[med-svn] [Git][med-team/jellyfish][master] 9 commits: Restore jellyfish-examples, needed for the autopkgtest
Michael R. Crusoe
gitlab at salsa.debian.org
Fri Sep 27 15:06:00 BST 2019
Michael R. Crusoe pushed to branch master at Debian Med / jellyfish
Commits:
cbdb9671 by Michael R. Crusoe at 2019-09-27T13:13:29Z
Restore jellyfish-examples, needed for the autopkgtest
- - - - -
68500c9e by Michael R. Crusoe at 2019-09-27T13:18:08Z
try big test
- - - - -
73025b0e by Michael R. Crusoe at 2019-09-27T13:36:02Z
Test needs bash
- - - - -
e6f6c20e by Michael R. Crusoe at 2019-09-27T13:36:29Z
big test fixup
- - - - -
a3418c6f by Michael R. Crusoe at 2019-09-27T13:36:37Z
enable htslib
- - - - -
0c3e8b5c by Michael R. Crusoe at 2019-09-27T13:37:41Z
bash fixup
- - - - -
5aef2763 by Michael R. Crusoe at 2019-09-27T13:57:55Z
htslib fixup
- - - - -
b525ed1c by Michael R. Crusoe at 2019-09-27T14:02:16Z
add two more tests to autopkgtests
- - - - -
f9bd3a80 by Michael R. Crusoe at 2019-09-27T14:05:27Z
update changelog
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/jellyfish-examples.examples
- debian/patches/series
- + debian/patches/test_needs_bash
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+jellyfish (2.3.0-2) UNRELEASED; urgency=medium
+
+ * Restore jellyfish-examples, needed for the autopkgtest (Closes: #941262)
+ * Enable an additional two test categories in the autopkgtests
+ * Enabled htslib, to read SAM/BAM/CRAM files
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Fri, 27 Sep 2019 15:00:00 +0200
+
jellyfish (2.3.0-1) unstable; urgency=medium
* Team upload
=====================================
debian/control
=====================================
@@ -16,7 +16,10 @@ Build-Depends: debhelper-compat (= 12),
python3-all-dev,
dh-python,
perl,
- chrpath
+ chrpath,
+ libhts-dev,
+ dos2unix,
+ samtools
Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/jellyfish
Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git
@@ -137,24 +140,24 @@ Description: count k-mers in DNA sequences (Perl bindings of jellyfish)
.
This package contains the Perl bindings of jellyfish.
-#Package: jellyfish-examples
-#Architecture: any
-#Depends: jellyfish,
-# ${shlibs:Depends},
-# ${misc:Depends}
-#Description: count k-mers in DNA sequences (examples for testing)
-# JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
-# DNA. A k-mer is a substring of length k, and counting the occurrences
-# of all such substrings is a central step in many analyses of DNA
-# sequence. JELLYFISH can count k-mers using an order of magnitude less
-# memory and an order of magnitude faster than other k-mer counting
-# packages by using an efficient encoding of a hash table and by
-# exploiting the "compare-and-swap" CPU instruction to increase
-# parallelism.
-# .
-# JELLYFISH is a command-line program that reads FASTA and multi-FASTA
-# files containing DNA sequences. It outputs its k-mer counts in an
-# binary format, which can be translated into a human-readable text
-# format using the "jellyfish dump" command.
-# .
-# This package contains examples to test the package
+Package: jellyfish-examples
+Architecture: any
+Depends: jellyfish,
+ ${shlibs:Depends},
+ ${misc:Depends}
+Description: count k-mers in DNA sequences (examples for testing)
+ JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
+ DNA. A k-mer is a substring of length k, and counting the occurrences
+ of all such substrings is a central step in many analyses of DNA
+ sequence. JELLYFISH can count k-mers using an order of magnitude less
+ memory and an order of magnitude faster than other k-mer counting
+ packages by using an efficient encoding of a hash table and by
+ exploiting the "compare-and-swap" CPU instruction to increase
+ parallelism.
+ .
+ JELLYFISH is a command-line program that reads FASTA and multi-FASTA
+ files containing DNA sequences. It outputs its k-mer counts in an
+ binary format, which can be translated into a human-readable text
+ format using the "jellyfish dump" command.
