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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