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Released as 20170422 ('Санкт-Петербу́рг')

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Ole Tange 2017-04-22 23:23:24 +02:00
parent 77da672741
commit e49dd0d5d0
11 changed files with 84 additions and 32 deletions
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43
NEWS
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@ -1,3 +1,46 @@
20170422
* --halt supports done in addition to success and fail.
* parset will set variables in parallel in Bash.
* Perl 5.6 on Irix is no longer supported.
* Vote for GNU Parallel's community ads on
http://meta.unix.stackexchange.com/a/4356/2972
http://meta.askubuntu.com/a/16750/22307
http://meta.serverfault.com/a/9040/45704
* GNU Parallel was cited in: Halvade-RNA: Parallel variant calling
from transcriptomic data using MapReduce
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0174575
* GNU Parallel was cited in: StrAuto: automation and parallelization
of STRUCTURE analysis
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1593-0
* GNU Parallel was cited in: Trespassing the Boundaries: Labeling
Temporal Bounds for Object Interactions in Egocentric Video
https://128.84.21.199/pdf/1703.09026.pdf
* GNU Parallel is used in: https://github.com/lucascbeyeler/zmbackup
* Using GNU Parallel
https://wiki.ncsa.illinois.edu/display/ROGER/Using+GNU+Parallel
* Find and xargs and parallel
http://helpful.knobs-dials.com/index.php/Find_and_xargs_and_parallel#Parallel
* Quick Introduction to GNU Parallel
https://github.com/mlangill/microbiome_helper/wiki/Quick-Introduction-to-GNU-Parallel
* Data science at the command line https://www.slideshare.net/sharatsc/data-science-at-the-command-line
* Bedtools笔记 http://www.jianshu.com/p/67b0665490ac
* Bug fixes and man page updates.
20170322 20170322
* --rpl can now take arguments by adding '(regexp)' in the replacement * --rpl can now take arguments by adding '(regexp)' in the replacement

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-20170322.tar.bz2 wget http://ftpmirror.gnu.org/parallel/parallel-20170422.tar.bz2
bzip2 -dc parallel-20170322.tar.bz2 | tar xvf - bzip2 -dc parallel-20170422.tar.bz2 | tar xvf -
cd parallel-20170322 cd parallel-20170422
./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-20170322.tar.bz2 wget http://ftpmirror.gnu.org/parallel/parallel-20170422.tar.bz2
bzip2 -dc parallel-20170322.tar.bz2 | tar xvf - bzip2 -dc parallel-20170422.tar.bz2 | tar xvf -
cd parallel-20170322 cd parallel-20170422
./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 20170322. # Generated by GNU Autoconf 2.69 for parallel 20170422.
# #
# 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='20170322' PACKAGE_VERSION='20170422'
PACKAGE_STRING='parallel 20170322' PACKAGE_STRING='parallel 20170422'
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 20170322 to adapt to many kinds of systems. \`configure' configures parallel 20170422 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 $ac_init_help in
short | recursive ) echo "Configuration of parallel 20170322:";; short | recursive ) echo "Configuration of parallel 20170422:";;
esac esac
cat <<\_ACEOF cat <<\_ACEOF
@ -1357,7 +1357,7 @@ fi
test -n "$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 20170322 parallel configure 20170422
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 20170322, which was It was created by parallel $as_me 20170422, which was
generated by GNU Autoconf 2.69. Invocation command line was generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@ $ $0 $@
@ -2237,7 +2237,7 @@ fi
# Define the identity of the package. # Define the identity of the package.
PACKAGE='parallel' PACKAGE='parallel'
VERSION='20170322' VERSION='20170422'
cat >>confdefs.h <<_ACEOF cat >>confdefs.h <<_ACEOF
@ -2880,7 +2880,7 @@ cat >>$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 20170322, which was This file was extended by parallel $as_me 20170422, 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 20170322 parallel config.status 20170422
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], [20170322], [bug-parallel@gnu.org]) AC_INIT([parallel], [20170422], [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([

5
doc/release_new_version
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@ -109,6 +109,9 @@ http://www.gnu.org/software/parallel/
http://www.gnu.org/software/parallel/man.html http://www.gnu.org/software/parallel/man.html
http://www.gnu.org/software/parallel/sql.html http://www.gnu.org/software/parallel/sql.html
http://www.gnu.org/software/parallel/sem.html http://www.gnu.org/software/parallel/sem.html
http://www.gnu.org/software/parallel/env_parallel.html
http://www.gnu.org/software/parallel/parset.html
http://www.gnu.org/software/parallel/parcat.html
http://www.gnu.org/software/parallel/niceload.html http://www.gnu.org/software/parallel/niceload.html
cp src/*.pdf src/*.html ../parallel-web/parallel cp src/*.pdf src/*.html ../parallel-web/parallel
@ -195,7 +198,7 @@ to:parallel@gnu.org, bug-parallel@gnu.org
Subject: GNU Parallel 20170422 ('Санкт-Петербу́рг') released <<[stable]>> Subject: GNU Parallel 20170422 ('Санкт-Петербу́рг') released <<[stable]>>
GNU Parallel 20170422 ('Paris/Stockholm/London/Санкт-Петербу́рг') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/ GNU Parallel 20170422 ('Санкт-Петербу́рг') <<[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.>>

