hisakatha / klab

Kasahara lab. public repository.

klab

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.

Installation

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

or::

$ ./configure --enable-perl

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

List

name	type	description	note
fatt	bio	FASTA/FASTQ manipulation tool.	see also doc/fatt.md
sieve	general	Random sampling of text files.	maybe useful for cross-validation
convertsequence	bio	Format conversion of sequence files.	see also perldoc
fixshebang	general	Fix shebang lines.	see also perldoc
gcc-color	general	Color the output of gcc/g++.	not extensively used.
icc-color	general	Color the output of Intel C++.
mydaemon	general	Automatically set ups crontab to ensure your daemon is running. (Works without root)
rep	general	Simple wrapper for different VCS such as svn/git/hg.	see also perldoc
sq	general	Execute SQL queries over CSV files.	see also perldoc. requires a bunch of Perl modules. DBD::CSV is required.
mddoc	general	Simple wrapper to view formatted Markdown (and restructured) texts via text browser	Requires Markdown.pl or pandoc.
gmddoc	general	Simple wrapper to view formatted GitHub-flavored Markdown via (graphic) web browser	Requires grip (python module).
sha_scan	general	Find duplicated files by collecting SHA1 hashes of files in a given directory.
rep	general	Repository utilitiy (one command, manage svn/cvs/git/hg at once!)
gfwhere	general	Find inconsistently replicated files in GlusterFS
json2csv	general	Convert JSON into CSV
csv2html	general	Convert CSV into HTML
csv2md	general	Convert CSV into a table in Markdown extra

Licenses

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/).