bowtie-0.12.8 ,we should get rid of Bowtie2,and the same as tophat/tophat2,and
if we keep all of the functions ,all of these we need to installed,right?
shenwiyn
From: greg
Date: 2013-02-22 01:22
To: Jennifer Jackson
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Problem running
...@bx.psu.edu
*CC:* galaxy-dev@lists.bx.psu.edu mailto:galaxy-dev@lists.bx.psu.edu
*Subject:* Re: [galaxy-dev] Problem running Tophat for Illumina
Ok, you're right, I did ask something similar before.
So is the simplest answer is to tell users to use Tophat2 instead of
Tophat for Illumina
Hi Greg,
The problem here and the confusion between the Bowtie loc files are
likely related. Do you have both bowtie/bowtie2 and tophat/tophat2
installed? And the tool wrappers for all versions are active? I though
we resolved this earlier but maybe you installed a new tool or updated?
The
Ok, you're right, I did ask something similar before.
So is the simplest answer is to tell users to use Tophat2 instead of
Tophat for Illumina? Or is there anything special in Tophat for
Illumina that they would be missing out on?
-Greg
Here's some info I dug up in case it's useful:
which
Hi Greg,
This is a good start, you will want to do which on bowtie2 and tophat2
as well. Each should point to proper binary. You don't seem to have all
of them installed, specifically Tophat v1.3.3-1.4.0, which is what
Tophat for Illumina uses.
Correct binary for the path name. See the
