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?

-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/ga!
 
laxy/installs/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

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