Hello Sachit,
For now, these are in the Galaxy Distribution at
http://bitbucket.org/galaxy/galaxy-dist. Look under:
tools / ngs_rna / tophat2*
tools / sr_mapping / bowtie2*
I believe that they will be migrated to the Galaxy Main Tool Shed
sometime soon: http://toolshed.g2.bx.psu.edu/
Hi everyone,
I am Didier Zoccola and i am marine biologist working on corals. I would like
to do a illumina mapping from RNA-seq coming from environmental conditions. For
that, i would like to use Bowtie but i have not a reference genome. We have
done a de novo transcriptome using trinity
I am getting this error in Bowtie2 and Tophat2:
Data table named 'bowtie2_indexes' is required by tool but not configured
Data table named 'tophat2_indexes' is required by tool but not configured.
How can I solve it? Thanks
___
The Galaxy
You'll need to update the tool_data_table_conf.xml file in your Galaxy home
directory.
If you haven't made changes to the file, you can copy
tool_data_table_conf.xml.sample to tool_data_table_conf.xml If you have made
changes, add these entries to the file:
--
table name=bowtie2_indexes
Thanks but after adding those lines when I stop and started the server
using --daemon mode, the server is not working? What might be the problem?
On Fri, Oct 19, 2012 at 9:01 AM, Jeremy Goecks jeremy.goe...@emory.eduwrote:
You'll need to update the tool_data_table_conf.xml file in your Galaxy
Hello ,
I tried everything possible according to the reply I got from Jen , helping
me fix my problem but is not working.Please see below .
Is it possible that because the usage shows 91% I am not able to retrieve
anything back to display? Might sound ridiculous but
have no clue !! I still have
Hello Didier,
A custom reference genome can be used with the RNA-seq tools. In short,
you load a fasta file (your custom reference genome) using FTP to the
public Galaxy server, then select it for use with the tools (genome
from the history). Help is in our wiki:
On Oct 18, 2012, at 1:43 AM, Todd Oakley wrote:
Yes, daemon/stop-daemon is the best way. However, to stop a process that was
not started with --daemon, this is what I do:
ps aux | grep galaxy
Identify the process numbers for 3 Galaxy processes, which will change every
time Galaxy is
I have had it happen occasionally, but didn't pay attention to the
details. Perhaps I forget to put --reload sometimes. Also, it seems
that sometimes the Galaxy processes do not all stop with --stop-daemon.
I wrote the text below as a recipe for people in my lab to restart in
those
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