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GNU Parallel Bug Reports GNU Parallel 20130822 ('Compostela') released

From: Ole Tange
Subject: GNU Parallel Bug Reports GNU Parallel 20130822 ('Compostela') released
Date: Thu, 22 Aug 2013 18:02:56 +0200

GNU Parallel 20130822 ('Compostela') has been released. It is
available for download at: http://ftp.gnu.org/gnu/parallel/

It includes a big code reorganization making this release beta quality.

New in this release:

* A tutorial showing much of GNU Parallel's functionality. Spend an
hour walking through the tutorial. Your commandline will love you for
it. man parallel_tutorial

* --line-buffer will buffer output on line basis. --group keeps the
output together for a whole job. --ungroup allows output to mixup with
half a line coming from one job and half a line coming from another
job. --line-buffer fits between these two; it prints a full line, but
will allow for mixing lines of different jobs.

* --record-env records all variables and functions set. Useful to
record the normal environment before using --env _.

* --env _ exports all functions and variables to the remote server
except for the ones recorded.

* New signing key. Due to recommendations from NIST
http://www.keylength.com/en/4/ the signing key was changed from
1024D/ID:FFFFFFF1 to 9888R/ID:88888888.

* Agalma: an automated phylogenomics workflow http://arxiv.org/pdf/1307.6432

* Job ad asking for GNU Parallel expertise

* Transient Beowulf Clustering with GNU Parallel and SSHfs

* Aligning to unique regions

* Top 10 scripting tricks for basic bioinformatics

* Using GNU Parallel to speed up and simplify data analyzes

* Compression of files in parallel using GNU parallel

* Using GNU Parallel to roll-your-own Map Reduce! http://www.rankfocus.com/?p=1

* Using GNU Parallel with Amazon

* Some useful comments on GNU Parallel

* Using GNU Parallel to count reads mapping to genes for multiple BAMs

* TimeMachineっぽいバックアップスクリプト http://rio.tc/2013/07/timemachine-1.html

* GNU ParallelでAndroid NDKの全バージョンを一括ダウンロード

* Bug fixes and man page updates.

= About GNU Parallel =

GNU Parallel is a shell tool for executing jobs in parallel using one
or more computers. A job is can be a single command or a small script
that has to be run for each of the lines in the input. The typical
input is a list of files, a list of hosts, a list of users, a list of
URLs, or a list of tables. A job can also be a command that reads from
a pipe. GNU Parallel can then split the input and pipe it into
commands in parallel.

If you use xargs and tee today you will find GNU Parallel very easy to
use as GNU Parallel is written to have the same options as xargs. If
you write loops in shell, you will find GNU Parallel may be able to
replace most of the loops and make them run faster by running several
jobs in parallel. GNU Parallel can even replace nested loops.

GNU Parallel makes sure output from the commands is the same output as
you would get had you run the commands sequentially. This makes it
possible to use output from GNU Parallel as input for other programs.

You can find more about GNU Parallel at: http://www.gnu.org/s/parallel/

You can install GNU Parallel in just 10 seconds with: wget -O - pi.dk/3 | sh

Watch the intro video on http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1

Walk through the tutorial (man parallel_tutorial). Your commandline
will love you for it.

When using GNU Parallel for a publication please cite:

O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login:
The USENIX Magazine, February 2011:42-47.

= About GNU SQL =

GNU sql aims to give a simple, unified interface for accessing
databases through all the different databases' command line clients.
So far the focus has been on giving a common way to specify login
information (protocol, username, password, hostname, and port number),
size (database and table size), and running queries.

The database is addressed using a DBURL. If commands are left out you
will get that database's interactive shell.

When using GNU SQL for a publication please cite:

O. Tange (2011): GNU SQL - A Command Line Tool for Accessing Different
Databases Using DBURLs, ;login: The USENIX Magazine, April 2011:29-32.

= About GNU Niceload =

GNU niceload slows down a program when the computer load average (or
other system activity) is above a certain limit. When the limit is
reached the program will be suspended for some time. If the limit is a
soft limit the program will be allowed to run for short amounts of
time before being suspended again. If the limit is a hard limit the
program will only be allowed to run when the system is below the

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