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Released as 20171022 ('Catalonia')

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Ole Tange 2017-10-23 09:08:28 +02:00
parent 746b4304a6
commit 823645285f
11 changed files with 66 additions and 37 deletions
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28
NEWS
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@ -1,14 +1,40 @@
20171022
* Initial support for XDG Base Directory $XDG_* environment variables.
* Validating half a million TIFF files. Part
Two
https://www.dpoc.ac.uk/2017/08/17/validating-half-a-million-tiff-files-part-two/
* Turing data science class: Cluster computing
https://www.turing.ac.uk/events/masterclass-cluster-computing/
* Butlin:Unix for Bioinformatics - advanced tutorial
https://openwetware.org/wiki/Butlin:Unix_for_Bioinformatics_-_advanced_tutorial
* พยายามใช้ CPU ให้ครบทุก CORE
https://veer66.wordpress.com/2017/09/02/use-multi-core/
* Examples on using GNU Parallel
https://gist.github.com/drmalex07/de8ff1379a560f6d84a0d863e60ae378
* Bug fixes and man page updates.
20170922 20170922
* Use '--limit myprog' to make a dynamic job limit. Just return 0 to * Use '--limit myprog' to make a dynamic job limit. Just return 0 to
spawn another job, 1 to not spawn another job, and 2 to kill the spawn another job, 1 to not spawn another job, and 2 to kill the
youngest job. youngest job.
* PARALLEL_RSYNC_OPTS and --rsync-opts sets the options for rsync (Default: -rlDzR). * PARALLEL_RSYNC_OPTS and --rsync-opts sets the options for rsync
(Default: -rlDzR).
* Download all of humble bundle books in parallel * Download all of humble bundle books in parallel
https://til.hashrocket.com/posts/ggt1jaes4y-download-all-of-humble-bundle-books-in-parallel https://til.hashrocket.com/posts/ggt1jaes4y-download-all-of-humble-bundle-books-in-parallel
* Bug fixes and man page updates.
20170822 20170822

12
README
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@ -44,9 +44,9 @@ document.
Full installation of GNU Parallel is as simple as: Full installation of GNU Parallel is as simple as:
wget http://ftpmirror.gnu.org/parallel/parallel-20170922.tar.bz2 wget http://ftpmirror.gnu.org/parallel/parallel-20171022.tar.bz2
bzip2 -dc parallel-20170922.tar.bz2 | tar xvf - bzip2 -dc parallel-20171022.tar.bz2 | tar xvf -
cd parallel-20170922 cd parallel-20171022
./configure && make && sudo make install ./configure && make && sudo make install
@ -55,9 +55,9 @@ Full installation of GNU Parallel is as simple as:
If you are not root you can add ~/bin to your path and install in If you are not root you can add ~/bin to your path and install in
~/bin and ~/share: ~/bin and ~/share:
wget http://ftpmirror.gnu.org/parallel/parallel-20170922.tar.bz2 wget http://ftpmirror.gnu.org/parallel/parallel-20171022.tar.bz2
bzip2 -dc parallel-20170922.tar.bz2 | tar xvf - bzip2 -dc parallel-20171022.tar.bz2 | tar xvf -
cd parallel-20170922 cd parallel-20171022
./configure --prefix=$HOME && make && make install ./configure --prefix=$HOME && make && make install
Or if your system lacks 'make' you can simply copy src/parallel Or if your system lacks 'make' you can simply copy src/parallel

