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: [email protected] [mailto:[email protected]] 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: [email protected] [[email protected]] On Behalf Of Mike Marchywka [[email protected]] Sent: Friday, May 07, 2010 20:12 To: [email protected] Subject: Re: [BiO BB] program for sequence length ---------------------------------------- > From: [email protected] > To: [email protected] > 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 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
