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 metadata? In either case, the ../shed_tools directory is the new one. Having this as the path in your .xml configuration files (as Bjoern suggested earlier) and moving all contents & data to be under the same location will be the simplest global solution ongoing. Links near the end of my reply can help explain how-to.

For the specific reason why bowtie2 indices are not working: I noticed that the reference genome ".fa" file is not linked from the directory containing the indexes. This is required. Adding it in, the same way that you did for the bowtie2 indexes, into this dir: "/global/referenceData/databases/bowtie2/hg19" will probably solve that part of the problem. I didn't see this posted - but I apologize if I am duplicating advice already given.

I also tend to advise keeping all data under the same master "data" directory - all indexes and sequence data - as symbolic links to additional file system paths that are unknown to the 'galaxy user' cause a different set of problems. However, that said, this doesn't seem to be an issue in your specific case: if the bowtie2 indexes are functioning correctly - then environment is set up so that the other dir hierarchy where the .fa files are kept must included in the 'galaxy' user's ENV. Symbolic links that go outside of the local dir structure are known to cause problems unless the ENV config is carefully set up, and to my knowledge are best avoided entirely for certain uses such as "upload by file path" into libraries.

For reference:

NGS data set-up is described in this wiki - including expected content for each type of index:
https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

For examples, you can rsync a genome or two and examine the contents. Or, our /location dir and have a look at the .loc files.
https://wiki.galaxyproject.org/Admin/DataIntegration

Tool Shed help (very detailed):
https://wiki.galaxyproject.org/Tool%20Shed
In particular, if you had previously installed repositories (this is not clear, just suspected from the duplications), updating the Metadata with certain distribution updates can be very important. This has been necessary for the last few releases to update to changes. The News Brief noted this, and included a link to this wiki page. Also see the "Related Pages" lower down on the wiki.
https://wiki.galaxyproject.org/ResettingMetadataForInstalledRepositories
This may also be useful:
https://wiki.galaxyproject.org/RepairingInstalledRepositories

Hopefully you have sorted most of this out by now, or this helps!

Jen
Galaxy team


On 3/4/14 12:21 PM, Ravi Alla wrote:
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
../shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/96d2e31a3938/bowtie2/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.
On Mar 4, 2014, at 11:28 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:

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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