Installing the PipTools Programs (mostly-C version)
TABLE OF CONTENTS
- Make sure you have the necessary software available on your system:
- An ANSI-compatible C compiler.
The PipTools programs are very simple, so just about any C or C++
compiler will do. If you are on a Unix-like system, you almost
certainly have one already (we used gcc ).
For Win32 systems, one option is to install the free
Cygwin package, which
provides common Unix development tools (including
gcc and make )
together with a DLL that allows them to run under Windows.
- The make utility.
This is a standard tool for automating compilation and
installation tasks based on instructions provided in a
"Makefile" . Unix-like systems, Cygwin, and
most C compilers will already include this, but if for some reason
you don't have it, you can still compile the programs manually.
- Perl.
Three of the tools ( genbank2exons ,
genbank2repeats , and
sort-exons ) are written in the Perl language,
so if you want to run them you will need a Perl interpreter (see
the Perl Home Page for more
information).
- The Boulder::Genbank module.
This is a Perl module that is used by
genbank2exons and
genbank2repeats to read GenBank files.
You can download it from the
Stein Laboratory.
- Download
piptools.zip and unpack it into a separate directory
or folder. We provide this file in a DOS-style PKZIP-compatible format,
because most platforms have readily available tools for handling this
(e.g., unzip on Unix.) Make sure your unzipper
program recreates the subdirectory structure (e.g., by using
pkunzip -d ).
- Examine the Makefile and
piplib/Makefile , and adjust them as necessary
for your operating system, compiler, and desired file locations.
The provided sample files are for Unix and gcc .
- Run make , and then if everything went smoothly,
run make install .
- Arrange for the Perl interpreter to be executed when you run the tools
that need it. On Unix-like systems that support the
"#!" syntax, this means making sure each program
file is executable, and adjusting the path to perl
in the first line. On other systems, you may need to set up wrapper
scripts, or remember to type perl -S at the
beginning of each command.
- Make sure the installed program files are in your path, so your
operating system can find them when you try to run them from another
directory or folder.
Cathy Riemer, January 2002