Hi Greg,

This is a good start, you will want to do "which" on bowtie2 and tophat2 as well. Each should point to proper binary. You don't seem to have all of them installed, specifically "Tophat v1.3.3-1.4.0", which is what "Tophat for Illumina" uses.


Correct binary for the path name. See the dependencies link for the tools wrappers that use this one (includes "Tophat for Illumina").
>> which bowtie
> /usr/local/galaxy/installs/bin/bowtie-0.12.8/bowtie

Incorrect binary for the path name and the tool wrapper "Tophat for Illumina". See the dependencies link. You probably need to install Tophat v1.3.3-1.4.0 or switch to using tool wrapper "Tophat2" and name the binary tophat2. The binary bowtie2 will also need to be correctly labeled if tophat2 is being used, to fully resolve the issue with locs.
>> which tophat
> /usr/local/galaxy/installs/bin/tophat-2.0.6.Linux_x86_64/tophat

I think you will find that the problems you were having with "Tophat for Illumina" are linked to the above and if you correct the dependencies, the loc problems and errors will sort themselves out.


On 2/21/13 9:22 AM, greg wrote:
Ok, you're right, I did ask something similar before.

So is the simplest answer is to tell users to use Tophat2 instead of
"Tophat for Illumina"?  Or is there anything special in "Tophat for
Illumina" that they would be missing out on?

I am not sure if leaving tools with improper tool wrapper/binary/loc mapping in the tool menu is the best solution. If you don't want them, you can of course remove them from the tool config file.

Which is better? The updated tools are different and most users will probably want to use the new versions just like most updated tools, but it really depends on what they are doing (if they need to reproduce an older study or not, are using a datatype not supported by the new tool, or are in the middle of a project, etc.). You are pretty close to having all of it configured correctly, if you also have the indexes for both created. But this is entirely your call. Maybe the scientists you support can help you make the decision - the user manuals for each describe the changes between the software versions. The wrappers in Galaxy have most if not all of the core functions implemented and the tool form's describe this in detail.

Take care,

Jen
Galaxy team



-Greg

Here's some info I dug up in case it's useful:

which bowtie
/usr/local/galaxy/installs/bin/bowtie-0.12.8/bowtie
which tophat
/usr/local/galaxy/installs/bin/tophat-2.0.6.Linux_x86_64/tophat

I do have all of these installed:

bowtie-0.12.8  bowtie2-2.0.2  bwa-0.6.2  cufflinks-2.0.2.Linux_x86_64
tophat-2.0.6.Linux_x86_64


Here's the PATH if it helps:

echo $PATH
/misc/local/galaxy/galaxy_python/bin:/sge/8.0.1p4/bin/lx-amd64:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/pinerog/bin:/usr/local.orig/bin:/usr/local/R-2.15.0/bin/:/usr/local/blast+:/usr/local/EMBOSS:/usr/local/galaxy/installs/bin/beam2:/usr/local/galaxy/installs/bin/bowtie2-2.0.2:/usr/local/galaxy/installs/bin/bowtie2-2.0.2/scripts:/usr/local/galaxy/installs/bin/bowtie-0.12.8:/usr/local/galaxy/installs/bin/bowtie-0.12.8/scripts:/usr/local/galaxy/installs/bin/tophat-2.0.6.Linux_x86_64:/usr/local/galaxy/installs/bin/samtools-0.1.18:/usr/local/galaxy/installs/bin/samtools-0.1.18/misc:/usr/local/galaxy/installs/bin/samtools-0.1.18/bcftools:/usr/local/galaxy/installs/bin/cufflinks-2.0.2.Linux_x86_64:/usr/local/galaxy/installs/bin/express-1.2.2-linux_x86_64:/usr/local/galaxy/installs/bin/bwa-0.6.2:/usr/local/galaxy/installs/bin/fastx:/usr/local/galaxy/installs/bin/lastz-distrib-1.02.00:/usr/local/!
galaxy/ins
talls/bin/lastz-distrib-1.02.00/tools:/misc/local/galaxy/galaxy_python/bin

On Thu, Feb 21, 2013 at 11:40 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:
Hi Greg,

The problem here and the confusion between the Bowtie loc files are likely
related. Do you have both bowtie/bowtie2 and tophat/tophat2 installed? And
the tool wrappers for all versions are active? I though we resolved this
earlier but maybe you installed a new tool or updated?

The wrappers for the tools that have dependencies on bowtie vs bowtie2 (and
the associated indexes) are not interchangeable. You will need to chech your
paths to see which tool is being used for each - be sure to check any
symbolic paths that may have been created when the tools were installed
(these tools are known to create links such as bowtie -> bowtie2, that you
will want to get rid of).

Reviewing tool dependencies is the best way to troubleshoot:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

Hopefully this helps. Be sure to keep any followup on the mailing list so
the dev community can continue to have input,

Jen
Galaxy team


On 2/21/13 7:50 AM, greg wrote:

Hi guys,

On our local galaxy install I'm getting the error below when I run
tophat for illumina like this:

http://snag.gy/HsWyS.jpg

Any ideas?

Thanks,

Greg


Error:

Dataset generation errors

Dataset 27: Tophat for Illumina on data 15: deletions

Tool execution generated the following error message:

Error in tophat:
tophat: option --no-closure-search not recognized
      for detailed help see http://tophat.cbcb.umd.edu/manual.html

cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/junctions.bed':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/insertions.bed':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/accepted_hits.bam':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/deletions.bed':
No such file or directory

The tool produced the following additional output:

TopHat v2.0.6
tophat -p 4  -a 8 -m 0 -i 70 -I 500000 -g 20 --library-type
fr-unstranded --max-insertion-length 3 --max-deletion-length 3
--coverage-search --min-coverage-intron 50 --max-coverage-intron 20000
--no-closure-search --initial-read-mismatches 2 --segment-mismatches 2
--segment-length 25 --min-segment-intron 50 --max-segment-intron
500000
/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome
/home/galaxy/000/dataset_306.dat
___________________________________________________________
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/


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org


On Thu, Feb 21, 2013 at 11:40 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:
Hi Greg,

The problem here and the confusion between the Bowtie loc files are likely
related. Do you have both bowtie/bowtie2 and tophat/tophat2 installed? And
the tool wrappers for all versions are active? I though we resolved this
earlier but maybe you installed a new tool or updated?

The wrappers for the tools that have dependencies on bowtie vs bowtie2 (and
the associated indexes) are not interchangeable. You will need to chech your
paths to see which tool is being used for each - be sure to check any
symbolic paths that may have been created when the tools were installed
(these tools are known to create links such as bowtie -> bowtie2, that you
will want to get rid of).

Reviewing tool dependencies is the best way to troubleshoot:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

Hopefully this helps. Be sure to keep any followup on the mailing list so
the dev community can continue to have input,

Jen
Galaxy team


On 2/21/13 7:50 AM, greg wrote:

Hi guys,

On our local galaxy install I'm getting the error below when I run
tophat for illumina like this:

http://snag.gy/HsWyS.jpg

Any ideas?

Thanks,

Greg


Error:

Dataset generation errors

Dataset 27: Tophat for Illumina on data 15: deletions

Tool execution generated the following error message:

Error in tophat:
tophat: option --no-closure-search not recognized
      for detailed help see http://tophat.cbcb.umd.edu/manual.html

cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/junctions.bed':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/insertions.bed':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/accepted_hits.bam':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/deletions.bed':
No such file or directory

The tool produced the following additional output:

TopHat v2.0.6
tophat -p 4  -a 8 -m 0 -i 70 -I 500000 -g 20 --library-type
fr-unstranded --max-insertion-length 3 --max-deletion-length 3
--coverage-search --min-coverage-intron 50 --max-coverage-intron 20000
--no-closure-search --initial-read-mismatches 2 --segment-mismatches 2
--segment-length 25 --min-segment-intron 50 --max-segment-intron
500000
/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome
/home/galaxy/000/dataset_306.dat
___________________________________________________________
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/


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
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/

Reply via email to