Hi David, I'm afraid I can't help you with this tool, but there is a metaphlan2 wrapper on the toolshed that is developed and tested by the iuc (intergalactic utility commission, https://galaxyproject.org/iuc/), you could give this a try. I'm pretty sure this tool is functional. In general galaxy will attempt to manage the tool dependencies for you. If possible you should let galaxy handle the tool dependency installation and avoid using system-installed binaries. You can find more information about the tool installation process here: https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/
Best, Marius On 24 March 2017 at 18:45, Lapointe, David <david.lapoi...@tufts.edu> wrote: > Thanks for that tip. I did restart galaxy and that problem went away, but.. > > bowtie2 is on the system path, but I am getting an error about bowtie2 not > being found, even though the path is given to the program in the call (see > below). Is this some weird config problem? Maybe try a different version. > Tool: MetaPhlAn > Name: MetaPhlAn on data 20 (rel_ab analysis) > Created: Fri Mar 24 15:10:47 2017 (UTC) > Filesize: 0 bytes > Dbkey: ? > Format: tabular > Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/dannon/metaphlan/metaphlan/1. > 7.0 > Galaxy Tool Version: 1.7.0 > Tool Version: > Tool Standard Output: stdout > <https://galaxy.tufts.edu/datasets/75732d013df69f30/stdout> > Tool Standard Error: stderr > <https://galaxy.tufts.edu/datasets/75732d013df69f30/stderr> > Tool Exit Code: 1 > History Content API ID: 75732d013df69f30 > Job API ID: 46c16c6e54962e29 > History API ID: 7ca8f1b7f24e5a2d > UUID: 42cc9323-4489-48f0-b419-72ce770925cb > Full Path: /mnt/galaxy/files/000/dataset_709.dat > Job Command-Line: python ${METAPHLAN_PATH}/metaphlan.py > /mnt/galaxy/files/000/dataset_700.dat -t rel_ab --tax_lev a --bowtie2_exe > /usr/bin/bowtie2 --bowtie2db ${METAPHLAN_PATH}/bowtie2db/mpa --no_map > --bt2_ps sensitive-local -o /mnt/galaxy/files/000/dataset_709.dat > Job Runtime (Wall Clock) 9 seconds > Cores Allocated 1 > Job Start Time 2017-03-24 15:10:49 > Job End Time 2017-03-24 15:10:58 > Input Parameter Value Note for rerun > Input metagenome (multi-fasta of metagenomic reads, loaded with the Get > Data module, see below for an example) http://huttenhower.sph. > harvard.edu/sites/default/files/LC1.fna > <https://galaxy.tufts.edu/datasets/4f005d042f4be528/show_params> > Type of analysis to perform rel_ab > Taxonomic level all taxonomic levels > Sensitivity options for read-marker similarity (as described by BowTie2) > Sensitive > Local > -- > David Lapointe Ph.D. > Sr. Bioinformatics Specialist > Research Technology (RT) > Tufts Technology Services (TTS) > 16 Dearborn Road > Somerville MA 02144 > > Phone: 617-627-5319 > Fax: 617-627-3667 > http://it.tufts.edu > > From: Marius van den Beek <m.vandenb...@gmail.com> > Date: Thursday, March 23, 2017 at 11:13 AM > To: David Lapointe <david.lapoi...@tufts.edu> > Cc: "galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists. > galaxyproject.org> > Subject: Re: [galaxy-dev] Dataset Generation Errors > > Hi David, > > this typically happens on older Galaxy versions (< 17.01) after installing > new or updated tools. > A galaxy restart should help. > > Best, > Marius > > On 23 March 2017 at 15:57, Lapointe, David <david.lapoi...@tufts.edu> > wrote: > >> I have installed the metaphlan tool ( dannon e951f9d38339) which >> installed with the dependancies seemingly satisfied. I am getting an error >> "This tool was disabled before the job completed" I can't determine why >> this happens. In the handler log is this: >> >> Tool 'toolshed.g2.bx.psu.edu/repos/dannon/metaphlan/metaphlan/1.7.0' >> removed from tool config, unable to run job >> >> >> David >> -- >> David Lapointe Ph.D. >> Sr. Bioinformatics Specialist >> Research Technology (RT) >> Tufts Technology Services (TTS) >> 16 Dearborn Road >> Somerville MA 02144 >> >> Phone: 617-627-5319 >> Fax: 617-627-3667 >> http://it.tufts.edu >> >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/ >> > >
___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
