 12 Feb 2018 14:32:29 -0500 +Subject: [PATCH] Added missing tests/small_mers.sh file. + +--- + tests/small_mers.sh | 11 +++++++++++ + 1 file changed, 11 insertions(+) + create mode 100644 tests/small_mers.sh + +diff --git a/tests/small_mers.sh b/tests/small_mers.sh +new file mode 100644 +index 0000000..5eb7db0 +--- /dev/null ++++ b/tests/small_mers.sh +@@ -0,0 +1,11 @@ ++#! /bin/sh ++ ++cd tests ++. ./compat.sh ++ ++sort -k2,2 > ${pref}.md5sum <<EOF ++ ++EOF ++ ++$JF count -t $nCPUs -o ${pref}_m10_10M.jf -s 1M -m 7 -C seq10m.fa ++$JF histo ${pref}_m10_10M.jf > ${pref}_m10_10M.histo ===================================== debian/patches/series ===================================== --- a/debian/patches/series +++ b/debian/patches/series @@ -6,4 +6,5 @@ spelling gcc-7.patch reproducible.patch portability.patch -skip_small_mers.sh +add_small_mers.sh.patch +6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch ===================================== debian/patches/skip_small_mers.sh deleted ===================================== --- a/debian/patches/skip_small_mers.sh +++ /dev/null @@ -1,22 +0,0 @@ -Author: Michael R. Crusoe <[email protected]> -Description: Skip missing test file from upstream ---- jellyfish.orig/Makefile.am -+++ jellyfish/Makefile.am -@@ -146,8 +146,7 @@ - TESTS = tests/generate_sequence.sh tests/parallel_hashing.sh \ - tests/merge.sh tests/bloom_filter.sh tests/big.sh \ - tests/subset_hashing.sh tests/multi_file.sh \ -- tests/bloom_counter.sh tests/large_key.sh tests/sam.sh \ -- tests/small_mers.sh -+ tests/bloom_counter.sh tests/large_key.sh tests/sam.sh - - EXTRA_DIST += $(TESTS) - clean-local: clean-local-check -@@ -165,7 +164,6 @@ - tests/large_key.log: tests/generate_sequence.log - tests/quality_filter.log: tests/generate_sequence.log - tests/sam.log: tests/generate_sequence.log --tests/small_mers.log: tests/generate_sequence.log - - # SWIG tests - TESTS += tests/swig_python.sh tests/swig_ruby.sh tests/swig_perl.sh View it on GitLab: https://salsa.debian.org/med-team/jellyfish/compare/c2cdb414c927d03d225db69bacd80490554c75fb...3952220cbaca160a19165bc19ea655ab5f66a6bc --- View it on GitLab: https://salsa.debian.org/med-team/jellyfish/compare/c2cdb414c927d03d225db69bacd80490554c75fb...3952220cbaca160a19165bc19ea655ab5f66a6bc You're receiving this email because of your account on salsa.debian.org.
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