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parallel: Small bug in {#prefix} replacement string.
This commit is contained in:
Ole Tange
parent
fb2a1753bf
commit
bbd336643c
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@ -196,17 +196,16 @@ file:///home/tange/privat/parallel/doc/release_new_version
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from:tange@gnu.org
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to:parallel@gnu.org, bug-parallel@gnu.org
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Subject: GNU Parallel 20170622 ('Grenfell') released <<[stable]>>
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Subject: GNU Parallel 20170822 ('<<>>') released <<[stable]>>
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GNU Parallel 20170622 ('Grenfell') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
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GNU Parallel 20170822 ('<<>>') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
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<<No new functionality was introduced so this is a good candidate for a stable release.>>
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Quote of the month:
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Haiku of the month:
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I don't care
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I just need to get shit done
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-- Sab
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<<>>
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New in this release:
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@ -215,21 +214,9 @@ New in this release:
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http://meta.askubuntu.com/a/16750/22307
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http://meta.serverfault.com/a/9040/45704
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* GNU Parallel was cited in: Hayabusa: Simple and Fast Full-Text Search Engine for Massive System Log Data http://dl.acm.org/citation.cfm?id=3095788
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* GNU Parallel was cited in:
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* コマンドの並列化を行える『GNU parallel』の個人的使い方まとめhttps://orebibou.com/2017/07/%E3%82%B3%E3%83%9E%E3%83%B3%E3%83%89%E3%81%AE%E4%B8%A6%E5%88%97%E5%8C%96%E3%82%92%E8%A1%8C%E3%81%88%E3%82%8B%E3%80%8Egnu-parallel%E3%80%8F%E3%81%AE%E5%80%8B%E4%BA%BA%E7%9A%84%E4%BD%BF%E3%81%84/
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* https://blog.archive.org/2017/07/10/how-to-play-and-play-with-78rpm-record-transfers/
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* https://gxnotes.com/article/130363.html
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* https://sgillies.net/2017/05/18/rfc-8142-geojson-text-sequences.html
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* https://lukas.zapletalovi.com/2017/07/git-auto-fetch-script-i-run-every-day.html
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* http://crazyhottommy.blogspot.de/2017/07/cores-cpus-and-threads.html
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' https://lukas.zapletalovi.com/2017/07/git-auto-fetch-script-i-run-every-day.html
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* https://medium.com/@nornagon/today-i-learned-gnu-parallel-plate-tectonics-9fcf24045e63
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<<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>>
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11
src/parallel
11
src/parallel
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@ -1042,6 +1042,7 @@ sub options_hash {
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"internal-pipe-means-argfiles" => \$opt::internal_pipe_means_argfiles,
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"Y" => \$opt::retired,
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"skip-first-line" => \$opt::skip_first_line,
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"bug" => \$opt::bug,
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"header=s" => \$opt::header,
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"cat" => \$opt::cat,
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"fifo" => \$opt::fifo,
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@ -1102,6 +1103,7 @@ sub parse_options {
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if($opt::nokeeporder) { $opt::keeporder = undef; }
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if(@opt::v) { $Global::verbose = $#opt::v+1; } # Convert -v -v to v=2
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if($opt::bug) { ::die_bug("test-bug"); }
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$Global::debug = $opt::D;
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$Global::shell = $ENV{'PARALLEL_SHELL'} || parent_shell($$)
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|| $ENV{'SHELL'} || "/bin/sh";
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@ -1419,7 +1421,7 @@ sub init_globals {
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# Bash ${a:2:3}
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'{:(\d+?):(\d+?)}' => '$_ = substr($_,$$1,$$2);',
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# Bash ${a#bc}
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'{#([^#][^}]*?)}' => 's/^$$1//;',
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'{#([^#}][^}]*?)}' => 's/^$$1//;',
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# Bash ${a%def}
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'{%([^}]+?)}' => 's/$$1$//;',
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# Bash ${a/def/ghi} ${a/def/}
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@ -3674,7 +3676,7 @@ sub onall {
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((defined $opt::timeout) ? "--timeout ".$opt::timeout : ""),
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((defined $opt::ungroup) ? "-u" : ""),
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((defined $opt::tee) ? "--tee" : ""),
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((defined $opt::workdir) ? "--wd ".$opt::workdir : ""),
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((defined $opt::workdir) ? "--wd ".::shell_quote_scalar($opt::workdir) : ""),
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(@Global::transfer_files ? map { "--tf ".::shell_quote_scalar($_) }
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@Global::transfer_files : ""),
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(@Global::ret_files ? map { "--return ".::shell_quote_scalar($_) }
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@ -4089,7 +4091,10 @@ sub die_bug {
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my $bugid = shift;
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print STDERR
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("$Global::progname: This should not happen. You have found a bug.\n",
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"Please contact <parallel\@gnu.org> and include:\n",
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"Please contact <parallel\@gnu.org> and follow\n",
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"https://www.gnu.org/software/parallel/man.html#REPORTING-BUGS\n",
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"\n",
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"Include this in the report:\n",
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"* The version number: $Global::version\n",
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"* The bugid: $bugid\n",
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"* The command line being run\n",
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@ -866,71 +866,292 @@ opposite GNU B<parallel> B<rush> does not clean up, if the process
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dies abnormally.
