Hi Moritz
I am not a galaxy tool shed expert, but I recommend you start with
reading these wiki pages:
http://wiki.galaxyproject.org/Tool%20Shed
http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy
and then try installing BWA via the tool shed and ask (if any) specific
questions (
1. Thanks, I'll try this out, after you reavealed me which version I should
use :)
2. Originally I had this workflow to start with
https://main.g2.bx.psu.edu/u/mj--/w/ngs
, but I at the sam-to-bam conversion I get the "sequences are not currently
available for specified build" error when using "lo
Hey,
now I am having a new problem: *Convert SAM to BAM
*Tool execution generated the following error message:
[samopen] SAM header is present: 93 sequences.
Parse error at line 106: sequence and quality are inconsistent
/bin/sh: line 1: 27934 Aborted samtools view -bS
"/home/trr/
Hey,
with the "tool file" line I got it working :)
Thanks a lot. Could you answer the question regarding Tool Shed: "If I
would use Tool Shed, could I skip all these manual steps? Is the
installation of BWA with Tool Shed also this complicated or is it more
simle?"
Best
Moritz
On 17 July 2013 0
On Mon, Jul 22, 2013 at 10:40 AM, Moritz Juchler
wrote:
> Hey,
>
> now I am having a new problem: Convert SAM to BAM
> Tool execution generated the following error message:
>
> [samopen] SAM header is present: 93 sequences.
> Parse error at line 106: sequence and quality are inconsistent
> /bin/sh
Hey,
no thats correct I did not use Tool Shed. If I would use it, could I skip
all these manual steps? Is the installation of BWA with Tool Shed also this
complicated or is it more simle?
How did you not follow my steps :) I wrote down everything clearly, at
least thats what I was hoping.
And no
Hi Moritz
I am struggling to follow what exactly you have done. As far as I can
see, you did not use the toolshed
(http://wiki.galaxyproject.org/Tool%20Shed) to install the BWA alinger
tool, but did all manually?
If so, have you added the following line:
to the "tool_conf.xml" file, and
