(We discussed this over IRC, but responding to the list posting for posterity/searchability) The JSON.pm file isn't found in your PERL5LIB path because the original version of my JBrowse tool failed to specify the full dependency list and assumed you had some perl modules manually installed. The latest version of my JBrowse tool now includes the full set of dependencies. Since chatting on IRC, this version has been uploaded to the MTS and is available here: https://toolshed.g2.bx.psu.edu/view/iuc/jbrowse/497c6bb3b717 (For the rest of the mailing list reading this, an unofficial release announcement) JBrowse 1.11.6 is available as a tool which can be run and can display: - bed/gff/gff3 - BAM - Blast XML data (automatically converted to gapped GFF3 and displayed with evalue-based intensities) - BigWig data - VCF data putting it closer to being on-par with trackster. It's an excellent end-of-workflow step to summarize all of your generated genomic analyses. If any of the community have feature requests, send them my way! NB: BAM/BigWigs do NOT play nicely with galaxy if you aren't using X-SendFile. 2015-06-18 5:42 GMT-05:00 Peter van Heusden <pvh@sanbi.ac.za>:

Thanks Bjoern

My initial install didn't pick up the Perl dependencies correctly, but I re-installed and now the install seems to have the required modules but is missing something in the environment variables. Specifically I get an error import JSON.pm, see below. Note that the jbrowse/1.11.6/iuc/package_jbrowse_1_11_6/d5ab749c9e97/lib/perl5 directory isn't included in @INC and in fact the paths that *are* included seem to imply that the wrong perl interpreter is being picked up.

Fatal error: Exit code 1 () Can't locate JSON.pm in @INC (you may need to install the JSON module) (@INC contains: /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/database/job_working_directory/000/29/dataset_29_files/JBrowse-1.11.6/bin/../src/perl5 /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/database/job_working_directory/000/29/dataset_29_files/JBrowse-1.11.6/bin/../src/perl5/Bio/JBrowse/JSON.pm line 10. BEGIN failed--compilation aborted at /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/database/job_working_directory/000/29/dataset_29_files/JBrowse-1.11.6/bin/../src/perl5/Bio/JBrowse/JSON.pm line 10. Compilation failed in require at /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/database/job_working_directory/000/29/dataset_29_files/JBrowse-1.11.6/bin/../src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm line 21. BEGIN failed--compilation aborted at /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/database/job_working_directory/000/29/dataset_29_files/JBrowse-1.11.6/bin/../src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm line 21. Compilation failed in require at bin/prepare-refseqs.pl line 7. BEGIN failed--compilation aborted at bin/prepare-refseqs.pl line 7. Traceback (most recent call last): File "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/2c9e5136b416/jbrowse/jbrowse.py", line 44, in <module> process_genome(jbrowse_dir, os.path.realpath(args.genome.name)) File "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/2c9e5136b416/jbrowse/jbrowse.py", line 17, in process_genome subprocess.check_output(['perl', 'bin/prepare-refseqs.pl', '--fasta', genome], cwd=jbrowse_dir) File "/usr/lib/python2.7/subprocess.py", line 573, in check_output raise CalledProcessError(retcode, cmd, output=output) subprocess.CalledProcessError: Command '['perl', 'bin/prepare-refseqs.pl', '--fasta', '/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/database/files/000/dataset_3.dat']' returned non-zero exit status 2

On 18 June 2015 at 10:01, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:

...

Peter,

I'm in a hurry ... have a look at https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse Developed by IUC member Eric Rasche.

Cheers, Bjoern

On 18.06.2015 10:00, Peter van Heusden wrote:

I've tried that - I've added the Environment Modules for the relevant tools to the local_env.sh file, so they're there in the environment when Galaxy runs. These tools are scheduled via our cluster, however, so I don't think the environment passes across to them. They depend on these Galaxy packages, however, and those (bedtools and ucsc-utils) are now installed, so I'm not sure why it can't pick them up from the shed_tools.

On 18 June 2015 at 09:10, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:

...

On 06/18/2015 09:06 AM, Peter van Heusden wrote:

...

Hi there

I'm trying to visualise some of our genome data using Trackster. Initial input is 790,000 lines of GFF3. When I try and create the visualisation, I get errors from two tools:

Convert GFF to Interval Index on data 3 -- an out of memory error - I'll try and fix this by upping the memory limit for our Galaxy jobs

Convert BED, GFF, or VCF to BigWig on data 3 -- bedtools and bedGraphToBigWig not found errors. I tried to resolve these by installing the ucsc-tools and bedtools packages - and they did install correctly - but I still get these file not found errors.

Hi Peter

make sure 'galaxy' (ie the user galaxy is running as) has the newly installed tools in its path. You might need to add them to "run.sh" and restart the server.

Hans-Rudolf

Any idea how to fix this second problem?

...

Thanks! Peter P.S. as an alternative to Trackster, does anyone have Galaxy interfaced to JBrowse?

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-- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu rasche.eric@yandex.ru