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B<rush> has some string manipulations that can be emulated by putting
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this into ~/.parallel/config (% is used instead of ^):
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this into ~/.parallel/config (/ is used instead of %, and % is used
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instead of ^ as that is closer to bash's ${var%postfix}):
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--rpl '{:} s:(\.[^/]+)*$::'
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--rpl '{:%([^}]+?)} s:$$1(\.[^/]+)*$::'
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--rpl '{/:%([^}]*?)} s:.*/(.*)$$1(\.[^/]+)*$:$1:'
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--rpl '{/:} s:(.*/)?([^/.]+)(\.[^/]+)*$:$2:'
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--rpl '{@(.*?)} /$$1/ and $_=$1;'
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Here are the examples from B<rush>'s website with the equivalent
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command in GNU B<parallel>.
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=head3 1. Simple run, quoting is not necessary
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$ seq 1 3 | rush echo {}
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$ seq 1 3 | parallel echo {}
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=head3 2. Read data from file (`-i`)
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$ rush echo {} -i data1.txt -i data2.txt
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$ cat data1.txt data2.txt | parallel echo {}
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=head3 3. Keep output order (`-k`)
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$ seq 1 3 | rush 'echo {}' -k
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$ seq 1 3 | parallel -k echo {}
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Here are the examples from B<rush>'s website:
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=head3 4. Timeout (`-t`)
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B<1> seq 1 10 | rush echo {}
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$ time seq 1 | rush 'sleep 2; echo {}' -t 1
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B<1> seq 1 10 | parallel echo {}
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$ time seq 1 | parallel --timeout 1 'sleep 2; echo {}'
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B<2> seq 1 10 | rush 'echo {}' -k
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=head3 5. Retry (`-r`)
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B<2> seq 1 10 | parallel -k 'echo {}'
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$ seq 1 | rush 'python unexisted_script.py' -r 1
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B<3> seq 1 | rush 'sleep 2; echo {}' -t 1
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$ seq 1 | parallel --retries 2 'python unexisted_script.py'
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B<3> seq 1 | parallel --timeout 1 'sleep 2; echo {}'
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Use B<-u> to see it is really run twice:
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B<4> seq 1 | rush 'python script.py' -r 3
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$ seq 1 | parallel -u --retries 2 'python unexisted_script.py'
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B<4> seq 1 | parallel --retries 4 'python script.py'
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=head3 6. Dirname (`{/}`) and basename (`{%}`) and remove custom
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suffix (`{^suffix}`)
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B<5> echo dir/file_1.txt.gz | rush 'echo {/} {%} {^_1.txt.gz}'
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$ echo dir/file_1.txt.gz | rush 'echo {/} {%} {^_1.txt.gz}'
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B<5> echo dir/file_1.txt.gz | parallel --plus 'echo {//} {/} {%_1.txt.gz}'
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$ echo dir/file_1.txt.gz |
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parallel --plus echo {//} {/} {%_1.txt.gz}
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B<6> echo dir.d/file.txt.gz | rush 'echo {.} {:} {%.} {%:}'
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=head3 7. Get basename, and remove last (`{.}`) or any (`{:}`) extension
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B<6> echo dir.d/file.txt.gz | parallel 'echo {.} {:} {/.} {/:}'
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$ echo dir.d/file.txt.gz | rush 'echo {.} {:} {%.} {%:}'
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B<7> echo 12 file.txt dir/s_1.fq.gz | rush 'echo job {#}: {2} {2.} {3%:^_1}'
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$ echo dir.d/file.txt.gz | parallel 'echo {.} {:} {/.} {/:}'
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B<7> echo 12 file.txt dir/s_1.fq.gz | parallel --colsep ' ' 'echo job {#}: {2} {2.} {3/:%_1}'
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=head3 8. Job ID, combine fields index and other replacement strings
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B<8> echo a=b=c | rush 'echo {1} {2} {3}' -d =
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$ echo 12 file.txt dir/s_1.fq.gz |
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rush 'echo job {#}: {2} {2.} {3%:^_1}'
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B<8> echo a=b=c | parallel --colsep = 'echo {1} {2} {3}'
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$ echo 12 file.txt dir/s_1.fq.gz |
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parallel --colsep ' ' 'echo job {#}: {2} {2.} {3/:%_1}'
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B<9> echo a=b=c | rush -D "=" -k 'echo {}'
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=head3 9. Capture submatch using regular expression (`{@regexp}`)
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B<9> echo -n a=b=c | parallel -d "=" -k 'echo {}'
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$ echo read_1.fq.gz | rush 'echo {@(.+)_\d}'
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B<9a> echo abc | rush -D "" -k 'echo {}'
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$ echo read_1.fq.gz | parallel 'echo {@(.+)_\d}'
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B<9a> echo -n abc | parallel --pipe --recend '' --block 1 -k parallel echo
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=head3 10. Custom field delimiter (`-d`)
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B<10> seq 1 | rush 'echo Hello, {fname} {lname}!' -v fname=Wei -v lname=Shen
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$ echo a=b=c | rush 'echo {1} {2} {3}' -d =
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B<10> seq 1 | parallel -N0 'fname=Wei; lname=Shen; echo Hello, ${fname} ${lname}!'
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$ echo a=b=c | parallel -d = echo {1} {2} {3}
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B<11> echo read_1.fq.gz | rush -v p={:^_1} 'echo {p} {p}_2.fq.gz'
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=head3 11. Send multi-lines to every command (`-n`)
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B<11> echo read_1.fq.gz | parallel 'p={:%_1}; echo ${p} ${p}_2.fq.gz'
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$ seq 5 | rush -n 2 -k 'echo "{}"; echo'
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B<12> seq 1 3 | rush 'sleep {}; echo {}' -c -t 2
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$ seq 5 |
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parallel -n 2 -k \
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'echo {=-1 $_=join"\n",@arg[1..$#arg] =}; echo'
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B<12> seq 1 3 | parallel --joblog mylog --timeout 2 'sleep {}; echo {}'
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$ seq 5 | rush -n 2 -k 'echo "{}"; echo' -J ' '
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B<12> Followed by:
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$ seq 5 | parallel -n 2 -k 'echo {}; echo'
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B<12> seq 1 3 | parallel --joblog mylog --retry-failed 'sleep {}; echo {}'
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=head3 12. Custom record delimiter (`-D`), note that empty records are not used.
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$ echo a b c d | rush -D " " -k 'echo {}'
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$ echo a b c d | parallel -d " " -k 'echo {}'
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$ echo abcd | rush -D "" -k 'echo {}'
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Cannot be done by GNU Parallel
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$ cat fasta.fa
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>seq1
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tag
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>seq2
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cat
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gat
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>seq3
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attac
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a
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cat
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$ cat fasta.fa | rush -D ">" \
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'echo FASTA record {#}: name: {1} sequence: {2}' -k -d "\n"
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# rush fails to join the multiline sequences
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$ cat fasta.fa | (read -n1 ignore_first_char;
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parallel -d '>' --colsep '\n' echo FASTA record {#}: \
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name: {1} sequence: '{=2 $_=join"",@arg[2..$#arg]=}'
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)
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=head3 13. Assign value to variable, like `awk -v` (`-v`)
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$ seq 1 |
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rush 'echo Hello, {fname} {lname}!' -v fname=Wei -v lname=Shen
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$ seq 1 |
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parallel -N0 \
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'fname=Wei; lname=Shen; echo Hello, ${fname} ${lname}!'
