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...
View ArticleXML::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...
View Article*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...
View ArticleControl 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,...
View ArticleUNIX & 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...
View ArticleFlush 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...
View ArticleHow 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...
View ArticleMacOS 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...
View ArticleCode 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...
View ArticleCode 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...
View Article
More Pages to Explore .....