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.prev...@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. >> >> >> >> ___________________________________________________________ >> 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 christopher.prev...@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. ___________________________________________________________ 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/