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$ for var in a b; do \
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$ seq 1 3 | rush -k -v var=$var 'echo var: {var}, data: {}'; \
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$ done
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In GNU B<parallel> you would typically do:
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$ seq 1 3 | parallel -k echo var: {1}, data: {2} ::: a b :::: -
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If you I<really> want the var:
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$ seq 1 3 |
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parallel -k var={1} ';echo var: $var, data: {}' ::: a b :::: -
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If you I<really> want the B<for>-loop:
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$ for var in a b; do
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> export var;
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> seq 1 3 | parallel -k 'echo var: $var, data: {}';
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> done
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Contrary to B<rush> this also works if the value is complex like:
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My brother's 12" records
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=head3 14. B<Preset variable> (`-v`), avoid repeatedly writing verbose replacement strings
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# naive way
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$ echo read_1.fq.gz | rush 'echo {:^_1} {:^_1}_2.fq.gz'
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$ echo read_1.fq.gz | parallel 'echo {:%_1} {:%_1}_2.fq.gz'
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# macro + removing suffix
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$ echo read_1.fq.gz |
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rush -v p='{:^_1}' 'echo {p} {p}_2.fq.gz'
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$ echo read_1.fq.gz |
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parallel 'p={:%_1}; echo $p ${p}_2.fq.gz'
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# macro + regular expression
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$ echo read_1.fq.gz | rush -v p='{@(.+?)_\d}' 'echo {p} {p}_2.fq.gz'
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$ echo read_1.fq.gz | parallel 'p={@(.+?)_\d}; echo $p ${p}_2.fq.gz'
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Contrary to B<rush> GNU B<parallel> works with complex values:
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echo "My brother's 12\"read_1.fq.gz" |
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parallel 'p={@(.+?)_\d}; echo $p ${p}_2.fq.gz'
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=head3 15. Interrupt jobs by `Ctrl-C`, rush will stop unfinished
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commands and exit.
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$ seq 1 20 | rush 'sleep 1; echo {}'
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^C
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$ seq 1 20 | parallel 'sleep 1; echo {}'
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^C
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=head3 16. Continue/resume jobs (`-c`). When some jobs failed (by
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execution failure, timeout, or cancelling by user with `Ctrl + C`),
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please switch flag `-c/--continue` on and run again, so that `rush`
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can save successful commands and ignore them in **NEXT** run.
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$ seq 1 3 | rush 'sleep {}; echo {}' -t 3 -c
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$ cat successful_cmds.rush
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$ seq 1 3 | rush 'sleep {}; echo {}' -t 3 -c
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$ seq 1 3 | parallel --joblog mylog --timeout 2 \
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'sleep {}; echo {}'
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$ cat mylog
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$ seq 1 3 | parallel --joblog mylog --retry-failed \
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'sleep {}; echo {}'
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Multi-line jobs:
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$ seq 1 3 | rush 'sleep {}; echo {}; \
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echo finish {}' -t 3 -c -C finished.rush
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$ cat finished.rush
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$ seq 1 3 | rush 'sleep {}; echo {}; \
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echo finish {}' -t 3 -c -C finished.rush
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$ seq 1 3 |
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parallel --joblog mylog --timeout 2 'sleep {}; echo {}; \
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echo finish {}'
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$ cat mylog
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$ seq 1 3 |
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parallel --joblog mylog --retry-failed 'sleep {}; echo {}; \
