Documentation update.

NEWS

@@ -84,9 +84,6 @@
   http://meta.askubuntu.com/a/16750/22307
   http://meta.serverfault.com/a/9040/45704
 
-* GNU Parallel was cited in:
-  https://springerplus.springeropen.com/articles/10.1186/s40064-016-2022-y
-
 * Edit images with GNU Parallel and ImageMagick
   https://fedoramagazine.org/edit-images-parallel-imagemagick/
 
@@ -1478,8 +1475,7 @@ New in this release:
   Substation Cable Installation Problem
   http://i11www.iti.uni-karlsruhe.de/_media/teaching/theses/ma-schmitz-14.pdf
 
-* GNU Parallel was used in: landsat-gifworks
+* GNU Parallel was used in: https://github.com/KAPPS-/landsat-gifworks
-  https://github.com/KAPPS-/landsat-gifworks
 
 * GNU Parallel was used in: https://github.com/exascience/elprep
 
@@ -2390,7 +2386,7 @@ New in this release:
 * --transfer and --basefile support paths relative to the --workdir by
   inserting /./ into the path. 
 
-* GNU Parallel was cited in: 'fastphylo: Fast tools for phylogenetics'
+* GNU Parallel was cited in: fastphylo: Fast tools for phylogenetics
   http://www.biomedcentral.com/1471-2105/14/334/abstract
 
 * Using GNU parallel

doc/release_new_version

@@ -210,6 +210,8 @@ Haiku of the month:
 
 New in this release:
 
+* 15分钟神器gnu parallel 入门观止 http://www.ezilin.com/2018/01/15gnu-parallel.html
+
 
 <<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>>
 

src/env_parallel.pod

@@ -23,7 +23,7 @@ instead that explains how to install the function.
 B<env_parallel> is beta quality and not production ready, but please
 use it for everyday use and report bugs.
 
-B<env_parallel> is 0.1 sec slower at startup than pure GNU
+B<env_parallel> is 100 ms slower at startup than pure GNU
 B<parallel>, and takes up to 30% longer to start a job (typically 15 ms).
 
 Due to the problem with environment space (see below) the recommended
@@ -88,10 +88,7 @@ Same as GNU B<parallel>.
 
 =head2 Ash
 
-B<--env> is supported to export only the variable, or alias with the
+=head3 Installation
-given name. Multiple B<--env>s can be given.
-
-Installation
 
 Put this in $HOME/.profile:
 
@@ -101,6 +98,11 @@ E.g. by doing:
 
   echo '. `which env_parallel.ash`' >> $HOME/.profile
 
+=head3 Supported use
+
+B<--env> is supported to export only the variable, or alias with the
+given name. Multiple B<--env>s can be given.
+
 =over 8
 
 =item aliases
@@ -138,10 +140,7 @@ Arrays are not supported by Ash.
 
 =head2 Bash
 
-B<--env> is supported to export only the variable, alias, function, or
+=head3 Installation
-array with the given name. Multiple B<--env>s can be given.
-
-Installation
 
 Put this in $HOME/.bashrc:
 
@@ -151,6 +150,11 @@ E.g. by doing:
 
   echo '. `which env_parallel.bash`' >> $HOME/.bashrc
 
+=head3 Supported use
+
+B<--env> is supported to export only the variable, alias, function, or
+array with the given name. Multiple B<--env>s can be given.
+
 =over 8
 
 =item aliases
@@ -194,24 +198,22 @@ E.g. by doing:
   env_parallel -k echo '${myarray[{}]}' ::: 0 1 2
   env_parallel -k -S server echo '${myarray[{}]}' ::: 0 1 2
   env_parallel -k --env myarray echo '${myarray[{}]}' ::: 0 1 2
-  env_parallel -k --env myarray -S server echo '${myarray[{}]}' ::: 0 1 2
+  env_parallel -k --env myarray -S server \
+    echo '${myarray[{}]}' ::: 0 1 2
 
 =back
 
 =head3 BUGS
 
-Due to a bug in Bash aliases containing newlines must be followed by a
+Due to a bug in Bash, aliases containing newlines must be followed by
-newline in the command.
+a newline in the command.
 
 =head2 csh
 
-B<--env> is supported to export only the variable, alias, or
-array with the given name. Multiple B<--env>s can be given.
-
 B<env_parallel> for B<csh> breaks B<$PARALLEL>, so do not use
 B<$PARALLEL>.
 
