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Released as 20160922 ('Christiania')

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Ole Tange 2016-09-23 01:15:11 +02:00
parent 74e35933f4
commit 0f8d12839f
8 changed files with 60 additions and 22 deletions
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35
NEWS
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@ -1,3 +1,38 @@
20160922
* parcat - cat files or fifos in parallel
* GNU Parallel was cited in: Velocity: A Netflow Based Optimized
Geo-IP Lookup Tool
https://mospace.umsystem.edu/xmlui/bitstream/handle/10355/50842/Thesis_2016_Pakhare.pdf?sequence=1&isAllowed=y
* GNU Parallel was cited in: Viral deep sequencing needs an adaptive
approach: IRMA, the iterative refinement meta-assembler
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011931/
* GNU Parallel is used in Gene Set Omic Analysis:
https://bitbucket.org/srp33/gsoa
* Using GNU Parallel and ImageMagick for Conversions
https://blog.fractalcomic.com/tutorials/using-gnu-parallel-and-imagemagick-for-conversions/
* Training in GNU Parallel
http://www.cism.ucl.ac.be/Services/Formations/parcomp.pdf
* Chown Ceph OSD data directory using GNU Parallel
http://blog.widodh.nl/2016/08/chown-ceph-osd-data-directory-using-gnu-parallel/
* FastGBS uses GNU Parallel https://bitbucket.org/jerlar73/fastgbs
* dDocent: A guide to ddRAD sequencing
https://ddocent.wordpress.com/ddocent-pipeline-user-guide/
* SOFTWARE GNU Parallel
http://msi-riss.readthedocs.io/en/latest/software/gnu-parallel.html
* Bug fixes and man page updates.
20160822 20160822
* --tmuxpane opens jobs in panes in tmux. Useful if you want to * --tmuxpane opens jobs in panes in tmux. Useful if you want to

12
README
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@ -40,9 +40,9 @@ 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-20160822.tar.bz2 wget http://ftpmirror.gnu.org/parallel/parallel-20160922.tar.bz2
bzip2 -dc parallel-20160822.tar.bz2 | tar xvf - bzip2 -dc parallel-20160922.tar.bz2 | tar xvf -
cd parallel-20160822 cd parallel-20160922
./configure && make && sudo make install ./configure && make && sudo make install
@ -51,9 +51,9 @@ 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-20160822.tar.bz2 wget http://ftpmirror.gnu.org/parallel/parallel-20160922.tar.bz2
bzip2 -dc parallel-20160822.tar.bz2 | tar xvf - bzip2 -dc parallel-20160922.tar.bz2 | tar xvf -
cd parallel-20160822 cd parallel-20160922
./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 20160822. # Generated by GNU Autoconf 2.69 for parallel 20160922.
# #
# 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='20160822' PACKAGE_VERSION='20160922'
PACKAGE_STRING='parallel 20160822' PACKAGE_STRING='parallel 20160922'
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 20160822 to adapt to many kinds of systems. \`configure' configures parallel 20160922 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 $ac_init_help in
short | recursive ) echo "Configuration of parallel 20160822:";; short | recursive ) echo "Configuration of parallel 20160922:";;
esac esac
cat <<\_ACEOF cat <<\_ACEOF
@ -1357,7 +1357,7 @@ fi
test -n "$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 20160822 parallel configure 20160922
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 20160822, which was It was created by parallel $as_me 20160922, which was
generated by GNU Autoconf 2.69. Invocation command line was generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@ $ $0 $@
@ -2237,7 +2237,7 @@ fi
# Define the identity of the package. # Define the identity of the package.
PACKAGE='parallel' PACKAGE='parallel'
VERSION='20160822' VERSION='20160922'
cat >>confdefs.h <<_ACEOF cat >>confdefs.h <<_ACEOF
@ -2880,7 +2880,7 @@ cat >>$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 20160822, which was This file was extended by parallel $as_me 20160922, 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 20160822 parallel config.status 20160922
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], [20160822], [bug-parallel@gnu.org]) AC_INIT([parallel], [20160922], [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([

7
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: 20160822 Version: 20160922
Release: 1.1 Release: 1.1
License: GPL License: GPL
Group: Productivity/File utilities Group: Productivity/File utilities
@ -62,6 +62,7 @@ rm $RPM_BUILD_ROOT%{_docdir}/parallel_design.html
rm $RPM_BUILD_ROOT%{_docdir}/niceload.html 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}/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
@ -69,6 +70,7 @@ rm $RPM_BUILD_ROOT%{_docdir}/parallel_design.texi
rm $RPM_BUILD_ROOT%{_docdir}/niceload.texi 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}/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
@ -76,6 +78,7 @@ rm $RPM_BUILD_ROOT%{_docdir}/parallel_design.pdf
rm $RPM_BUILD_ROOT%{_docdir}/niceload.pdf 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
%clean %clean
rm -rf $RPM_BUILD_ROOT rm -rf $RPM_BUILD_ROOT
@ -85,7 +88,7 @@ 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/sem.html src/sql.html src/niceload.html src/parallel.texi src/env_parallel.texi src/parallel_tutorial.texi src/parallel_design.texi src/niceload.texi src/sem.texi src/sql.texi src/parallel.pdf src/env_parallel.pdf src/parallel_tutorial.pdf src/parallel_design.pdf src/niceload.pdf src/sem.pdf src/sql.pdf %doc README NEWS src/parallel.html src/env_parallel.html src/parallel_tutorial.html src/parallel_design.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/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/niceload.pdf src/sem.pdf src/sql.pdf src/parcat.pdf
%changelog %changelog
* Sat Jan 22 2011 Ole Tange * Sat Jan 22 2011 Ole Tange

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 = 20160823; $Global::version = 20160922;
Getopt::Long::Configure("bundling","require_order"); Getopt::Long::Configure("bundling","require_order");
get_options_from_array(\@ARGV) || die_usage(); get_options_from_array(\@ARGV) || die_usage();
if($opt::version) { if($opt::version) {

2
src/parallel
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@ -1210,7 +1210,7 @@ sub check_invalid_option_combinations {
sub init_globals { sub init_globals {
# Defaults: # Defaults:
$Global::version = 20160824; $Global::version = 20160922;
$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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@ -566,7 +566,7 @@ $Global::Initfile && unlink $Global::Initfile;
exit ($err); exit ($err);
sub parse_options { sub parse_options {
$Global::version = 20160823; $Global::version = 20160922;
$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