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