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 toolshed and see if that will fix your problem?
More information on ways to debug this are below (wrote email before checking the repository):
You’ll need to check that the various location files are being loaded into the proper data tables, see:
https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables. Galaxy has 2 files that specify the link between a location file and a data table:
tool_data_table_conf.xml and
shed_tool_data_table_conf.xml, for distribution/locally defined data tables and shed installed data tables, respectively — these are merged together during run time for each named data table from the various specified location files.
Can you check these files to confirm that you have a data table named ‘bowtie2_indexes’ defined and that one of the files referenced from there has your additions?
Thanks for using Galaxy,
Dan
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
What is the difference between these 3 files?
I changed the 2nd file to include the path to the indices and this shows up as a valid preloaded index for tophat2 but does not for bowtie2. I also changed the normal bowtie_indices.loc file at the second location and this works and I can see the bowtie1 indices for that bowtie tool. Currently only the bowtie2 indices are acting up.
I wish this was easier.
Thanks
Ravi.
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.gruening@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.gruening@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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