-Installation
+=head3 Installation
 
 Put this in $HOME/.cshrc:
 
@@ -221,6 +223,11 @@ E.g. by doing:
 
   echo 'source `which env_parallel.csh`' >> $HOME/.cshrc
 
+=head3 Supported use
+
+B<--env> is supported to export only the variable, alias, or
+array with the given name. Multiple B<--env>s can be given.
+
 =over 8
 
 =item aliases
@@ -249,17 +256,15 @@ Not supported by B<csh>.
   env_parallel -k echo \$'{myarray[{}]}' ::: 1 2 3
   env_parallel -k -S server echo \$'{myarray[{}]}' ::: 1 2 3
   env_parallel -k --env myarray echo \$'{myarray[{}]}' ::: 1 2 3
-  env_parallel -k --env myarray -S server echo \$'{myarray[{}]}' ::: 1 2 3
+  env_parallel -k --env myarray -S server \
+    echo \$'{myarray[{}]}' ::: 1 2 3
 
 =back
 
 
 =head2 Dash
 
-B<--env> is supported to export only the variable, or alias with the
+=head3 Installation
-given name. Multiple B<--env>s can be given.
-
-Installation
 
 Put this in $HOME/.profile:
 
@@ -269,6 +274,11 @@ E.g. by doing:
 
   echo '. `which env_parallel.dash`' >> $HOME/.profile
 
+=head3 Supported use
+
+B<--env> is supported to export only the variable, or alias with the
+given name. Multiple B<--env>s can be given.
+
 =over 8
 
 =item aliases
@@ -307,10 +317,7 @@ E.g. by doing:
 
 =head2 fish
 
-B<--env> is supported to export only the variable, alias, function, or
+=head3 Installation
-array with the given name. Multiple B<--env>s can be given.
-
-Installation
 
 Put this in $HOME/.config/fish/config.fish:
 
@@ -318,7 +325,13 @@ Put this in $HOME/.config/fish/config.fish:
 
 E.g. by doing:
 
-  echo 'source (which env_parallel.fish)' >> $HOME/.config/fish/config.fish
+  echo 'source (which env_parallel.fish)' \
+    >> $HOME/.config/fish/config.fish
+
+=head3 Supported use
+
+B<--env> is supported to export only the variable, alias, function, or
+array with the given name. Multiple B<--env>s can be given.
 
 =over 8
 
@@ -354,17 +367,15 @@ E.g. by doing:
   env_parallel -k echo '$myarray[{}]' ::: 1 2 3
   env_parallel -k -S server echo '$myarray[{}]' ::: 1 2 3
   env_parallel -k --env myarray echo '$myarray[{}]' ::: 1 2 3
-  env_parallel -k --env myarray -S server echo '$myarray[{}]' ::: 1 2 3
+  env_parallel -k --env myarray -S server \
+    echo '$myarray[{}]' ::: 1 2 3
 
 =back
 
 
 =head2 ksh
 
-B<--env> is supported to export only the variable, alias, function, or
+=head3 Installation
-array with the given name. Multiple B<--env>s can be given.
-
-Installation
 
 Put this in $HOME/.kshrc:
 
@@ -374,6 +385,11 @@ E.g. by doing:
 
   echo 'source `which env_parallel.ksh`' >> $HOME/.kshrc
 
+=head3 Supported use
+
+B<--env> is supported to export only the variable, alias, function, or
+array with the given name. Multiple B<--env>s can be given.
+
 =over 8
 
 =item aliases
@@ -413,17 +429,15 @@ E.g. by doing:
   env_parallel -k echo '${myarray[{}]}' ::: 0 1 2
   env_parallel -k -S server echo '${myarray[{}]}' ::: 0 1 2
   env_parallel -k --env myarray echo '${myarray[{}]}' ::: 0 1 2
-  env_parallel -k --env myarray -S server echo '${myarray[{}]}' ::: 0 1 2
+  env_parallel -k --env myarray -S server \
+    echo '${myarray[{}]}' ::: 0 1 2
 
 =back
 
 
 =head2 pdksh
 
-B<--env> is supported to export only the variable, alias, function, or
+=head3 Installation
-array with the given name. Multiple B<--env>s can be given.
-
-Installation
 
 Put this in $HOME/.profile:
 
