galaxy-dev October 2017

galaxy-dev@lists.galaxyproject.org

25 participants
28 discussions

contribute to tools without github
by Matthias Bernt 20 Oct '17

20 Oct '17

I noticed that the sparql_uniprot tool does not run (python3 incompatibility). Since there is no github page I do not know how to contribute to such a tool. I have a similar problem with the lefse tool. What would be the best way to fix sich tools? Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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Re: [galaxy-dev] galaxy-dev Digest, Vol 136, Issue 11
by Matthias Enders 20 Oct '17

20 Oct '17

Dear Galaxy-Dev List, the problem disappeared this day, as our IT was rebuilding the whole with galaxy-docker container. Mit freundlichen Grüßen Matthias Enders ----------------------------------------------------------------------- GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.enders(a)german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844 -----Ursprüngliche Nachricht----- Von: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] Im Auftrag von galaxy-dev-request(a)lists.galaxyproject.org Gesendet: Mittwoch, 18. Oktober 2017 18:00 An: galaxy-dev(a)lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 136, Issue 11 Priorität: Hoch Send galaxy-dev mailing list submissions to galaxy-dev(a)lists.galaxyproject.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-request(a)lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-owner(a)lists.galaxyproject.org When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Problems with the test tool shed? (Von Kuster, Greg) 2. Re: Problems with the test tool shed? (Martin Čech) 3. Re: the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8 (Hans-Rudolf Hotz) 4. Re: MACS2 Error (Deepak Tanwar) 5. Re: MACS2 Error (Devon Ryan) 6. Problems with BlastDB.loc (Enders Matthias) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Oct 2017 18:21:40 +0000 From: "Von Kuster, