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The beauty of screen
How to launch analyses in background on a *nix system ? You can use the « & » at the end of your command, but the screen output of your analyses will be messy and you cannot close your session. You...
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XML::SAX conflict between Debian & CPAN
If you have made a previous install of XML::SAX via CPAN and then you try to install a debian package that required this module, you will probably get this error: Fatal: cannot call...
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*nix command line tips
One thing which is definitively amazing with *nix OS is that you always learn new things… Let have a look at these commands: bc : a nice command-line calculator… To my mind, I’ve always considered that...
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Control your jobs!
Let’s explain the situation: you have a lot of analyses to compute on your SMP computer (same analysis on different files, many different analyses or same analysis many times, for simulation purpose,...
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UNIX & PERL starter kit…
If you’re looking for a nice introductory lesson to learn the basis of UNIX commands and PERL programming aspects, I recommend you to get the PDF file that you would find on the Korf lab website. The...
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Flush file output
If you want to write something to a file (i.e write to a log file), PERL will handle a buffer and won’t write instantly to the file. In most case, this behaviour is the best (since writing to a file...
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How to mirror a FTP site?
For research purposes, I want to mirror the GEO directory of the NCBI FTP site. These data are huge: more than 1,000 annotation platforms files and more than 20,000 GSE files! Platforms files are...
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MacOS X 10.6.x, FINK, Macport, DBD::mysql and PERL…
Recently, I updated my laptop to snow leopard. After installing a bunch of softwares, I made some test with PERL… And then, with a PERL program working with a SQL database : dyld: lazy symbol binding...
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Code more shell scripts (Part. I)
I’ve noticed, that I didn’t code a lot using shell language: very few sh scripts (for multiple commands executions), only basic commands. It’s a mistake, since for file management (for instance), shell...
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Code more shell scripts (Part. II)
With NGS data, we are experiencing to handle very (very very) large datasets. Whatever the coding language used (PERL, python, C…), the open/read part of a program is (always) very slow. Thus, the...
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