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

christopher.previti@dkfz.de <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

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-- *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@dkfz.de <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.