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 2014-03-04 10:14:33,335 Data table named 'bowtie2_indexes' is required by tool but not configured

Hope you can figure it out,
Bjoern

Am 04.03.2014 19:19, schrieb Ravi Alla:
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_indexes', attempting to merge content.
galaxy.tools.parameters.dynamic_options WARNING 2014-03-04 10:14:33,335 Data 
table named 'bowtie2_indexes' is required by tool but not configured

And ls -l /global/referenceData/databases/bowtie2/hg19 is
drwxr-xr-x 2 ralla cgrl      2048 Sep 10 11:14 .
drwxr-xr-x 3 ralla cgrl      2048 Sep 10 11:06 ..
-rw-rw-r-- 1 ralla cgrl 960018873 May  2  2012 hg19.1.bt2
-rw-rw-r-- 1 ralla cgrl 716863572 May  2  2012 hg19.2.bt2
-rw-rw-r-- 1 ralla cgrl      3833 May  2  2012 hg19.3.bt2
-rw-rw-r-- 1 ralla cgrl 716863565 May  2  2012 hg19.4.bt2
-rw-rw-r-- 1 ralla cgrl 960018873 May  2  2012 hg19.rev.1.bt2
-rw-rw-r-- 1 ralla cgrl 716863572 May  2  2012 hg19.rev.2.bt2

and ls -l /global/referenceData/databases/bowtie/hg19 is
drwxr-xr-x 2 ralla cgrl      2048 Mar  4 10:07 .
drwxr-xr-x 3 ralla cgrl      2048 Nov 30  2012 ..
-rw-rw-r-- 1 ralla cgrl 821725563 Nov 13  2009 hg19.1.ebwt
-rw-rw-r-- 1 ralla cgrl 357667968 Nov 13  2009 hg19.2.ebwt
-rw-rw-r-- 1 ralla cgrl      3284 Nov 13  2009 hg19.3.ebwt
-rw-rw-r-- 1 ralla cgrl 715335926 Nov 13  2009 hg19.4.ebwt
lrwxrwxrwx 1 ralla cgrl        45 Aug 21  2013 hg19.fa -> 
/global/referenceData/genomes/hs/hg19/hg19.fa
-rw-rw-r-- 1 ralla cgrl 821725563 Nov 13  2009 hg19.rev.1.ebwt
-rw-rw-r-- 1 ralla cgrl 357667968 Nov 13  2009 hg19.rev.2.ebwt

Thanks for looking into this.
Ravi.
On Mar 4, 2014, at 9:13 AM, Björn Grüning <bjoern.gruen...@gmail.com> wrote:

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 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 galaxy. I tried the same 
edits to .loc file with bwa and the indices show right up, but not with bowtie2 
and even bowtie for that matter. I really don't know what to do about this.
Thanks
Ravi
On Mar 4, 2014, at 3:06 AM, Björn Grüning <bjoern.gruen...@gmail.com> wrote:

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?

Only two, or? Please make sure you are using the main toolshed. bowtie2 and 
package_bowtie2_2_1_0 are connected together. One is the binary and the other 
contains the wrapper. Use devteam respositories is always a good choice.

- What are repository dependencies? Why would I need these if bowtie2 is 
already installed on my system?

repository dependecies containing all dependencies of your wrappers, that can 
be some binaries, but also R, Perl, python libraries that are needed to execute 
your wrappers. We recommend you to use the dependencies because then you have 
full control over all your used versions (wrapper, dependencies, tool) and that 
enables reproducibility. To put in other words: With the toolshed you can have 
different tool and wrappers versions with different dependencies at the same 
time.

- I have been installing bowtie2 by unchecking the repository dependencies and 
tool dependencies boxes. Is this correct?

It will work, if you have a system installed version. But you need to take care 
about binary updates by your own. And reproducibility of your results is not 
guaranteed.

- Finally when I install bowtie2 this way it creates 2 bowtie2_indices.loc 
files, one in galaxy/tool-data and the other in 
shed_tools/toolshed.g2.gx.psu.edu/dev/bowtie2, which one do I need to edit to 
point to my index files? No matter which one I change I can't seem to see the 
indices.

That is strange. Are you sure you don't have a spelling mistake in it. It 
should be the bowtie2_indices.los I think. I will CC Greg, he is one of the 
Tool Shed Developers and should know more about it.
Please do not forget to restart your Galaxy instance once you have update the 
*loc files.

I hope someone on here can help me out.

Hope it helped a little bit,
Bjoern

Thanks a lot
Ravi.
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