EPOR is an extensible package organiser for Unix-like systems. It's written to trace filesystem changes (something being installed) and save this information in a simple text database (this, as any other provided feature, is customisable via the embedded Guile interpreter). Database entries contain information supplied by the command line (package name, version, etc.) and traced by filesystem changes (new directories, files, etc.). This is achieved using the "LD_PRELOAD method''.
ProteomeCommons.org IO Framework is a proper Java framework for handling spectra and peak lists. The framework can read and write to a number of different spectra and peak list formats, and it provides a simple, intuitive Java object model for working with spectra or peak lists. All classes support two methods of handling peak list and spectrum data: in-memory or stream. The goal of this framework is to support all the popular MS and MSMS data formats, and to eliminate any time or effort involved in figuring out how to read and write peak list or spectrum files.
tzls and tzx are commandline utilities for quickly unpacking or listing the contents of various types of common Unix archive files, which may be compressed in any of several ways. The supported compression types are bzip2, gzip, and compress. The supported archive types are tar, cpio, zip, rar, and arj. The tools are implemented as shell scripts, so no compilation is required.
fff and ffl are tools for searching for files and directories from the Unix shell with more integrated "shell-like" behaviour and simpler syntax than find(1), though find(1) is still used to perform the actual searches. In particular, there is no need to quote wildcards, and searches are case-insensitive. Matching results are shown one per line. fff displays full paths, and ffl relative paths. Detailed find(1) options can be appended to the fff/ffl command line if desired. These utilities are based entirely on shell aliases and functions, so no compliation is required.