@@ -433,6 +447,11 @@ E.g. by doing:
 
   echo 'source `which env_parallel.pdksh`' >> $HOME/.profile
 
+=head3 Supported use
+
+B<--env> is supported to export only the variable, alias, function, or
+array with the given name. Multiple B<--env>s can be given.
+
 =over 8
 
 =item aliases
@@ -465,17 +484,15 @@ E.g. by doing:
   env_parallel -k echo "\${myarray[{}]}" ::: 0 1 2;
   env_parallel -k -S server echo "\${myarray[{}]}" ::: 0 1 2;
   env_parallel -k --env myarray echo "\${myarray[{}]}" ::: 0 1 2;
-  env_parallel -k --env myarray -S server echo "\${myarray[{}]}" ::: 0 1 2
+  env_parallel -k --env myarray -S server \
+    echo "\${myarray[{}]}" ::: 0 1 2
 
 =back
 
 
 =head2 sh
 
-B<--env> is supported to export only the variable, or alias with the
+=head3 Installation
-given name. Multiple B<--env>s can be given.
-
-Installation
 
 Put this in $HOME/.profile:
 
@@ -485,6 +502,11 @@ E.g. by doing:
 
   echo '. `which env_parallel.sh`' >> $HOME/.profile
 
+=head3 Supported use
+
+B<--env> is supported to export only the variable, or alias with the
+given name. Multiple B<--env>s can be given.
+
 =over 8
 
 =item aliases
@@ -516,13 +538,10 @@ E.g. by doing:
 
 =head2 tcsh
 
-B<--env> is supported to export only the variable, alias, or
-array with the given name. Multiple B<--env>s can be given.
-
 B<env_parallel> for B<tcsh> breaks B<$PARALLEL>, so do not use
 B<$PARALLEL>.
 
-Installation
+=head3 Installation
 
 Put this in $HOME/.tcshrc:
 
@@ -532,6 +551,11 @@ E.g. by doing:
 
   echo 'source `which env_parallel.tcsh`' >> $HOME/.tcshrc
 
+=head3 Supported use
+
+B<--env> is supported to export only the variable, alias, or
+array with the given name. Multiple B<--env>s can be given.
+
 =over 8
 
 =item aliases
@@ -560,17 +584,15 @@ Not supported by B<tcsh>.
   env_parallel -k echo \$'{myarray[{}]}' ::: 1 2 3
   env_parallel -k -S server echo \$'{myarray[{}]}' ::: 1 2 3
   env_parallel -k --env myarray echo \$'{myarray[{}]}' ::: 1 2 3
-  env_parallel -k --env myarray -S server echo \$'{myarray[{}]}' ::: 1 2 3
+  env_parallel -k --env myarray -S server \
+    echo \$'{myarray[{}]}' ::: 1 2 3
 
 =back
 
 
 =head2 Zsh
 
-B<--env> is supported to export only the variable, alias, function, or
+=head3 Installation
-array with the given name. Multiple B<--env>s can be given.
-
-Installation
 
 Put this in $HOME/.zshrc:
 
@@ -580,6 +602,11 @@ E.g. by doing:
 
   echo '. `which env_parallel.zsh`' >> $HOME/.zshenv
 
+=head3 Supported use
+
+B<--env> is supported to export only the variable, alias, function, or
+array with the given name. Multiple B<--env>s can be given.
+
 =over 8
 
 =item aliases
@@ -619,7 +646,8 @@ E.g. by doing:
   env_parallel -k echo '${myarray[{}]}' ::: 1 2 3
   env_parallel -k -S server echo '${myarray[{}]}' ::: 1 2 3
   env_parallel -k --env myarray echo '${myarray[{}]}' ::: 1 2 3
-  env_parallel -k --env myarray -S server echo '${myarray[{}]}' ::: 1 2 3
+  env_parallel -k --env myarray -S server \
+    echo '${myarray[{}]}' ::: 1 2 3
 
 =back
 
@@ -763,10 +791,8 @@ B<env_parallel> uses GNU B<parallel>.
 
 =head1 SEE ALSO
 
-B<parallel>(1), 
+B<parallel>(1), B<ash>(1), B<bash>(1), B<csh>(1), B<dash>(1),
-
+B<fish>(1), B<ksh>(1), B<pdksh>(1) B<tcsh>(1), B<zsh>(1).
-B<ash>(1), B<bash>(1), B<csh>(1), B<dash>(1), B<fish>(1), B<ksh>(1),
-B<pdksh>(1) B<tcsh>(1), B<zsh>(1).
 
