[BiO BB] program for sequence length

[Bossers, Alex]

For simple joining up manipulation and analysis tools into workflows
(without programming experience) have a look at Galaxy developed by
PennState University (http://galaxy.psu.edu/). You can have a local
instance but there are also public instances available (all free).
http://main.g2.bx.psu.edu/ Including demonstration video snippets.
{This is no advertisement.... I am not associated in any way to the
group or development :)}
Almost all commandline scripts/utilities/services can be added quite
easy into the page by a simple config file.

Alex

-----Original Message-----
From: bbb-bounces at bioinformatics.org
[mailto:bbb-bounces at bioinformatics.org] On Behalf Of Karger, Amir
Sent: Tuesday, May 11, 2010 2:49 AM
To: General Forum at Bioinformatics.Org
Subject: Re: [BiO BB] program for sequence length

Scriptome has several purposes:
1) Help experienced coders avoid reinventing the wheel and silly bugs.
2) Help non-programmers do simple munging using cut and paste, without
learning how to program. (And by "simple" I mean somewhere between
Notepad find/replace and real programming.)
3) Help novice programmers get some examples of Perl idioms, or starting
points to work with. (I had this whole plan of commenting the tools, but
never got the tuits.)

Re #1, with the command-line Scriptome tool, so when I'm working with a
client (or even by myself) I can just do:
    Scriptome -t change_fasta_to_tab blah.fasta > blah.tab

And some of the merge and choose tools are great when exploring data.

And no, arguing about languages is only slightly less stupid than
fighting a land war in Asia.

-Amir
________________________________________
From: bbb-bounces at bioinformatics.org [bbb-bounces at bioinformatics.org] On
Behalf Of Mike Marchywka [marchywka at hotmail.com]
Sent: Friday, May 07, 2010 20:12
To: bbb at bioinformatics.org
Subject: Re: [BiO BB] program for sequence length

----------------------------------------
> From: akarger at CGR.Harvard.edu
> To: bbb at bioinformatics.org
> Date: Fri, 7 May 2010 09:36:49 -0400
> Subject: Re: [BiO BB] program for sequence length
>
> Check out the Scriptome (yes, this is an advertisement.) at
http://sysbio.harvard.edu/csb/resources/computational/scriptome/ , which
is a set of Perl one-liners you cut and paste onto your command line to
do bio-y text-y thigns.

I hadn't thought of this before but it is a good idea if you can search
it easily, I often use google for
sed/awk one liners for stuff like this and its a great way to learn the
tools and get your work done.
You seem to have a bit more than flat lists of one-liners but off hand
I'd think this would be
a generally good idea. Now to argue," you should have done that in
{perl,awk,sed,java,c++} instead of {perl, awk, sed, java, c++}"
LOL

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