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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