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 resides in the galaxy-dist folder and uses tool_conf.xml to 
load tools into the side bar and tool_data_table_conf.xml to load indices (and 
other data) for the default tools that come with galaxy.

The shed tools reside in the ../shed_tools/ directory and use 
shed_tools_conf.xml to load tools into the side bar and the 
shed_tools_data_table_conf.xml to load indices.

The shed_tool xml is setup in the universe.ini file.

The .loc files for default main tools reside in galaxy-dist/tool-data and the 
.loc files for the shed_tools reside in 
../shed_tools/......./<tool-name>/<tool_id>/<tool-name>/

And when I uninstall tools and reinstall I would have to update the metadata 
for that tool.

If ../shed_tools dir is not present then shed-tools get installed under 
galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/


And it is always better to install tools as wrappers + dependencies when 
possible.

Am I on the right track with this tool organization?
Thanks
Ravi



On Mar 5, 2014, at 11:06 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:

> 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.gruen...@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.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.
>>>>>>>> ___________________________________________________________
>>>>>>>> Please keep all replies on the list by using "reply all"
>>>>>>>> in your mail client.  To manage your subscriptions to this
>>>>>>>> and other Galaxy lists, please use the interface at:
>>>>>>>>   http://lists.bx.psu.edu/
>>>>>>>> 
>>>>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>>>>   http://galaxyproject.org/search/mailinglists/
>>>>>>>> 
>>>>>> 
>>>> 
>>>> 
>> 
>> 
>> 
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
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> 
> -- 
> Jennifer Hillman-Jackson
> http://galaxyproject.org

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