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
<http://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
<http://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
<mailto: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
<mailto: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 <mailto: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
<http://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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