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Released as 20150822 ('HansVibeke')
This commit is contained in:
Ole Tange
parent
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commit
074ed8bfc6
43
NEWS
43
NEWS
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@ -1,3 +1,46 @@
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20150822
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* If $job->skip() is called in {= =} the job will not be run.
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* @arg can now be used in {= =}: parallel echo '{= $arg[2] < 5 and
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$_="j" =}' ::: 1 2 3 ::: 4 5 6
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* Version of GNU Parallel that uses PostgreSQL as backend
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https://github.com/stephen-fralich/parallel-sql/
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* A composite genome approach to identify phylogenetically informative
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data from next-generation sequencing
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http://www.biomedcentral.com/content/pdf/s12859-015-0632-y.pdf
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* SpeedSeq: ultra-fast personal genome analysis and interpretation
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http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html
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* GNU Parallel is used in elPrep: https://github.com/ExaScience/elprep
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* Who actually reads the code?
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http://www.fsf.org/blogs/community/who-actually-reads-the-code
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* Introduction to GNU Parallel
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http://erictleung.com/2015/08/06/intro-to-gnu-parallel/
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* ¿Alguien se lee el código?
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http://www.taringa.net/post/linux/18854759/Alguien-se-lee-el-codigo.html
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* ¿Quién se lee el código fuente?
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https://victorhckinthefreeworld.wordpress.com/2015/08/12/quien-se-lee-el-codigo-fuente/
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* Distribution des traitements avec GNU Parallel
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http://blog.inovia-conseil.fr/?p=226#4
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* Эксперимент по проверке, читают ли код открытых проектов
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http://www.opennet.ru/opennews/art.shtml?num=42718
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* 多核心主機搭配 GNU parallel
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http://blog.zeroplex.tw/2015/08/gnu-parallel.html
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* Bug fixes and man page updates.
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20150722
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* If a record fits in a block, --block only reads upto the size of
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12
README
12
README
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@ -40,9 +40,9 @@ document.
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Full installation of GNU Parallel is as simple as:
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wget http://ftpmirror.gnu.org/parallel/parallel-20150722.tar.bz2
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bzip2 -dc parallel-20150722.tar.bz2 | tar xvf -
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cd parallel-20150722
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wget http://ftpmirror.gnu.org/parallel/parallel-20150822.tar.bz2
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bzip2 -dc parallel-20150822.tar.bz2 | tar xvf -
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cd parallel-20150822
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./configure && make && sudo make install
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@ -51,9 +51,9 @@ Full installation of GNU Parallel is as simple as:
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If you are not root you can add ~/bin to your path and install in
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~/bin and ~/share:
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wget http://ftpmirror.gnu.org/parallel/parallel-20150722.tar.bz2
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bzip2 -dc parallel-20150722.tar.bz2 | tar xvf -
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cd parallel-20150722
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wget http://ftpmirror.gnu.org/parallel/parallel-20150822.tar.bz2
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bzip2 -dc parallel-20150822.tar.bz2 | tar xvf -
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cd parallel-20150822
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./configure --prefix=$HOME && make && make install
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Or if your system lacks 'make' you can simply copy src/parallel
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20
configure
vendored
20
configure
vendored
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@ -1,6 +1,6 @@
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#! /bin/sh
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# Guess values for system-dependent variables and create Makefiles.
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# Generated by GNU Autoconf 2.69 for parallel 20150722.
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# Generated by GNU Autoconf 2.69 for parallel 20150822.
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#
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# Report bugs to <bug-parallel@gnu.org>.
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#
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@ -579,8 +579,8 @@ MAKEFLAGS=
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# Identity of this package.
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PACKAGE_NAME='parallel'
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PACKAGE_TARNAME='parallel'
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PACKAGE_VERSION='20150722'
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PACKAGE_STRING='parallel 20150722'
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PACKAGE_VERSION='20150822'
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PACKAGE_STRING='parallel 20150822'
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PACKAGE_BUGREPORT='bug-parallel@gnu.org'
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PACKAGE_URL=''
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@ -1203,7 +1203,7 @@ if test "$ac_init_help" = "long"; then
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# Omit some internal or obsolete options to make the list less imposing.
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# This message is too long to be a string in the A/UX 3.1 sh.
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cat <<_ACEOF
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\`configure' configures parallel 20150722 to adapt to many kinds of systems.
