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
Tool Standard Error: 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
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.vandenbeek@gmail.com>
Date: Thursday, March 23, 2017 at 11:13 AM
To: David Lapointe <david.lapointe@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.Lapointe@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:

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

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