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<mailto:m.vandenb...@gmail.com>> Date: Thursday, March 23, 2017 at 11:13 AM To: David Lapointe <david.lapoi...@tufts.edu<mailto:david.lapoi...@tufts.edu>> Cc: "galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>" <galaxy-dev@lists.galaxyproject.org<mailto: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<mailto: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<http://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/
