commandlinefu.com

I just rediscovered this excellent site. Well worth the occasional browse:

• Commandlinefu - main page
• Commandlinefu_byvote - sorted by vote count

There are some real gems in there! For example:

> python -m SimpleHTTPServer
Serve current directory tree at http://$HOSTNAME:8000/

Useful for tiding up your workspace whilst keeping jobs running:

> disown -a && exit
Close shell keeping all subprocess running

I do love a bit of process substitution:

> diff <(sort file1) <(sort file2)
diff two unsorted files without creating temporary files

Handy:

> rm !(*.foo|*.bar|*.baz)
Delete all files in a folder that don't match a certain file extension

And a "I should have thought of this; it's so obvious now!" trick:

> some_very_long_and_complex_command # label

Easy and fast access to often executed commands that are very long
and complex. When using reverse-i-search you have to type some 
part of the command that you want to retrieve. However, if the
command is very complex it might be difficult to recall the parts
that will uniquely identify this command. Using the above trick
it's possible to label your commands and access them easily by 
pressing ^R and typing the label (should be short and descriptive).

Linux: command line cut and paste

It's always annoyed me that I have to open up a file in order to cut and paste the contents into a web browser (I use this a lot for capturing information on an internal wiki). As of 2010-03-23 there are no default command line access utilities for this (on CentOs anyway).

However, download and install xclip and the clipboard is yours to command.

xclip allows access to both the PRIMARY (middle mouse button) and SECONDARY (standard copy/paste) selections.

By default piping into xclip puts the text in the PRIMARY clipboard (middle mousebutton).

> echo $RANDOM | xclip
> xclip -o
4807

You can define which selection to input to. Say you want to store text in the SECONDARY selection (accessed using standard cut and paste commands):

> echo $RANDOM | xclip -sel 'clipboard'
> xclip -o -sel 'clipboard'
4807

You can now use edit->paste to output the text. Note that the random number was the same as before. I guess this is some shell caching mechanism. For a new random number each time you have to use a new shell:

> (echo $RANDOM) | cat
1297

Command line R

Sometimes I just want to print out a histogram from a file, or create a simple summary of some numeric data. It's good to be able to just bash off an R script from the command line to do this for you.

There are a couple of easy ways to invoke R to run in 'batch' mode (i.e. non-interactive):
1. R CMD BATCH <scriptname>
2. R --vanilla --slave <scriptname>

For 1. the output is saved in a file named <scriptname>.Rout, in 2. the output comes to STDOUT - which, for me, is much more useful.

Also, you can use the standard shell 'tricks' to create quick scripts without having to save a script file:

e.g.

1. Create a numeric summary of the input data (in this case for a file with the format - "name,value"):

R --vanilla --slave <<< "d=read.table('data.scores', sep=',');summary(d);q()"
V1
Min. :1.333
1st Qu.:4.037
Median :4.651
Mean :4.634
3rd Qu.:5.282
Max. :8.000


2. Create a histogram for the data and save to a PNG (don't forget to escape any special shell characters).

R --vanilla --slave <<< "d=read.table('data.scores', sep=',');png('data.png');hist(d\$V1);q()"


converting postscript to an image

This is something I've meant to learn how to do for ages. I needed to do this to produce summaries for a shit load of PDFs (containing related molecules) and wanted to have an image of a structure to represent each PDF. Anyway, I print structures as postscript files, so I needed a way to create a PNG of the first structure for each PDF.

I saw a few solutions on line which used ghostview to first output a jpeg and then 'mogrify' to cut down the hunormous result to something useful. It turns out you can just do this:

convert molecule.ps -trim molecule.png

This creates a png from the ps file. Blimey! Really simple!

The -trim tag is a great addition as well, since a direct conversion results in a lot of extra whitespace.

jvisualvm instead of kill -3

Whenever I need to see what's going on under the hood of a process I issue a kill -3 to get a stack-trace. Well, I was just introduced to jvisualvm! This is a great way to see what's going on with a running java process.

Histograms in gnuplot

I'm pretty new to gnuplot, but have found it to be a handy tool for simple plots.  

Today I needed to generate a simple histogram.  Rather than creating a permanent script I've just been piping a string into gnuplot from echo.

echo "set terminal png;\
 set output 'timings.png';\
 set style fill solid 0.5 border -1;\
 set xlabel 'chunks';\
 set ylabel 'time to complete (m)';\
 set key autotitle columnhead;\
 set title 'timings on 20 nodes';\
 set auto x;\
 plot 'timings.tsv' u 2:xticlabels(1) with boxes lt 2;"\
 |  gnuplot

and out pops a nice histogram (sorry, can't post this example as it's work related).

The input file had column headers and the first column was used as the xlabels (see the xticlabels call above?)