Yes, that's how I started. Install from the toolshed, check manage 
dependancies, restart galaxy..  Error says bowtie2 not in system path, put 
bowtie2 in system path, still get the error even though it is in the *xml file  
as a parameter.
--
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: Friday, March 24, 2017 at 3:13 PM
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,

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<mailto: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<http://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

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