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echo finish {}'
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=head3 17. A comprehensive example: downloading 1K+ pages given by
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three URL list files using `phantomjs save_page.js` (some page
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contents are dynamicly generated by Javascript, so `wget` does not
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work). Here I set max jobs number (`-j`) as `20`, each job has a max
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running time (`-t`) of `60` seconds and `3` retry changes
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(`-r`). Continue flag `-c` is also switched on, so we can continue
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unfinished jobs. Luckily, it's accomplished in one run :)
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$ for f in $(seq 2014 2016); do \
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$ /bin/rm -rf $f; mkdir -p $f; \
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$ cat $f.html.txt | rush -v d=$f -d = \
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'phantomjs save_page.js "{}" > {d}/{3}.html' \
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-j 20 -t 60 -r 3 -c; \
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$ done
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GNU B<parallel> can append to an existing joblog with '+':
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$ rm mylog
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$ for f in $(seq 2014 2016); do
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/bin/rm -rf $f; mkdir -p $f;
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cat $f.html.txt |
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parallel -j20 --timeout 60 --retries 4 --joblog +mylog \
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--colsep = \
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phantomjs save_page.js {1}={2}={3} '>' $f/{3}.html
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done
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=head3 18. A bioinformatics example: mapping with `bwa`, and
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processing result with `samtools`:
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$ ref=ref/xxx.fa
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$ threads=25
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$ ls -d raw.cluster.clean.mapping/* \
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| rush -v ref=$ref -v j=$threads -v p='{}/{%}' \
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'bwa mem -t {j} -M -a {ref} {p}_1.fq.gz {p}_2.fq.gz > {p}.sam; \
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samtools view -bS {p}.sam > {p}.bam; \
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samtools sort -T {p}.tmp -@ {j} {p}.bam -o {p}.sorted.bam; \
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samtools index {p}.sorted.bam; \
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||||
samtools flagstat {p}.sorted.bam > {p}.sorted.bam.flagstat; \
|
||||
/bin/rm {p}.bam {p}.sam;' \
|
||||
-j 2 --verbose -c -C mapping.rush
|
||||
|
||||
GNU B<parallel> would use a function:
|
||||
|
||||
$ ref=ref/xxx.fa
|
||||
$ export ref
|
||||
$ thr=25
|
||||
$ export thr
|
||||
$ bwa_sam() {
|
||||
p="$1"
|
||||
bam="$p".bam
|
||||
sam="$p".sam
|
||||
sortbam="$p".sorted.bam
|
||||
bwa mem -t $thr -M -a $ref ${p}_1.fq.gz ${p}_2.fq.gz > "$sam"
|
||||
samtools view -bS "$sam" > "$bam"
|
||||
samtools sort -T ${p}.tmp -@ $thr "$bam" -o "$sortbam"
|
||||
samtools index "$sortbam"
|
||||
samtools flagstat "$sortbam" > "$sortbam".flagstat
|
||||
/bin/rm "$bam" "$sam"
|
||||
}
|
||||
$ export -f bwa_sam
|
||||
$ ls -d raw.cluster.clean.mapping/* |
|
||||
parallel -j 2 --verbose --joblog mylog bwa_sam
|
||||
|
||||
=head3 Other B<rush> features
|
||||
|
||||
B<rush> has:
|
||||
|
||||
|
|
@ -978,6 +1199,13 @@ With GNU B<parallel> this can be emulated by:
|
|||
|
||||
parallel --plus echo '{%.bar.gz}' ::: foo.ext.bar.gz
|
||||
|
||||
=item {@regexp}, capture submatch using regular expression
|
||||
|
||||
With GNU B<parallel> this can be emulated by:
|
||||
|
||||
parallel --rpl '{@(.*?)} /$$1/ and $_=$1;' \
|
||||
echo '{@\d_(.*).gz}' ::: 1_foo.gz
|
||||
|
||||
=item {%.}, {%:}, basename without extension
|
||||
|
||||
With GNU B<parallel> this can be emulated by:
|
||||
|
|
@ -1015,7 +1243,8 @@ double space, ' and ":
|
|||
|
||||
=item * Commands of multi-lines
|
||||
|
||||
To improve readibilty GNU B<parallel> encourages not to use multi-line
|
||||
While you I<can> use multi-lined commands in GNU B<parallel>, to
|
||||
improve readibilty GNU B<parallel> encourages not to use multi-line
|
||||
commands. In most cases it can be written as a function:
|
||||
|
||||
seq 1 3 | parallel --timeout 2 --joblog my.log 'sleep {}; echo {}; \
|
||||
|
|
|
|||
|
|
@ -1077,7 +1077,7 @@ users:
|
|||
https://lists.gnu.org/archive/html/parallel/2013-11/msg00006.html
|
||||
|
||||
There is no doubt that this is not an ideal solution, but no one has
|
||||
so far come up with an ideal solution - neither for maintaining GNU
|
||||
so far come up with an ideal solution - neither for funding GNU
|
||||
B<parallel> nor other free software.
|
||||
|
||||
If you believe you have the perfect solution, you should try it out,
|
||||
|
|
|
|||
Loading…
Reference in a new issue