10
packager/obs/home:tange/parallel/.osc/_files
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@ -1,6 +1,6 @@
<directory name="parallel" rev="200" srcmd5="ef8094ec2de88060bf1e32d83bfc1a1f" vrev="1"> <directory name="parallel" rev="202" srcmd5="fda429cef02d9586acbd456694e0fe73" vrev="2">
<entry md5="0910ea89703cd4fee443f5a2403325bb" mtime="1490135663" name="parallel-20170322.tar.bz2" size="1490362" /> <entry md5="86a0368be2f9ed06578c0e7802eda47e" mtime="1492895884" name="parallel-20170422.tar.bz2" size="1543933" />
<entry md5="c80f0634d4841dd85133b077b421146e" mtime="1490135663" name="parallel.spec" size="4314" /> <entry md5="84c26447ed56c65df3bb936de0549bac" mtime="1492895885" name="parallel.spec" size="4483" />
<entry md5="e9080ce05862bd69bc2d9a3fdfc0766b" mtime="1490135664" name="parallel_20170322.dsc" size="556" /> <entry md5="4b675733211ff4c1d16a1966b025e9c6" mtime="1492895885" name="parallel_20170422.dsc" size="556" />
<entry md5="af85898a49a8311de8bf11718d4ab4b2" mtime="1490135664" name="parallel_20170322.tar.gz" size="1670238" /> <entry md5="2955c6e4e7e6ef8bbcfe3cfd018a6d6d" mtime="1492895885" name="parallel_20170422.tar.gz" size="1725824" />
</directory> </directory>