20
configure vendored
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@ -1,6 +1,6 @@
#! /bin/sh #! /bin/sh
# Guess values for system-dependent variables and create Makefiles. # Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for parallel 20170922. # Generated by GNU Autoconf 2.69 for parallel 20171022.
# #
# Report bugs to <bug-parallel@gnu.org>. # Report bugs to <bug-parallel@gnu.org>.
# #
@ -579,8 +579,8 @@ MAKEFLAGS=
# Identity of this package. # Identity of this package.
PACKAGE_NAME='parallel' PACKAGE_NAME='parallel'
PACKAGE_TARNAME='parallel' PACKAGE_TARNAME='parallel'
PACKAGE_VERSION='20170922' PACKAGE_VERSION='20171022'
PACKAGE_STRING='parallel 20170922' PACKAGE_STRING='parallel 20171022'
PACKAGE_BUGREPORT='bug-parallel@gnu.org' PACKAGE_BUGREPORT='bug-parallel@gnu.org'
PACKAGE_URL='' PACKAGE_URL=''
@ -1214,7 +1214,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing. # Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh. # This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF cat <<_ACEOF
\`configure' configures parallel 20170922 to adapt to many kinds of systems. \`configure' configures parallel 20171022 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]... Usage: $0 [OPTION]... [VAR=VALUE]...
@ -1281,7 +1281,7 @@ fi
if test -n "$ac_init_help"; then if test -n "$ac_init_help"; then
case $ac_init_help in case $ac_init_help in
short | recursive ) echo "Configuration of parallel 20170922:";; short | recursive ) echo "Configuration of parallel 20171022:";;
esac esac
cat <<\_ACEOF cat <<\_ACEOF
@ -1357,7 +1357,7 @@ fi
test -n "$ac_init_help" && exit $ac_status test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then if $ac_init_version; then
cat <<\_ACEOF cat <<\_ACEOF
parallel configure 20170922 parallel configure 20171022
generated by GNU Autoconf 2.69 generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc. Copyright (C) 2012 Free Software Foundation, Inc.
@ -1374,7 +1374,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake. running configure, to aid debugging if configure makes a mistake.
It was created by parallel $as_me 20170922, which was It was created by parallel $as_me 20171022, which was
generated by GNU Autoconf 2.69. Invocation command line was generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@ $ $0 $@
@ -2237,7 +2237,7 @@ fi
# Define the identity of the package. # Define the identity of the package.
PACKAGE='parallel' PACKAGE='parallel'
VERSION='20170922' VERSION='20171022'
cat >>confdefs.h <<_ACEOF cat >>confdefs.h <<_ACEOF
@ -2880,7 +2880,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their # report actual input values of CONFIG_FILES etc. instead of their
# values after options handling. # values after options handling.
ac_log=" ac_log="
This file was extended by parallel $as_me 20170922, which was This file was extended by parallel $as_me 20171022, which was
generated by GNU Autoconf 2.69. Invocation command line was generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES CONFIG_FILES = $CONFIG_FILES
@ -2942,7 +2942,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\ ac_cs_version="\\
parallel config.status 20170922 parallel config.status 20171022
configured by $0, generated by GNU Autoconf 2.69, configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\" with options \\"\$ac_cs_config\\"

2
configure.ac
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@ -1,4 +1,4 @@
AC_INIT([parallel], [20170922], [bug-parallel@gnu.org]) AC_INIT([parallel], [20171022], [bug-parallel@gnu.org])
AM_INIT_AUTOMAKE([-Wall -Werror foreign]) AM_INIT_AUTOMAKE([-Wall -Werror foreign])
AC_CONFIG_HEADERS([config.h]) AC_CONFIG_HEADERS([config.h])
AC_CONFIG_FILES([ AC_CONFIG_FILES([

21
doc/release_new_version
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@ -199,27 +199,30 @@ to:parallel@gnu.org, bug-parallel@gnu.org
stable-bcc: Jesse Alama <jessealama@fastmail.fm> stable-bcc: Jesse Alama <jessealama@fastmail.fm>
Subject: GNU Parallel 20171022 ('Peter Madsen/Catalonia/Las Vegas') released <<[stable]>> Subject: GNU Parallel 20171022 ('Catalonia') released <<[stable]>>
GNU Parallel 20171022 ('Peter Madsen') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/ GNU Parallel 20171022 ('Catalonia') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
<<No new functionality was introduced so this is a good candidate for a stable release.>> <<No new functionality was introduced so this is a good candidate for a stable release.>>
Haiku of the month: Haiku of the month:
<<>> Cores should never sit
--ole-tange idle - you have work to do!
Use GNU Parallel.
-- Ole Tange
New in this release: New in this release:
* * Validating half a million TIFF files. Part Two. https://www.dpoc.ac.uk/2017/08/17/validating-half-a-million-tiff-files-part-two/
https://www.turing.ac.uk/events/masterclass-cluster-computing/
https://openwetware.org/wiki/Butlin:Unix_for_Bioinformatics_-_advanced_tutorial * Turing data science class: Cluster computing https://www.turing.ac.uk/events/masterclass-cluster-computing/
https://veer66.wordpress.com/2017/09/02/use-multi-core/ * Butlin:Unix for Bioinformatics - advanced tutorial https://openwetware.org/wiki/Butlin:Unix_for_Bioinformatics_-_advanced_tutorial
https://gist.github.com/drmalex07/de8ff1379a560f6d84a0d863e60ae378 * พยายามใช้ CPU ให้ครบทุก CORE https://veer66.wordpress.com/2017/09/02/use-multi-core/
* Examples on using GNU Parallel https://gist.github.com/drmalex07/de8ff1379a560f6d84a0d863e60ae378
<<Citation not OK: BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing https://www.nature.com/articles/s41598-017-01703-6>> <<Citation not OK: BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing https://www.nature.com/articles/s41598-017-01703-6>>

