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/galaxy/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 jen@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:
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:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
On Thu, Feb 21, 2013 at 11:40 AM, Jennifer Jackson jen@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:
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:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org