9
packager/obs/home:tange/parallel/.osc/parallel.spec
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@ -1,8 +1,8 @@
Summary: Shell tool for executing jobs in parallel Summary: Shell tool for executing jobs in parallel
Name: parallel Name: parallel
Version: 20170322 Version: 20170422
Release: 1.1 Release: 1.2
License: GPL License: GPL
Group: Productivity/File utilities Group: Productivity/File utilities
URL: ftp://ftp.gnu.org/gnu/parallel URL: ftp://ftp.gnu.org/gnu/parallel
@ -65,6 +65,7 @@ rm $RPM_BUILD_ROOT%{_docdir}/niceload.html
rm $RPM_BUILD_ROOT%{_docdir}/sem.html rm $RPM_BUILD_ROOT%{_docdir}/sem.html
rm $RPM_BUILD_ROOT%{_docdir}/sql.html rm $RPM_BUILD_ROOT%{_docdir}/sql.html
rm $RPM_BUILD_ROOT%{_docdir}/parcat.html rm $RPM_BUILD_ROOT%{_docdir}/parcat.html
rm $RPM_BUILD_ROOT%{_docdir}/parset.html
rm $RPM_BUILD_ROOT%{_docdir}/parallel.texi rm $RPM_BUILD_ROOT%{_docdir}/parallel.texi
rm $RPM_BUILD_ROOT%{_docdir}/env_parallel.texi rm $RPM_BUILD_ROOT%{_docdir}/env_parallel.texi
rm $RPM_BUILD_ROOT%{_docdir}/parallel_tutorial.texi rm $RPM_BUILD_ROOT%{_docdir}/parallel_tutorial.texi
@ -74,6 +75,7 @@ rm $RPM_BUILD_ROOT%{_docdir}/niceload.texi
rm $RPM_BUILD_ROOT%{_docdir}/sem.texi rm $RPM_BUILD_ROOT%{_docdir}/sem.texi
rm $RPM_BUILD_ROOT%{_docdir}/sql.texi rm $RPM_BUILD_ROOT%{_docdir}/sql.texi
rm $RPM_BUILD_ROOT%{_docdir}/parcat.texi rm $RPM_BUILD_ROOT%{_docdir}/parcat.texi
rm $RPM_BUILD_ROOT%{_docdir}/parset.texi
rm $RPM_BUILD_ROOT%{_docdir}/parallel.pdf rm $RPM_BUILD_ROOT%{_docdir}/parallel.pdf
rm $RPM_BUILD_ROOT%{_docdir}/env_parallel.pdf rm $RPM_BUILD_ROOT%{_docdir}/env_parallel.pdf
rm $RPM_BUILD_ROOT%{_docdir}/parallel_tutorial.pdf rm $RPM_BUILD_ROOT%{_docdir}/parallel_tutorial.pdf
@ -83,6 +85,7 @@ rm $RPM_BUILD_ROOT%{_docdir}/niceload.pdf
rm $RPM_BUILD_ROOT%{_docdir}/sem.pdf rm $RPM_BUILD_ROOT%{_docdir}/sem.pdf
rm $RPM_BUILD_ROOT%{_docdir}/sql.pdf rm $RPM_BUILD_ROOT%{_docdir}/sql.pdf
rm $RPM_BUILD_ROOT%{_docdir}/parcat.pdf rm $RPM_BUILD_ROOT%{_docdir}/parcat.pdf
rm $RPM_BUILD_ROOT%{_docdir}/parset.pdf
%clean %clean
rm -rf $RPM_BUILD_ROOT rm -rf $RPM_BUILD_ROOT
@ -92,7 +95,7 @@ rm -rf $RPM_BUILD_ROOT
/usr/bin/* /usr/bin/*
/usr/share/man/man1/* /usr/share/man/man1/*
/usr/share/man/man7/* /usr/share/man/man7/*
%doc README NEWS src/parallel.html src/env_parallel.html src/parallel_tutorial.html src/parallel_design.html src/parallel_alternatives.html src/sem.html src/sql.html src/parcat.html src/niceload.html src/parallel.texi src/env_parallel.texi src/parallel_tutorial.texi src/parallel_design.texi src/parallel_alternatives.texi src/niceload.texi src/sem.texi src/sql.texi src/parcat.texi src/parallel.pdf src/env_parallel.pdf src/parallel_tutorial.pdf src/parallel_design.pdf src/parallel_alternatives.pdf src/niceload.pdf src/sem.pdf src/sql.pdf src/parcat.pdf %doc README NEWS src/parallel.html src/env_parallel.html src/parallel_tutorial.html src/parallel_design.html src/parallel_alternatives.html src/sem.html src/sql.html src/parcat.html src/parset.html src/niceload.html src/parallel.texi src/env_parallel.texi src/parallel_tutorial.texi src/parallel_design.texi src/parallel_alternatives.texi src/niceload.texi src/sem.texi src/sql.texi src/parcat.texi src/parset.texi src/parallel.pdf src/env_parallel.pdf src/parallel_tutorial.pdf src/parallel_design.pdf src/parallel_alternatives.pdf src/niceload.pdf src/sem.pdf src/sql.pdf src/parcat.pdf src/parset.pdf
%changelog %changelog
* Sat Jan 22 2011 Ole Tange * Sat Jan 22 2011 Ole Tange