+ .
+ This package contains examples to test the package
=====================================
debian/copyright
=====================================
@@ -5,7 +5,7 @@ Source: http://www.cbcb.umd.edu/software/jellyfish/
Files: *
Copyright: Copyright 2011-2014 Guillaume Marçais1, Carl Kingsford
-License: GPL-3+
+License: GPL-3+ or BSD-3-clause
Files: jellyfish/randomc.h
Copyright: Copyright 2008 Agner Fog
@@ -71,6 +71,8 @@ Files: unit_tests/gtest/src/gtest_main.cc
unit_tests/gtest/src/gtest-all.cc
unit_tests/gtest/gtest.h
Copyright: 2005-2008 Google Inc.
+License: BSD-3-clause
+
License: BSD-3-clause
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
=====================================
debian/jellyfish-examples.examples
=====================================
@@ -1,2 +1,3 @@
tests/*.sh*
unit_tests/unit_tests.sh
+compat.sh
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ portability.patch
#Apparently fixed upstream
#fix_catch.patch
fix_replacement_of_-L_option.patch
+test_needs_bash
=====================================
debian/patches/test_needs_bash
=====================================
@@ -0,0 +1,12 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: small_mers needs bash
+
+Due to process substitution. Thanks to https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/jellyfish.html for highlighting this.
+--- jellyfish.orig/tests/small_mers.sh
++++ jellyfish/tests/small_mers.sh
+@@ -1,4 +1,4 @@
+-#! /bin/sh
++#! /bin/bash
+
+ cd tests
+ . ../compat.sh
=====================================
debian/rules
=====================================
@@ -10,6 +10,7 @@ export DH_OPTIONS
export PKG_CONFIG_LIBDIR=${CURDIR}
export PKG_CONFIG_ALLOW_SYSTEM_LIBS=true
export PKG_CONFIG_SYSROOT_DIR=${CURDIR}/debian/tmp/
+export PKG_CONFIG_PATH=$(shell pkg-config --variable pc_path pkg-config)
export PERL_MM_OPT=INSTALLDIRS=vendor
export PYBUILD_BUILD_ARGS=build_ext --rpath "${CURDIR}/debian/tmp/usr/lib/${DEB_HOST_MULTIARCH}"
@@ -52,7 +53,7 @@ override_dh_install:
sed -i "/dependency_libs/ s/'.*'/''/" ./debian/libjellyfish-2.0-dev/usr/lib/${DEB_HOST_MULTIARCH}/*.la
override_dh_auto_configure:
- dh_auto_configure -- --enable-swig --enable-perl-binding # --enable-python-binding
+ dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib # --enable-python-binding
override_dh_clean:
dh_clean
@@ -86,4 +87,5 @@ override_dh_auto_build:
# if you have a *really* large machine you can try to activate this test by
# uncommenting the following.
#override_dh_auto_test:
-# BIG=1 dh_auto_test
+# BIG=1 dh_auto_test
+# false
=====================================
debian/tests/run-unit-test
=====================================
@@ -8,7 +8,8 @@ fi
cd $ADTTMP
mkdir tests
cp -a /usr/share/doc/jellyfish-examples/examples/* tests
-sed -i "s#DIR=../bin#DIR=/usr/lib/${pkg}/bin#" tests/compat.sh
+mv tests/compat.sh ./
+sed -i "s#DIR=../bin#DIR=/usr/lib/${pkg}/bin#" compat.sh
tests/generate_sequence.sh
sh tests/parallel_hashing.sh
sh tests/merge.sh
@@ -33,4 +34,6 @@ sh tests/multi_file.sh
#############################################################################################
sh tests/bloom_counter.sh
sh tests/large_key.sh
+sh tests/sam.sh
+bash tests/small_mers.sh
/usr/lib/jellyfish/bin/test_all
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/compare/ad75843dcb4ba66e7e9be5d34309a9894d96fd5b...f9bd3a805462e729a28442847950f29a0e76419c
--
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/compare/ad75843dcb4ba66e7e9be5d34309a9894d96fd5b...f9bd3a805462e729a28442847950f29a0e76419c
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