Contents: Click a blue triangle to expand or collapse a list

• Downloads and Links for the Scriptome
• Command-line Scriptome Executables
• Feedback and Mailing Lists

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Downloads and Links for the Scriptome

Command-line Scriptome Executables

These programs allow you to run Scriptome tools from a Windows/Mac/UNIX command line without browsing the web pages. Click below to download Scriptome and ScriptPack:

Download Scriptome command-line executables

Requirements: You need to have the HTML::Tree module installed. This is automatically installed as part of ActiveState (Windows Perl), and will be installed on many UNIX machines as well. If you don't have it, you can download it from CPAN. Go to http://search.cpan.org and type HTML::Tree into the search box; click on the first link, then click on the "Download" link and follow the instructions.

Installation: Scriptome_exe.tar.gz has four files inside. Put Scriptome and ScriptPack into a directory that is in your PATH. If you're using Windows, then also put the two .bat files into that same directory.

That's it! Ask the mailing list if you have questions.

Usage: Just input a tool name and input and output file names. The program will ask you for any needed parameters (if you didn't enter them using the -p flag), then run the code for the tool as if you had cut and paste it from the website. For more information, type Scriptome -h.

Examples:

 # List names and short descriptions of all 'change' tools
        Scriptome -t change

 # Change FASTA file to tabular file. No parameters needed, just filenames
        Scriptome -t change_fasta_to_tab in.fasta > out.tab

 # Choose first and third column from tabular file (Columns start at 0!)
        Scriptome -t choose_cols -p '@cols=(0, 2)' all_cols.tab > some.tab

 # Choose first & third column, same as above - interactive version.
 # Results will be the same as using -p above
        Scriptome -t choose_cols all_cols.tab > some.tab
 # The program asks you to enter paramaters
        @cols = [ Hit Enter to use (1, -1, 2) ]:
 # Type in (0, 2), including the paretheses, and hit Enter
        @cols = [ Hit Enter to use (1, -1, 2) ]: (0, 2)

Scriptome and ScriptPack work exactly the same way. The only difference is that Scriptome actually goes to the Scriptome website to retrieve the tool code. Scriptpack contains a copy of all the tools, so it does not require Internet access to function.

Feedback and Mailing Lists

The best place to discuss the Scriptome is the Scriptome-users mailing list. It's a good place to ask how to solve a certain problem using the Scriptome, or to suggest ways the Scriptome could be better. Subscribe or see archives at http://bioinformatics.org/mailman/listinfo/scriptome-users.

There is also a very low-traffic announcement-only mailing list about major updates or changes to the Scriptome. Subscribe or see archives at http://bioinformatics.org/mailman/listinfo/scriptome-announce.

Submit bug reports at http://bioinformatics.org/bugs/.