10
packager/obs/home:tange/parallel/.osc/_files
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@ -1,6 +1,6 @@
<directory name="parallel" rev="209" srcmd5="8fab105254f47a893b92e8e198387499" vrev="1"> <directory name="parallel" rev="211" srcmd5="58244bb8926ba4034e5d6b7412f2e88d" vrev="2">
<entry md5="c4d3446284a6268bc1a0d342e5f42cde" mtime="1506035470" name="parallel-20170922.tar.bz2" size="1633997" /> <entry md5="ba6e92a95f4bf45af1f450b727581ded" mtime="1508657698" name="parallel-20171022.tar.bz2" size="1665461" />
<entry md5="9c8b18adabc23f0d76a25b46248daee4" mtime="1506035470" name="parallel.spec" size="4482" /> <entry md5="d4abff90624453b9434ebfb09be7e90c" mtime="1508657699" name="parallel.spec" size="4482" />
<entry md5="bf74d68c873b1d21c143a002b341b5b0" mtime="1506035471" name="parallel_20170922.dsc" size="556" /> <entry md5="40ca59a0bad881333ac2d3bdb2e6318a" mtime="1508657699" name="parallel_20171022.dsc" size="556" />
<entry md5="3e1a471c8f5ed9b11a1ac360b483b307" mtime="1506035471" name="parallel_20170922.tar.gz" size="1839209" /> <entry md5="59c4cf7d017efd0841f7b49c89e6a3bf" mtime="1508657703" name="parallel_20171022.tar.gz" size="1833707" />
</directory> </directory>

2
packager/obs/home:tange/parallel/.osc/parallel.spec
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@ -1,6 +1,6 @@
Summary: Shell tool for executing jobs in parallel Summary: Shell tool for executing jobs in parallel
Name: parallel Name: parallel
Version: 20170922 Version: 20171022
Release: 1.2 Release: 1.2
License: GPL License: GPL
Group: Productivity/File utilities Group: Productivity/File utilities

2
packager/obs/home:tange/parallel/parallel.spec
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@ -1,6 +1,6 @@
Summary: Shell tool for executing jobs in parallel Summary: Shell tool for executing jobs in parallel
Name: parallel Name: parallel
Version: 20170922 Version: 20171022
Release: 1.2 Release: 1.2
License: GPL License: GPL
Group: Productivity/File utilities Group: Productivity/File utilities

2
src/niceload
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@ -24,7 +24,7 @@
use strict; use strict;
use Getopt::Long; use Getopt::Long;
$Global::progname="niceload"; $Global::progname="niceload";
$Global::version = 20170923; $Global::version = 20171022;
Getopt::Long::Configure("bundling","require_order"); Getopt::Long::Configure("bundling","require_order");
get_options_from_array(\@ARGV) || die_usage(); get_options_from_array(\@ARGV) || die_usage();
if($opt::version) { if($opt::version) {

2
src/parallel
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@ -1381,7 +1381,7 @@ sub check_invalid_option_combinations {
sub init_globals { sub init_globals {
# Defaults: # Defaults:
$Global::version = 20170923; $Global::version = 20171022;
$Global::progname = 'parallel'; $Global::progname = 'parallel';
$Global::infinity = 2**31; $Global::infinity = 2**31;
$Global::debug = 0; $Global::debug = 0;

2
src/sql
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@ -576,7 +576,7 @@ $Global::Initfile && unlink $Global::Initfile;
exit ($err); exit ($err);
sub parse_options { sub parse_options {
$Global::version = 20170923; $Global::version = 20171022;
$Global::progname = 'sql'; $Global::progname = 'sql';
# This must be done first as this may exec myself # This must be done first as this may exec myself