9
packager/obs/home:tange/parallel/parallel.spec
View file

@ -1,8 +1,8 @@
Summary: Shell tool for executing jobs in parallel Summary: Shell tool for executing jobs in parallel
Name: parallel Name: parallel
Version: 20170322 Version: 20170422
Release: 1.1 Release: 1.2
License: GPL License: GPL
Group: Productivity/File utilities Group: Productivity/File utilities
URL: ftp://ftp.gnu.org/gnu/parallel URL: ftp://ftp.gnu.org/gnu/parallel
@ -65,6 +65,7 @@ rm $RPM_BUILD_ROOT%{_docdir}/niceload.html
rm $RPM_BUILD_ROOT%{_docdir}/sem.html rm $RPM_BUILD_ROOT%{_docdir}/sem.html
rm $RPM_BUILD_ROOT%{_docdir}/sql.html rm $RPM_BUILD_ROOT%{_docdir}/sql.html
rm $RPM_BUILD_ROOT%{_docdir}/parcat.html rm $RPM_BUILD_ROOT%{_docdir}/parcat.html
rm $RPM_BUILD_ROOT%{_docdir}/parset.html
rm $RPM_BUILD_ROOT%{_docdir}/parallel.texi rm $RPM_BUILD_ROOT%{_docdir}/parallel.texi
rm $RPM_BUILD_ROOT%{_docdir}/env_parallel.texi rm $RPM_BUILD_ROOT%{_docdir}/env_parallel.texi
rm $RPM_BUILD_ROOT%{_docdir}/parallel_tutorial.texi rm $RPM_BUILD_ROOT%{_docdir}/parallel_tutorial.texi
@ -74,6 +75,7 @@ rm $RPM_BUILD_ROOT%{_docdir}/niceload.texi
rm $RPM_BUILD_ROOT%{_docdir}/sem.texi rm $RPM_BUILD_ROOT%{_docdir}/sem.texi
rm $RPM_BUILD_ROOT%{_docdir}/sql.texi rm $RPM_BUILD_ROOT%{_docdir}/sql.texi
rm $RPM_BUILD_ROOT%{_docdir}/parcat.texi rm $RPM_BUILD_ROOT%{_docdir}/parcat.texi
rm $RPM_BUILD_ROOT%{_docdir}/parset.texi
rm $RPM_BUILD_ROOT%{_docdir}/parallel.pdf rm $RPM_BUILD_ROOT%{_docdir}/parallel.pdf
rm $RPM_BUILD_ROOT%{_docdir}/env_parallel.pdf rm $RPM_BUILD_ROOT%{_docdir}/env_parallel.pdf
rm $RPM_BUILD_ROOT%{_docdir}/parallel_tutorial.pdf rm $RPM_BUILD_ROOT%{_docdir}/parallel_tutorial.pdf
@ -83,6 +85,7 @@ rm $RPM_BUILD_ROOT%{_docdir}/niceload.pdf
rm $RPM_BUILD_ROOT%{_docdir}/sem.pdf rm $RPM_BUILD_ROOT%{_docdir}/sem.pdf
rm $RPM_BUILD_ROOT%{_docdir}/sql.pdf rm $RPM_BUILD_ROOT%{_docdir}/sql.pdf
rm $RPM_BUILD_ROOT%{_docdir}/parcat.pdf rm $RPM_BUILD_ROOT%{_docdir}/parcat.pdf
rm $RPM_BUILD_ROOT%{_docdir}/parset.pdf
%clean %clean
rm -rf $RPM_BUILD_ROOT rm -rf $RPM_BUILD_ROOT
@ -92,7 +95,7 @@ rm -rf $RPM_BUILD_ROOT
/usr/bin/* /usr/bin/*
/usr/share/man/man1/* /usr/share/man/man1/*
/usr/share/man/man7/* /usr/share/man/man7/*
%doc README NEWS src/parallel.html src/env_parallel.html src/parallel_tutorial.html src/parallel_design.html src/parallel_alternatives.html src/sem.html src/sql.html src/parcat.html src/niceload.html src/parallel.texi src/env_parallel.texi src/parallel_tutorial.texi src/parallel_design.texi src/parallel_alternatives.texi src/niceload.texi src/sem.texi src/sql.texi src/parcat.texi src/parallel.pdf src/env_parallel.pdf src/parallel_tutorial.pdf src/parallel_design.pdf src/parallel_alternatives.pdf src/niceload.pdf src/sem.pdf src/sql.pdf src/parcat.pdf %doc README NEWS src/parallel.html src/env_parallel.html src/parallel_tutorial.html src/parallel_design.html src/parallel_alternatives.html src/sem.html src/sql.html src/parcat.html src/parset.html src/niceload.html src/parallel.texi src/env_parallel.texi src/parallel_tutorial.texi src/parallel_design.texi src/parallel_alternatives.texi src/niceload.texi src/sem.texi src/sql.texi src/parcat.texi src/parset.texi src/parallel.pdf src/env_parallel.pdf src/parallel_tutorial.pdf src/parallel_design.pdf src/parallel_alternatives.pdf src/niceload.pdf src/sem.pdf src/sql.pdf src/parcat.pdf src/parset.pdf
%changelog %changelog
* Sat Jan 22 2011 Ole Tange * Sat Jan 22 2011 Ole Tange

2
src/niceload
View file

@ -24,7 +24,7 @@
use strict; use strict;
use Getopt::Long; use Getopt::Long;
$Global::progname="niceload"; $Global::progname="niceload";
$Global::version = 20170323; $Global::version = 20170422;
Getopt::Long::Configure("bundling","require_order"); Getopt::Long::Configure("bundling","require_order");
get_options_from_array(\@ARGV) || die_usage(); get_options_from_array(\@ARGV) || die_usage();
if($opt::version) { if($opt::version) {

2
src/parallel
View file

@ -1363,7 +1363,7 @@ sub check_invalid_option_combinations {
sub init_globals { sub init_globals {
# Defaults: # Defaults:
$Global::version = 20170417; $Global::version = 20170422;
$Global::progname = 'parallel'; $Global::progname = 'parallel';
$Global::infinity = 2**31; $Global::infinity = 2**31;
$Global::debug = 0; $Global::debug = 0;

2
src/sql
View file

@ -576,7 +576,7 @@ $Global::Initfile && unlink $Global::Initfile;
exit ($err); exit ($err);
sub parse_options { sub parse_options {
$Global::version = 20170323; $Global::version = 20170422;
$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