[med-svn] [Git][med-team/jellyfish][master] 4 commits: Some nitty-gritty
Steffen Möller
gitlab at salsa.debian.org
Sat Sep 21 13:59:51 BST 2019
Steffen Möller pushed to branch master at Debian Med / jellyfish
Commits:
1670579b by Steffen Moeller at 2019-09-21T12:33:09Z
Some nitty-gritty
- - - - -
7584c14c by Steffen Moeller at 2019-09-21T12:34:50Z
Adjusted patches
- - - - -
11a0a62c by Steffen Moeller at 2019-09-21T12:36:54Z
No dependency on python2, please!
- - - - -
ad75843d by Steffen Moeller at 2019-09-21T12:52:42Z
Some cleanups for 2.3 to build
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/patches/fix_replacement_of_-L_option.patch
- debian/patches/manpage_whatis_entry.patch
- debian/patches/portability.patch
- debian/patches/reproducible.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,18 @@
-jellyfish (2.3.0-1) UNRELEASED; urgency=medium
+jellyfish (2.3.0-1) unstable; urgency=medium
+ * Team upload
+
+ [Andreas Tille]
* Install config.h which is needed by sailfish package
* New upstream version
* debhelper-compat 12
+ [Steffen Moeller]
+ * Standards-Version: 4.4.0
+ * d/u/metadata: Added ref to conda
+ * deactivated installation of examples, which have changed considerably
+ * removed build-dependency on python2 (prime reason to upload)
+
-- Andreas Tille <tille at debian.org> Thu, 01 Aug 2019 13:37:07 +0200
jellyfish (2.2.10-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -14,11 +14,10 @@ Build-Depends: debhelper-compat (= 12),
procps,
swig,
python3-all-dev,
- python-all-dev,
dh-python,
perl,
chrpath
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/jellyfish
Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git
Homepage: http://www.cbcb.umd.edu/software/jellyfish/
@@ -138,24 +137,24 @@ 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/patches/fix_replacement_of_-L_option.patch
=====================================
@@ -3,8 +3,10 @@ Bug-Debian: https://bugs.debian.org/907819
Author: Andreas Tille <tille at debian.org>
Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
---- a/examples/count_in_file/Makefile
-+++ b/examples/count_in_file/Makefile
+Index: jellyfish/examples/count_in_file/Makefile
+===================================================================
+--- jellyfish.orig/examples/count_in_file/Makefile
++++ jellyfish/examples/count_in_file/Makefile
@@ -1,6 +1,6 @@
CC = g++
CXXFLAGS = $(shell pkg-config --cflags jellyfish-2.0) -std=c++0x -Wall -O3
@@ -13,8 +15,10 @@ Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
LDLIBS = $(shell pkg-config --libs jellyfish-2.0)
all: count_in_file
---- a/examples/jf_count_dump/Makefile
-+++ b/examples/jf_count_dump/Makefile
+Index: jellyfish/examples/jf_count_dump/Makefile
+===================================================================
+--- jellyfish.orig/examples/jf_count_dump/Makefile
++++ jellyfish/examples/jf_count_dump/Makefile
@@ -1,6 +1,6 @@
CC = g++
CXXFLAGS = $(shell pkg-config --cflags jellyfish-2.0) -std=c++0x -Wall -O3
@@ -23,8 +27,10 @@ Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
LDLIBS = $(shell pkg-config --libs jellyfish-2.0)
all: jf_count_dump
---- a/examples/query_per_sequence/Makefile
-+++ b/examples/query_per_sequence/Makefile
+Index: jellyfish/examples/query_per_sequence/Makefile
+===================================================================
+--- jellyfish.orig/examples/query_per_sequence/Makefile
++++ jellyfish/examples/query_per_sequence/Makefile
@@ -1,6 +1,6 @@
CC = g++
CXXFLAGS = $(shell pkg-config --cflags jellyfish-2.0) -std=c++0x -Wall -O3
@@ -33,9 +39,11 @@ Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
LDLIBS = $(shell pkg-config --libs jellyfish-2.0)
all: query_per_sequence
---- a/swig/Tuprules.tup
-+++ b/swig/Tuprules.tup
-@@ -80,7 +80,7 @@ endif
+Index: jellyfish/swig/Tuprules.tup
+===================================================================
+--- jellyfish.orig/swig/Tuprules.tup
++++ jellyfish/swig/Tuprules.tup
+@@ -86,7 +86,7 @@ endif
ifdef JELLYFISH_RPATH
JELLYFISH_RPATH = @(JELLYFISH_RPATH)
else
@@ -44,8 +52,10 @@ Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
endif
ifdef RUBY_CFLAGS
---- a/swig/perl5/Makefile.PL
-+++ b/swig/perl5/Makefile.PL
+Index: jellyfish/swig/perl5/Makefile.PL
+===================================================================
+--- jellyfish.orig/swig/perl5/Makefile.PL
++++ jellyfish/swig/perl5/Makefile.PL
@@ -19,7 +19,7 @@ my $pkg = "jellyfish-2.0";
my $jf_cflags = pkgconfig("--cflags $pkg");
my $jf_libs = pkgconfig("--libs $pkg");
@@ -55,9 +65,11 @@ Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
print("$jf_cflags\n$jf_libs\n$jf_rpath\n");
---- a/swig/ruby/extconf.rb
-+++ b/swig/ruby/extconf.rb
-@@ -13,7 +13,7 @@ end
+Index: jellyfish/swig/ruby/extconf.rb
+===================================================================
+--- jellyfish.orig/swig/ruby/extconf.rb
++++ jellyfish/swig/ruby/extconf.rb
+@@ -19,7 +19,7 @@ end
$defs << pkgconfig("--cflags jellyfish-2.0") << '-std=c++0x'
libs = [pkgconfig("--libs jellyfish-2.0"),
@@ -66,9 +78,11 @@ Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
if Array === $libs
$libs += libs
---- a/swig/python/setup.py
-+++ b/swig/python/setup.py
-@@ -17,7 +17,7 @@ def pkgconfig(s):
+Index: jellyfish/swig/python/setup.py
+===================================================================
+--- jellyfish.orig/swig/python/setup.py
++++ jellyfish/swig/python/setup.py
+@@ -23,7 +23,7 @@ def pkgconfig(s):
jf_libs = [re.sub(r'-l', '', x) for x in pkgconfig("--libs-only-l jellyfish-2.0")]
jf_include = [re.sub(r'-I', '', x) for x in pkgconfig("--cflags-only-I jellyfish-2.0")]
jf_cflags = pkgconfig("--cflags-only-other jellyfish-2.0")
=====================================
debian/patches/manpage_whatis_entry.patch
=====================================
@@ -2,8 +2,10 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Mon, 28 Aug 2017 14:10:27 +0200
Description: Fix whatis entry in manpage (also fix some spelling issues)
---- a/doc/jellyfish.man
-+++ b/doc/jellyfish.man
+Index: jellyfish/doc/jellyfish.man
+===================================================================
+--- jellyfish.orig/doc/jellyfish.man
++++ jellyfish/doc/jellyfish.man
@@ -12,11 +12,8 @@
..
.TH "JELLYFISH" "1" "2010/10/1" "k\-mer counter " "k\-mer counter "
=====================================
debian/patches/portability.patch
=====================================
@@ -4,9 +4,11 @@ Bug-Debian: https://bugs.debian.org/871697
Description: Replace asm statements by C code to increase portability
Note: Does not work as described - needs verification
+Index: jellyfish/include/jellyfish/rectangular_binary_matrix.hpp
+===================================================================
--- jellyfish.orig/include/jellyfish/rectangular_binary_matrix.hpp
+++ jellyfish/include/jellyfish/rectangular_binary_matrix.hpp
-@@ -302,13 +302,20 @@
+@@ -296,13 +296,20 @@ namespace jellyfish {
// #pragma GCC diagnostic pop
// i is the lower 2 bits of x, and an index into the smear array. Compute res ^= smear[i] & p[j].
