Hi mates!!
I have a problem with Galaxy... FastQC doesn't run because the file FastQC.py
cann't find executable file FastQC.xml. Almost, that file is in the same
directory called rgenetics, (seeing Linux terminal) .
someone can help me?
thanks and have a nice day :)
Hi, Jorge,
Galaxy source includes the Galaxy interfaces but not the third party
executables for tools like fastqc or bwa. They can be automagically
installed if you install the tool from a tool shed but at a guess, you are
working on your desktop with the fastqc tool in a recent clone of galaxy?
thanks for the information Ross but I'm lost with the guide for the fastqc
tool. I don't understand how to resolve missing tool dependecies
Date: Mon, 9 Dec 2013 22:30:58 +1100
Subject: Re: [galaxy-user] Problem with executable file in FastQC
From: ross.laza...@gmail.com
To:
HI Jorge,
I am going to assume that you are working with a local instance, but
please correct us if that is wrong. Going forward, you will want to ask
local install questions at: galaxy-...@bx.psu.edu, as that is where the
development community is most active.
Lists:
Hello,
If the data was in .fastqsanger format, you could use the tool
Manipulate FASTQ, but with .fasta, this is a good way.
But watch your regular expression - test it out on a smaller set to make
sure it is doing what you want. I see a start of the line character in
the middle of your
Hi,
It indeed helps.Your regular expression looks brief and more useful.BTW, a
start of line (^) between [] and in the first location, for example,
[^ATCGatcg] means a character not [ATCGatcg], which maybe not work in the tool
SELECT.
Thank you for your help!
Date: Mon, 9 Dec 2013 06:34:28
Hello,
You are right! I forgot about that. Aren't regular expressions fun? And
please test it out, if you prefer your method or are just curious, I
didn't try it that way. There are usually a few ways to do the same
thing when using a regex.
But, I am glad that this helped a bit and good luck
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