- galaxy-dev - lists.galaxyproject.org

conda not installing deps.
by Jochen Bick 29 Jul '19

29 Jul '19

Hi we have a new galaxy 19.01 instance and conda is somehow not running correctly: galaxy.yml #dependency_resolvers_config_file: config/dependency_resolvers_conf.xml conda_prefix: /opt/galaxy/tools/_conda #conda_exec: null #conda_debug: false #conda_ensure_channels: 'iuc,conda-forge,bioconda,defaults' #conda_use_local: false conda_auto_install: true conda_auto_init: true conda_copy_dependencies: true job_working_directory: /opt/galaxy/daten/jobs_directory any ideas? Thanks Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 8092 Zurich, Switzerland Office: Eschikon 27 8315 Lindau, Switzerland Phone +41 52 354 92 06 jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch

3 4

Memory limit for a Travis CI build
by Jin Li 29 Jul '19

29 Jul '19

Hi all, I submitted a PR to Galaxy Tools IUC (https://github.com/galaxyproject/tools-iuc/pull/2506) The Travis CI build exited with an error code 35072. The error may be caused by running out of memory. https://travis-ci.org/galaxyproject/tools-iuc/jobs/564531462 In fact, my program does not use too much memory on the test case (< 1GB). May I ask what is the memory limit to pass a Travis CI build? How could I request more memory if it is too small? Thank you. Best regards, Jin

2 2

Installing a database on local instance Galaxy
by goutham sarovaram 28 Jul '19

28 Jul '19

Hello, My name is Goutham I'm currently doing RNA-Seq analysis on a local instance of Galaxy installed on a workstation at our research center. As I have been tasked with adminstrative duties for this system I would like to know how I can install databases on to the local instance (Databases download from Uniprot and Pfam etc.) For running blast+ and other tools associated with the trinotate pipeline which I'm trying to operate through Galaxy. Best regards. (The instance is hosted on a Kubuntu 18 LTS with a dual Xeon E series and 64 DDR4 memory, any suggestions for better optimizations are welcome)

2 1

Re: How to resolve the dependency of self-compiled C++ programs when publishing a tool?
by Jin Li 25 Jul '19

25 Jul '19

Hi Devon, Thank you for your instant reply. May I ask how could I quickly put a C++ program in either conda-forge or bioconda? I am new to these package repositories. Thank you. Best regards, Jin On Thu, Jul 11, 2019 at 2:03 AM Devon Ryan <dpryan(a)dpryan.com> wrote: > > Put your tool in either conda-forge or bioconda, that will take care > of the issue. > -- > Devon Ryan, Ph.D. > Email: dpryan(a)dpryan.com > Data Manager/Bioinformatician > Max Planck Institute of Immunobiology and Epigenetics > Stübeweg 51 > 79108 Freiburg > Germany > > On Thu, Jul 11, 2019 at 8:44 AM Jin Li <lijin.abc(a)gmail.com> wrote: > > > > Hi all, > > > > I want to publish our own tool to the Galaxy Tool Shed. Our tool is > > our own developed C++ program. Our compiled binaries may not > > necessarily run in other machines due to different OS platforms. How > > could I resolve the tool dependency of our own compiled binaries? > > Thank you. > > > > Best regards, > > Jin > > ___________________________________________________________ > > 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/

5 9

trouble running the new galaxy instance
by Jochen Bick 23 Jul '19

23 Jul '19

Hi since we updated some loc files our galaxy (19.01) does start but is unavailable in the browser. # systemctl status galaxy ? galaxy.service - SYSV: Galaxy http://galaxyproject.org/ Loaded: loaded (/etc/rc.d/init.d/galaxy; bad; vendor preset: disabled) Active: active (exited) since Mon 2019-07-15 10:23:11 CEST; 1 weeks 0 days ago Docs: man:systemd-sysv-generator(8) Process: 5840 ExecStop=/etc/rc.d/init.d/galaxy stop (code=exited, status=0/SUCCESS) Process: 5957 ExecStart=/etc/rc.d/init.d/galaxy start (code=exited, status=0/SUCCESS) Jul 15 10:23:11 green-galaxy galaxy[5957]: File "/opt/galaxy/galaxy/.venv/li...n Jul 15 10:23:11 green-galaxy galaxy[5957]: self.fetch_more_tokens() Jul 15 10:23:11 green-galaxy galaxy[5957]: File "/opt/galaxy/galaxy/.venv/li...s Jul 15 10:23:11 green-galaxy galaxy[5957]: return self.fetch_value() Jul 15 10:23:11 green-galaxy galaxy[5957]: File "/opt/galaxy/galaxy/.venv/li...e Jul 15 10:23:11 green-galaxy galaxy[5957]: self.get_mark()) Jul 15 10:23:11 green-galaxy galaxy[5957]: yaml.scanner.ScannerError: mappin...e Jul 15 10:23:11 green-galaxy galaxy[5957]: in "/opt/galaxy/galaxy/config/gal...0 Jul 15 10:23:11 green-galaxy galaxy[5957]: ...done. Jul 15 10:23:11 green-galaxy systemd[1]: Started SYSV: Galaxy http://galaxyp.... Hint: Some lines were ellipsized, use -l to show in full. Has anyone a good hint? Cheers Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 8092 Zurich, Switzerland Office: Eschikon 27 8315 Lindau, Switzerland Phone +41 52 354 92 06 jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch

2 2

backing up old histories
by Pat Gillevet 23 Jul '19

23 Jul '19

Is there an easy way to backup old histories before deleting them. Just in case one wants to reload them. thanks Pat ******************************************************************************** Patrick M. Gillevet, Ph.D Director, Microbiome Analysis Center Professor, Department of Biology George Mason University, Science & Technology Campus 10900 University Boulevard, MSN 4D4 Manassas, Virginia 20110 Office 703-993-1057 Room Colgan Hall-426 FAX 703-993-8430 http://mbac.gmu.edu **********************************************************************************

1 0

2 accounts by mistake
by Rattray, Alison (NIH/NCI) [C] 23 Jul '19

23 Jul '19

I forgot that I had set up an account a while ago, but came across the old account tonight. Problem is that as I was trying to merge them it seems all my files are now gone. Neither of my sign in addresses gets me back to my data (ouch!). How can I get beyond this. (Yes I tried what is suggested when it says that my data is deleted... nothing shows up. Would appreciate some input into how to merge my two accounts into one and hopefully rescue my data as well!!!! Thank you Alison J. Rattray, Ph.D. Contractor RNA Biology Laboratory 1050 Boyles St. Bldg 539 Rm 222 Frederick, Maryland 21701 (301)846-6715 Cell 240-529-7172 Alternative email: rattray56(a)gmail.com

2 1

Still problems running ML tools from toolshed
by Nancy Ide 18 Jul '19

18 Jul '19

Running the ml_performance_plots tool I get this error: Fatal error: Exit code 1 () Traceback (most recent call last): File "/Users/ide/Projects/GitHub/GalaxyMods/tools/learning/ml_performance.py", line 156, in <module> main(args.infile_input, args.infile_output, args.infile_trained_model) File "/Users/ide/Projects/GitHub/GalaxyMods/tools/learning/ml_performance.py", line 83, in main model = pickle.load(model_file) File "/usr/local/Cellar/python@2/2.7.16/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 1384, in load return Unpickler(file).load() File "/usr/local/Cellar/python@2/2.7.16/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 864, in load dispatch[key](self) File "/usr/local/Cellar/python@2/2.7.16/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 892, in load_proto raise ValueError, "unsupported pickle protocol: %d" % proto ValueError: unsupported pickle protocol: 3 Please help! ----------------------------------------------------- Nancy Ide Professor of Computer Science Department of Computer Science Vassar College Poughkeepsie, New York 12604-0520 USA tel: (+1 845) 437 5988 fax: (+1 845) 437 7498 email: ide(a)cs.vassar.edu http://www.cs.vassar.edu/~ide -----------------------------------------------------

1 0

Re: Bismark - Bug in Bismark Pretty Report ?
by Previti 15 Jul '19

15 Jul '19

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(a)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.previti(a)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.

1 0

How to resolve the dependency of self-compiled C++ programs when publishing a tool?
by Jin Li 11 Jul '19

11 Jul '19

Hi all, I want to publish our own tool to the Galaxy Tool Shed. Our tool is our own developed C++ program. Our compiled binaries may not necessarily run in other machines due to different OS platforms. How could I resolve the tool dependency of our own compiled binaries? Thank you. Best regards, Jin

1 0