Kasahara lab. public repository.
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This public repository contains a suite of programs that are used in research in Kasahara lab.

The programs include various codes such as small utilities or tools for bioinformatics.


This package follows the standard installation process of waf::

$ ./waf configure
$ ./waf build
$ ./waf install

If you like GNU autotools-style configure, you can instead do like this::

$ ./configure
$ make
$ make install

although these commands are just a wrapper for the former commands.

When you wish to use scripts that use Perl modules, you need to add --enable-perl for waf configure, namely::

$ ./waf configure --enable-perl


$ ./configure --enable-perl

You may need to be root for installing the Perl libraries.


fattbioFASTA/FASTQ manipulation tool.see also doc/fatt.md
sievegeneralRandom sampling of text files.maybe useful for cross-validation
convertsequencebioFormat conversion of sequence files.see also perldoc
fixshebanggeneralFix shebang lines.see also perldoc
gcc-colorgeneralColor the output of gcc/g++.not extensively used.
icc-colorgeneralColor the output of Intel C++.
mydaemongeneralAutomatically set ups crontab to ensure your daemon is running. (Works without root)
repgeneralSimple wrapper for different VCS such as svn/git/hg.see also perldoc
sqgeneralExecute SQL queries over CSV files.see also perldoc. requires a bunch of Perl modules. DBD::CSV is required.
mddocgeneralSimple wrapper to view formatted Markdown (and restructured) texts via text browserRequires Markdown.pl or pandoc.
gmddocgeneralSimple wrapper to view formatted GitHub-flavored Markdown via (graphic) web browserRequires grip (python module).
sha_scangeneralFind duplicated files by collecting SHA1 hashes of files in a given directory.
repgeneralRepository utilitiy (one command, manage svn/cvs/git/hg at once!)
gfwheregeneralFind inconsistently replicated files in GlusterFS
json2csvgeneralConvert JSON into CSV
csv2htmlgeneralConvert CSV into HTML
csv2mdgeneralConvert CSV into a table in Markdown extra


The programs are licensed under the modified BSD Licenses unless otherwise stated in source code.

The princple is that 3rd party libraries and their derivatives are basically licensed under their original licenses, while what we developed from scratch are licensed under the modified BSD. The 3rd party libraries include SQLite3 (http://www.sqlite.org/), sqdbcpp (http://code.google.com/p/sqdbcpp/).