@@ -29,7 +31,7 @@ Note: Does not work as described - needs verification
uint64_t i, j = 0, x = 0;
for(unsigned int w = 0; w < nb_words(); ++w) {
-@@ -320,16 +327,16 @@
+@@ -314,16 +321,16 @@ namespace jellyfish {
}
for( ; j > 7; j -= 8, p -= 8) {
i = (x & (uint64_t)0x3) << 4;
@@ -50,7 +52,7 @@ Note: Does not work as described - needs verification
x >>= 2;
}
}
-@@ -339,18 +346,19 @@
+@@ -333,18 +340,19 @@ namespace jellyfish {
switch(j) {
case 6:
i = (x & (uint64_t)0x3) << 4;
@@ -73,7 +75,7 @@ Note: Does not work as described - needs verification
uint64_t res1, res2;
asm("movd %[acc], %[res1]\n\t"
"psrldq $8, %[acc]\n\t"
-@@ -358,6 +366,10 @@
+@@ -352,6 +360,10 @@ namespace jellyfish {
: [res1]"=r"(res1), [res2]"=r"(res2)
: [acc]"x"(acc));
return res1 ^ res2;
=====================================
debian/patches/reproducible.patch
=====================================
@@ -4,9 +4,11 @@ Bug-Debian: https://bugs.debian.org/863015
Description: Enable reproducible build by avoiding the current
date with time zone in json output
+Index: jellyfish/include/jellyfish/generic_file_header.hpp
+===================================================================
--- jellyfish.orig/include/jellyfish/generic_file_header.hpp
+++ jellyfish/include/jellyfish/generic_file_header.hpp
-@@ -180,6 +180,8 @@
+@@ -172,6 +172,8 @@ public:
protected:
std::string get_hostname() const {
@@ -15,7 +17,7 @@ Description: Enable reproducible build by avoiding the current
struct utsname buf;
if(uname(&buf) == -1)
return "";
-@@ -187,6 +189,8 @@
+@@ -179,6 +181,8 @@ protected:
}
std::string get_pwd() const {
@@ -24,7 +26,7 @@ Description: Enable reproducible build by avoiding the current
#ifdef PATH_MAX
size_t len = PATH_MAX;
#else
-@@ -202,6 +206,16 @@
+@@ -194,6 +198,16 @@ protected:
std::string get_localtime() const {
time_t t = time(0);
std::string res(ctime(&t));
=====================================
debian/patches/series
=====================================
@@ -1,5 +1,6 @@
manpage_whatis_entry.patch
reproducible.patch
portability.patch
-fix_catch.patch
+#Apparently fixed upstream
+#fix_catch.patch
fix_replacement_of_-L_option.patch
=====================================
debian/rules
=====================================
@@ -21,11 +21,11 @@ export DEB_LDFLAGS_MAINT_APPEND = -lpthread
override_dh_auto_install:
dh_auto_install -- install-data
-override_dh_installexamples:
- dh_installexamples
- sed '/SRCDIR=/d' debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/compat.sh*
- sed '/BUILDDIR=/d' debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/compat.sh*
- rm -f debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/swig*
+#override_dh_installexamples:
+# dh_installexamples
+# sed '/SRCDIR=/d' debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/compat.sh*
+# sed '/BUILDDIR=/d' debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/compat.sh*
+# rm -f debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/swig*
override_dh_install:
# dh_install -X*.a -X*.la -Xpkgconfig
@@ -62,6 +62,18 @@ override_dh_clean:
fi
rm -f tests/compat.sh
rm -f swig/python/jellyfish* # swig/python/dna_jellyfish.py
+ rm -f swig/perl5/blib/arch/auto/jellyfish/jellyfish.so
+ rm -f swig/perl5/blib/bin/.exists
+ rm -f swig/perl5/blib/lib/.exists
+ rm -f swig/perl5/blib/lib/auto/jellyfish/.exists
+ rm -f swig/perl5/blib/man1/.exists
+ rm -f swig/perl5/blib/man3/.exists
+ rm -f swig/perl5/blib/script/.exists
+ rm -f swig/perl5/jellyfish.bs
+ rm -f swig/perl5/pm_to_blib
+ rm -rf swig/perl5/MYMETA.json swig/perl5/MYMETA.yml swig/perl5/Makefile swig/perl5/blib/
+
+
override_dh_auto_build:
mkdir -p debian/tmp_save_tests
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/compare/c42a849fda537f45f75e15329c4468d6b9bab072...ad75843dcb4ba66e7e9be5d34309a9894d96fd5b
--
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/compare/c42a849fda537f45f75e15329c4468d6b9bab072...ad75843dcb4ba66e7e9be5d34309a9894d96fd5b
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