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\`configure' configures parallel 20150822 to adapt to many kinds of systems.
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Usage: $0 [OPTION]... [VAR=VALUE]...
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@ -1269,7 +1269,7 @@ fi
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if test -n "$ac_init_help"; then
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case $ac_init_help in
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short | recursive ) echo "Configuration of parallel 20150722:";;
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short | recursive ) echo "Configuration of parallel 20150822:";;
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esac
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cat <<\_ACEOF
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@ -1345,7 +1345,7 @@ fi
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test -n "$ac_init_help" && exit $ac_status
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if $ac_init_version; then
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cat <<\_ACEOF
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parallel configure 20150722
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parallel configure 20150822
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generated by GNU Autoconf 2.69
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Copyright (C) 2012 Free Software Foundation, Inc.
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@ -1362,7 +1362,7 @@ cat >config.log <<_ACEOF
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This file contains any messages produced by compilers while
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running configure, to aid debugging if configure makes a mistake.
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It was created by parallel $as_me 20150722, which was
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It was created by parallel $as_me 20150822, which was
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generated by GNU Autoconf 2.69. Invocation command line was
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$ $0 $@
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@ -2225,7 +2225,7 @@ fi
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# Define the identity of the package.
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PACKAGE='parallel'
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VERSION='20150722'
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VERSION='20150822'
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cat >>confdefs.h <<_ACEOF
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@ -2867,7 +2867,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
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# report actual input values of CONFIG_FILES etc. instead of their
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# values after options handling.
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ac_log="
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This file was extended by parallel $as_me 20150722, which was
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This file was extended by parallel $as_me 20150822, which was
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generated by GNU Autoconf 2.69. Invocation command line was
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CONFIG_FILES = $CONFIG_FILES
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@ -2929,7 +2929,7 @@ _ACEOF
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cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
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ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
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ac_cs_version="\\
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parallel config.status 20150722
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parallel config.status 20150822
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configured by $0, generated by GNU Autoconf 2.69,
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with options \\"\$ac_cs_config\\"
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@ -1,4 +1,4 @@
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AC_INIT([parallel], [20150722], [bug-parallel@gnu.org])
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AC_INIT([parallel], [20150822], [bug-parallel@gnu.org])
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AM_INIT_AUTOMAKE([-Wall -Werror foreign])
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AC_CONFIG_HEADERS([config.h])
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AC_CONFIG_FILES([
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@ -209,11 +209,9 @@ cc:Tim Cuthbertson <tim3d.junk@gmail.com>,
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Ryoichiro Suzuki <ryoichiro.suzuki@gmail.com>,
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Jesse Alama <jesse.alama@gmail.com>
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Subject: GNU Parallel 20150822 ('天津') released <<[stable]>>
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Subject: GNU Parallel 20150822 ('Hans Vibeke') released
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GNU Parallel 20150822 ('天津') <<[stable]>> has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
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<<No new functionality was introduced so this is a good candidate for a stable release.>>
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GNU Parallel 20150822 ('Hans Vibeke') has been released. It is available for download at: http://ftp.gnu.org/gnu/parallel/
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Haiku of the month:
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@ -230,12 +228,6 @@ New in this release:
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* Version of GNU Parallel that uses PostgreSQL as backend https://github.com/stephen-fralich/parallel-sql/
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* <<Har angiveligt submittet ny version - afventer opdatering>> GNU Parallel was used (unfortunately without citation) in: MUGBAS: a species free gene-based programme suite for post-GWAS analysis http://www.ncbi.nlm.nih.gov/pubmed/25765345
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* <<Afventer updateret publisering>> GNU Parallel was used in: Large Scale Author Name Disambiguation in Digital Libraries http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?tp=&arnumber=7004487&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D7004487
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* <<kontaktet 2015-06-22 Afventer svar fra journal>> GNU Parallel was used (unfortunately with wrong citation) in: TADSim: Discrete Event-Based Performance Prediction for Temperature-Accelerated Dynamics http://vruehle.de/publications/2015c.pdf
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* A composite genome approach to identify phylogenetically informative data from next-generation sequencing http://www.biomedcentral.com/content/pdf/s12859-015-0632-y.pdf
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* SpeedSeq: ultra-fast personal genome analysis and interpretation http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html
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Summary: Shell tool for executing jobs in parallel
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Name: parallel
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Version: 20150722
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Version: 20150822
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Release: 1
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License: GPL
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Group: Productivity/File utilities
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@ -24,7 +24,7 @@
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use strict;
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use Getopt::Long;
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$Global::progname="niceload";
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$Global::version = 20150722;
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$Global::version = 20150822;
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Getopt::Long::Configure("bundling","require_order");
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get_options_from_array(\@ARGV) || die_usage();
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if($opt::version) {
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sub init_globals {
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# Defaults:
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$Global::version = 20150813;
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$Global::version = 20150822;
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$Global::progname = 'parallel';
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$Global::infinity = 2**31;
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$Global::debug = 0;
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@ -85,7 +85,10 @@ B<Bash functions>: B<export -f> the function first.
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B<Bash aliases>: Copy the full environment using this and use B<env_parallel> instead of B<parallel>.
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env_parallel() {
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export PARALLEL_ENV="$(echo "shopt -s expand_aliases 2>/dev/null"; alias;typeset -p | grep -vFf <(readonly; echo GROUPS; echo FUNCNAME; echo DIRSTACK; echo _; echo PIPESTATUS; echo USERNAME) | grep -v BASH_;typeset -f)";
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export PARALLEL_ENV="$(echo "shopt -s expand_aliases 2>/dev/null"; alias;typeset -p |
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grep -vFf <(readonly) |
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grep -v 'declare .. (GROUPS|FUNCNAME|DIRSTACK|_|PIPESTATUS|USERNAME|BASH_[A-Z_]+) ';
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typeset -f)";
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`which parallel` "$@";
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unset PARALLEL_ENV;
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}
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@ -103,7 +106,7 @@ B<Ksh functions>: If it is a Ksh function you can encode the function in a varia
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To export all functions and also make them available when running remote:
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env_parallel() {
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export PARALLEL_ENV="$(alias | perl -pe 's/^/alias /';typeset -p;typeset -f)";
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export PARALLEL_ENV="$(alias | perl -pe 's/^/alias /';typeset -p|egrep -v 'typeset( -i)? -r|PIPESTATUS';typeset -f)";
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`which parallel` "$@";
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unset PARALLEL_ENV;
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}
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@ -122,9 +125,11 @@ B<Zsh functions>: If it is a Zsh function you can encode the function in a varia
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To export all functions and also make them available when running remote:
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env_parallel() {
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PARALLEL_ENV="$(alias | perl -pe 's/^/alias /';typeset -f)";
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export PARALLEL_ENV
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`which parallel` "$@";
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export PARALLEL_ENV="$(alias | perl -pe 's/^/alias /';typeset -p |
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grep -aFvf <(typeset -pr)|egrep -iav 'ZSH_EVAL_CONTEXT|LINENO=| _=|aliases|^typeset [a-z_]+$'|
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egrep -av '^(typeset IFS=|..$)|cyan';
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typeset -f)";
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parallel "$@";
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unset PARALLEL_ENV;
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}
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# call as:
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2
src/sql
2
src/sql
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exit ($err);
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sub parse_options {
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$Global::version = 20150722;
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$Global::version = 20150822;
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$Global::progname = 'sql';
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# This must be done first as this may exec myself
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}
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env_parallel() {
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unset PARALLEL_ENV;
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export PARALLEL_ENV="$(alias | perl -pe 's/^/alias /';typeset -p |
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grep -aFvf <(typeset -pr)|egrep -iav 'ZSH_EVAL_CONTEXT|LINENO=| _=|aliases|^typeset [a-z_]+$'|
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egrep -av '^(typeset IFS=|..$)|cyan';
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typeset -f)";
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parallel "$@";
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unset PARALLEL_ENV;
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}
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# alias does not work: http://unix.stackexchange.com/questions/223534/defining-an-alias-and-immediately-use-it
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}
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env_parallel() {
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unset PARALLEL_ENV;
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export PARALLEL_ENV="$(alias | perl -pe 's/^/alias /';typeset -p|egrep -v 'typeset( -i)? -r|PIPESTATUS';typeset -f)";
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`which parallel` "$@";
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unset PARALLEL_ENV;
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}
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env_parallel alias_echo ::: alias_works
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env_parallel func_echo ::: function_works
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