Hi Nate
Thanks for the clarifications. Is there anything specific I should watch out
for when updating and deleting tools? The reason I ask is that Jennifer
mentioned in previous emails the need to update metadata for tools, which I am
sure I follow.
Thanks
Ravi
On Mar 14, 2014, at 9:02 AM, Nat
On Wed, Mar 5, 2014 at 8:18 PM, Ravi Alla wrote:
> Hi Jennifer,
> Thank you for this information. I was able to troubleshoot the
> bowtie2_indices. Like Bjoern said the bowtie2 tool needed to be reinstalled
> because the tool_table does not load the correct indices.
>
> I am still trying to wrap m
Hi Jennifer,
Thank you for this information. I was able to troubleshoot the bowtie2_indices.
Like Bjoern said the bowtie2 tool needed to be reinstalled because the
tool_table does not load the correct indices.
I am still trying to wrap my head around the different toolsheds.
The main tool shed
Hi Ravi,
The directory structure for the installation of ToolShed tools changed,
which is why you have three directories. You perhaps had bowtie2
installed once before, then reinstalled (without completely removing the
older version and associated data)? Or updated without resetting the
metad
Hi Ravi,
I checked and the bowtie2 tool repository had a misconfigured data table name
in its tool_data_table_conf.xml.sample file that was erroneously creating a
tophat2_indexes data table, whereas the tool itself uses bowtie2_indexes.
Can you try to uninstall and reinstall bowtie2 from the t
Bjoern,
This is getting frustrating.
There are three places bowtie2_indices.loc file is expected. I really don't
know which one is the one I should modify.
galaxy-dist/tool-data/bowtie2_indices.loc
galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/96d2e31a3938/bowtie2_indices.loc
Hi,
can you check if the file tool_data_table_conf.xml contains an entry
about bowtie2_indexes ... or the table shed_data_table_conf.xml ... in
one of them should be one entry with bowtie2_indexes.
That warning should not be there I think:
> galaxy.tools.parameters.dynamic_options WARNING 2
Hi Bjoern,
Please find the bowtie2 and bowtie .loc files. In the paster.log file I see
these entries for bowtie
galaxy.tools.data DEBUG 2014-03-04 10:14:11,048 Loaded tool data table
'bowtie_indexes'
galaxy.tools.data DEBUG 2014-03-04 10:14:11,051 Loading another instance of
data table 'bowtie_
Hi Ravi,
can you attach the loc file, do you see anything in the Galaxy log files
about bowtie2, try grepping for "bowtie2".
Cheers,
Bjoern
Am 04.03.2014 18:07, schrieb Ravi Alla:
Hi Bjoern,
Thank you for your clarifications. I have tried installing bowtie2 using both
variations, once with
Hi Bjoern,
Thank you for your clarifications. I have tried installing bowtie2 using both
variations, once with both wrapper and dependencies and once with only wrapper
(since I have dependencies installed on the system). In either case even after
editing the .loc file I cannot see the indices in
Hi Ravi,
Hi guys,
I am new to galaxy and am in the process of setting it up on a cluster with
some help. I am trying to install bowtie2 to my local galaxy through the
toolshed. I have a few questions.
- Which bowtie2 should I install? When I search for bowtie2 a bunch of results
come up?
O
Hi guys,
I am new to galaxy and am in the process of setting it up on a cluster with
some help. I am trying to install bowtie2 to my local galaxy through the
toolshed. I have a few questions.
- Which bowtie2 should I install? When I search for bowtie2 a bunch of results
come up?
- What are repo
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