Bismark - Bug in Bismark Pretty Report ?

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Bismark - Bug in Bismark Pretty Report ?

Previti
Dear Galaxy Community,

I just recently started testing the Bismark methylation tools, everything works fine until I try to make a "pretty report".
Some information is not included in the report, instead you see placeholders
I attached the output I  get and shown below are the job parameters.
Does anybody know where to fix this?

Best regards,
Christopher

Bismark Pretty Report

Dataset Information

Number: 198
Name: Bismark Pretty Report on data 190, data 189, and others: Download pretty html report
Created: Thu 07 Mar 2019 03:24:40 PM (UTC)
Filesize: 2.7 MB
Dbkey: ?
Format: html

Job Information

Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_pretty_report/0.20.0
Galaxy Tool Version: 0.20.0
Tool Version:
Tool Standard Output: stdout
Tool Standard Error: stderr
Tool Exit Code: 0
History Content API ID: 971c2f882eb14ac3 (41433)
Job API ID: 58816697357e736f (22051)
History API ID: 5fccce9c1b3793da (807)
UUID: 45bedd12-6ce5-4d63-a1e2-e05883b0c356
Full Path: /opt/galaxy/galaxy/database/files/038/dataset_38737.dat

Tool Parameters

Input Parameter Value Note for rerun
Submit a Bismark mapping report 191: Bismark Meth. Extractor on data 60 and data 133: Genome-wide methylation report.
additional_reports
Submit the corresponding Bismark deduplication report 197: Bismark Deduplicate on data 133: deduplication report
Submit the corresponding Bismark splitting report 189: Bismark Meth. Extractor on data 60 and data 133: Splitting Report
Submit the corresponding Bismark M-bias report 190: Bismark Meth. Extractor on data 60 and data 133: Mbias Report
Submit the corresponding Bismark nucleotide report

Create a separate logfile, otherwise logs are added to the dataset info. False

Inheritance Chain

Bismark Pretty Report on data 190, data 189, and others: Download pretty html report

Command Line

python '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/bismark/7bffcb6fc81d/bismark/bismark2report_wrapper.py'  --alignment_report '/opt/galaxy/galaxy/database/files/038/dataset_38715.dat'  --dedup_report '/opt/galaxy/galaxy/database/files/038/dataset_38736.dat' --splitting_report '/opt/galaxy/galaxy/database/files/038/dataset_38713.dat' --mbias_report '/opt/galaxy/galaxy/database/files/038/dataset_38714.dat'  --output_html_report '/opt/galaxy/galaxy/database/files/038/dataset_38737.dat'

Job Metrics

core

Cores Allocated 8
Job End Time 2019-03-07 16:49:58
Job Runtime (Wall Clock) 25 minutes
Job Start Time 2019-03-07 16:24:43
Memory Allocated (MB) 510000

Job Dependencies

Dependency Dependency Type Version
bismark conda 0.20.0


--
Dr. Christopher Previti
Genomics and
Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.previti@...
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.



    

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Bismark_Pretty_Report_on_data_190,_data_189,_and_others__Download_pretty_html_report_html.html (3M) Download Attachment
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Re: Bismark - Bug in Bismark Pretty Report ?

Previti
Dear Björn,

This works now...but I don't know why...
Maybe a combination of a Galaxy update and correctly whitelisting the
tool for displaying html output....

Thanks for getting back to me!

Christopher


On 7/13/19 1:45 PM, Björn Grüning wrote:

> Uha, this looks like a upstream bug, not sure how this can be Galaxy
> related.
>
> Is this still a problem?
>
> Cheers,
> Bjoern
>
> Am 08.03.19 um 09:23 schrieb Previti:
>> Dear Galaxy Community,
>>
>> I just recently started testing the Bismark methylation tools,
>> everything works fine until I try to make a "pretty report".
>> Some information is not included in the report, instead you see
>> placeholders
>> I attached the output I  get and shown below are the job parameters.
>> Does anybody know where to fix this?
>>
>> Best regards,
>> Christopher
>>
>>
>>     Bismark Pretty Report
>>
>>
>>       Dataset Information
>>
>> Number:     198
>> Name:     Bismark Pretty Report on data 190, data 189, and others:
>> Download pretty html report
>> Created:     Thu 07 Mar 2019 03:24:40 PM (UTC)
>> Filesize:     2.7 MB
>> Dbkey:     ?
>> Format:     html
>>
>>
>>       Job Information
>>
>> Galaxy Tool ID:
>> toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_pretty_report/0.20.0
>> Galaxy Tool Version:     0.20.0
>> Tool Version:    
>> Tool Standard Output:     stdout
>> <http://dkfzgalaxy/datasets/971c2f882eb14ac3/stdout>
>> Tool Standard Error:     stderr
>> <http://dkfzgalaxy/datasets/971c2f882eb14ac3/stderr>
>> Tool Exit Code:     0
>> History Content API ID:     971c2f882eb14ac3 (41433)
>> Job API ID:     58816697357e736f (22051)
>> History API ID:     5fccce9c1b3793da (807)
>> UUID:     45bedd12-6ce5-4d63-a1e2-e05883b0c356
>> Full Path:     /opt/galaxy/galaxy/database/files/038/dataset_38737.dat
>>
>>
>>       Tool Parameters
>>
>> Input Parameter     Value     Note for rerun
>> Submit a Bismark mapping report     191: Bismark Meth. Extractor on
>> data 60 and data 133: Genome-wide methylation report.
>> <http://dkfzgalaxy/datasets/c53067deacfc4f28/show_params>    
>> additional_reports    
>> Submit the corresponding Bismark deduplication report     197:
>> Bismark Deduplicate on data 133: deduplication report
>> <http://dkfzgalaxy/datasets/622377f5e70addd2/show_params>    
>> Submit the corresponding Bismark splitting report     189: Bismark
>> Meth. Extractor on data 60 and data 133: Splitting Report
>> <http://dkfzgalaxy/datasets/aa40ffd063a4645f/show_params>    
>> Submit the corresponding Bismark M-bias report     190: Bismark Meth.
>> Extractor on data 60 and data 133: Mbias Report
>> <http://dkfzgalaxy/datasets/47db6b20871008b9/show_params>    
>> Submit the corresponding Bismark nucleotide report    
>>     
>> Create a separate logfile, otherwise logs are added to the dataset
>> info.     False    
>>
>>
>>       Inheritance Chain
>>
>> Bismark Pretty Report on data 190, data 189, and others: Download
>> pretty html report
>>
>>
>>       Command Line
>>
>> python
>> '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/bismark/7bffcb6fc81d/bismark/bismark2report_wrapper.py' 
>> --alignment_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38715.dat' 
>> --dedup_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38736.dat'
>> --splitting_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38713.dat'
>> --mbias_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38714.dat' 
>> --output_html_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38737.dat'
>>
>>
>>       Job Metrics
>>
>>
>>         core
>>
>> Cores Allocated     8
>> Job End Time     2019-03-07 16:49:58
>> Job Runtime (Wall Clock)     25 minutes
>> Job Start Time     2019-03-07 16:24:43
>> Memory Allocated (MB)     510000
>>
>>
>>       Job Dependencies
>>
>> Dependency     Dependency Type     Version
>> bismark     conda     0.20.0
>>
>>
>>
>> -- 
>> *Dr. Christopher Previti*
>> Genomics and Proteomics Core Facility
>> High Throughput Sequencing (W190)
>> Bioinformatician
>>
>> German Cancer Research Center (DKFZ)
>> Foundation under Public Law
>> Im Neuenheimer Feld 580
>> 69120 Heidelberg
>> Germany
>> Room: B2.102 (INF580/TP3)
>> Phone: +49 6221 42-4661
>>
>> [hidden email] <http://www.dkfz.de/>
>> www.dkfz.de <http://www.dkfz.de/>
>>
>> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
>> VAT-ID No.: DE143293537
>>
>> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
>> Personen bestimmt, an die sie adressiert ist.
>> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
>> Informationen enthalten. Sollten Sie nicht
>> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
>> Absender und löschen Sie die Mitteilung.
>> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht
>> ist untersagt.
>>
>>
>>
>> ___________________________________________________________
>> 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:
>>    %(web_page_url)s
>>
>> To search Galaxy mailing lists use the unified search at:
>>    http://galaxyproject.org/search/
>>

--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

[hidden email] <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.


___________________________________________________________
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:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/