Contents: Click a blue triangle to expand or collapse a list
Are you using the Scriptome on UNIX/Mac or Windows? Decide this based on where
your data is sitting. So, for example, if you're sitting at a Windows machine,
using telnet (or putty, or whatever) to access a UNIX machine that has your
data on it, use the UNIX tools.
You do not need to install or download these tools; you just cut
and paste each tool into a terminal window.
A few of the tools
use Bioperl. If you do bio, you may already have Bioperl installed, but if you
get an error message like "Can't find Bio::something.pm in ..." then you may
need to download it from http://bioperl.org.
Note: if you're sitting at a Windows machine, but your data is on a UNIX
computer that you log into (with ssh, telnet, etc.) then use the UNIX tools.
On Windows machines you probably need to install Perl. It's a free
download from http://www.activestate.com/Products/ActivePerl/ and
a one-click install.
If you're using UNIX or Mac, you already have Perl. For a few tools, you may
need to download Bioperl from http://bioperl.org.
Scriptome tools are little UNIX/Mac or Windows commands. You run them by
cutting and pasting from the website onto the "command line". To get a
command line, you need to:
- UNIX
-
Open a terminal or xterm (or telnet or Putty from elsewhere).
- Mac OS X
-
Open a terminal window. (In the Finder, go to File->Find, and search for
"Terminal". The icon looks like a computer monitor.)
- Windows
-
Open a Command prompt: Open your Start menu, go to Run, type cmd, and
click OK.
Now use the "cd" command to change directories to where your data is sitting.
For example, cd my/data/directory.
Solve all of my data manipulation problems with just one tool that
takes two important parameters
As you can see, the Scriptome tools are in colored boxes. (The boxes are
green for Windows, Blue for Unix. On some versions of
IE, the boxes aren't colored. But they still have a dashed line around them,
and a larger margin than the rest of the text.)
The parameters that you might want to change - such as filenames, which
column to read in tabular data, etc. - are written in bold, red text in the
box. (Most scripts have one or two input files, an output file, and one or two
other parameters. Others have fewer parameters.) The other stuff is gray, which
means you can safely ignore it, unless you want to learn some Perl.
Use the form above the box to edit the parameters as needed. When you change
the text in the form, the text of the tool in the colored box will be
updated.
Cut and paste the text of the tool - i.e., everything in the colored box - onto
the command line. Go ahead, try it! Then look at what the tool prints to
the screen, and what it puts in the output file you specified. (This tool
doesn't actually care whether the input files exist.)
The "Expand code" button inside the colored box is not required for using the
tool. If you click it, the tool's Perl code is split onto many lines. You won't
be able to cut and paste this tool onto the command line, but this format is
much more readable. This is useful for people who want to see exactly what
the tool is doing, or learn a bit of Perl. Click the "Shrink code" button
to collapse the tool again.
The tools for Windows are a tiny bit different from the Unix/Mac tools.
(See the FAQ.)
Use the links in the top left of the page to switch from Unix/Mac to
Windows and back. The page colors (and the upper left of the page) will
let you know which section of the site you're in.
All scripts that work on tabular data assume the data is tab-separated.
Use a Change script to change, e.g.,
comma-separated data to tab-separated before using these scripts.
Or save Excel files as tab-separated.
When working with tabular data, remember that the first column is called
column 0, NOT 1. (Sorry.) The second column is column 1, the third is 2, etc.
As a shortcut, the last column can also be referred to as column -1,
second-to-last column is -2, etc.
More tips are available on the Tips Page.
A protocol is a series of steps to solve a biological problem,
such as extracting DNA:
http://www.genome.ou.edu/protocol_book/protocol_partI.html. A Scriptome
protocol is a series of steps that are used to solve a data manipulation
problem. Each step is carried out by running a Scriptome tool - often by
running the tool on the output generated in an earlier step in the protocol.
This site has "canned" protocols for Sequence Analysis
or Microarray Data. The protocols are just lists of atoms
in a row, and are used the same way an atom is. Namely, cut and paste
everything in the colored box onto the Unix/Mac/Windows command line.
If you're less brave, cut and paste the single tools one at a time.
This will allow you to edit each tool before executing it.
If you want to edit the filenames or other parameters in a protocol,
you'll need to paste the protocol into a text editor or Word, edit, and
then cut and paste from there onto the command line.
You can add a tool into the middle of a protocol by (using a text editor,
as described above and) pasting the tool in. Or you can build a protocol
from scratch.
