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:

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

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