 
 =cut

src/parallel

@@ -1391,7 +1391,7 @@ sub check_invalid_option_combinations {
 
 sub init_globals {
     # Defaults:
-    $Global::version = 20171224;
+    $Global::version = 20180107;
     $Global::progname = 'parallel';
     $Global::infinity = 2**31;
     $Global::debug = 0;
@@ -2240,7 +2240,7 @@ sub perl_quote_scalar {
     # Inputs:
     #   $string = string to be quoted
     # Returns:
-    #   $shell_quoted = string quoted with \ as needed by perl's eval
+    #   $perl_quoted = string quoted with \ as needed by perl's eval
     my $a = $_[0];
     if(defined $a) {
 	$a =~ s/[\\\"\$\@]/\\$&/go;
@@ -4101,7 +4101,7 @@ sub citation_notice {
 	     "This helps funding further development; AND IT WON'T COST YOU A CENT.",
 	     "If you pay 10000 EUR you should feel free to use GNU Parallel without citing.",
 	     "",
-	     "To silence this citation notice: run 'parallel --citation'.",
+	     "To silence this citation notice: run 'parallel --citation' once.",
 	     ""
 	    );
     }
@@ -9072,7 +9072,7 @@ sub set_exitsignal {
 	} elsif($Global::halt_success) {
 	    ::status("$Global::progname: This job succeeded:",
 		     $job->replaced());
-	    $limit = $Global::total_completed-$Global::total_failed;
+	    $limit = $Global::total_completed - $Global::total_failed;
 	}
 	if($Global::halt_done) {
 	    ::status("$Global::progname: This job finished:",

src/parallel.pod

@@ -555,7 +555,7 @@ B<--return>.
 =item B<-C> I<regexp>
 
 Column separator. The input will be treated as a table with I<regexp>
-separating the columns. The n'th column can be access using
+separating the columns. The n'th column can be accessed using
 B<{>I<n>B<}> or B<{>I<n>.B<}>. E.g. B<{3}> is the 3rd column.
 
 If there are more input sources, each input source will be separated,
@@ -3974,7 +3974,7 @@ A mutex is a counting semaphore allowing only one job to run. This
 will edit the file I<myfile> and prepends the file with lines with the
 numbers 1 to 3.
 
-  seq 3 | parallel sem sed -i -e 'i{}' myfile
+  seq 3 | parallel sem sed -i -e '1i{}' myfile
 
 As I<myfile> can be very big it is important only one process edits
 the file at the same time.
@@ -4552,7 +4552,7 @@ host in serial, so if your B<--sshloginfile> contains many hosts it may
 be slow.
 
 If your jobs are short you may see that there are fewer jobs running
-on the remove systems than expected. This is due to time spent logging
+on the remote systems than expected. This is due to time spent logging
 in and out. B<-M> may help here.
 
 =head3 Disk access
@@ -4583,7 +4583,7 @@ of the jobs will be stuck waiting for disk access.
 The current implementation of B<--nice> is too pessimistic in the max
 allowed command length. It only uses a little more than half of what
 it could. This affects B<-X> and B<-m>. If this becomes a real problem for
-you file a bug-report.
+you, file a bug-report.
 
 =head2 Aliases and functions do not work
 
@@ -4595,10 +4595,14 @@ or:
 
   open3: exec of by command failed
 
+or:
+
+  /bin/bash: command: command not found
+
 it may be because I<command> is not known, but it could also be
 because I<command> is an alias or a function. If it is a function you
-need to B<export -f> the function first. An alias will only work if
+need to B<export -f> the function first or use B<env_parallel>. An
-you use B<env_parallel>.
+alias will only work if you use B<env_parallel>.
 
 
 =head1 REPORTING BUGS

src/parset.pod

@@ -131,18 +131,18 @@ but must instead use a tempfile:
 
   seq 3 > parallel_input
   parset res1,res2,res3 echo :::: parallel_input
-  echo "res1"
+  echo "$res1"
-  echo "res2"
+  echo "$res2"
-  echo "res3"
+  echo "$res3"
 
 or a FIFO:
 
   mkfifo input_fifo
   seq 3 > input_fifo &
   parset res1,res2,res3 echo :::: input_fifo
-  echo "res1"
+  echo "$res1"
-  echo "res2"
+  echo "$res2"
-  echo "res3"
+  echo "$res3"
 
 =head3 Installation