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Dataset Generation Errors

Lapointe, David
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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Re: Dataset Generation Errors

Marius van den Beek
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 <[hidden email]> 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

___________________________________________________________
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/


___________________________________________________________
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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/
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Re: Dataset Generation Errors

Lapointe, David
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 <[hidden email]>
Date: Thursday, March 23, 2017 at 11:13 AM
To: David Lapointe <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
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 <[hidden email]> 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

___________________________________________________________
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/
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Re: Dataset Generation Errors

Marius van den Beek
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 <[hidden email]> 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
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

From: Marius van den Beek <[hidden email]>
Date: Thursday, March 23, 2017 at 11:13 AM
To: David Lapointe <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
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 <[hidden email]> 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

___________________________________________________________
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/
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Re: Dataset Generation Errors

Lapointe, David
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 <[hidden email]>
Date: Friday, March 24, 2017 at 3:13 PM
To: David Lapointe <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
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 <[hidden email]> 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
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

From: Marius van den Beek <[hidden email]>
Date: Thursday, March 23, 2017 at 11:13 AM
To: David Lapointe <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
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 <[hidden email]> 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

___________________________________________________________
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/
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