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/ >>>>>> >>>> >> >>
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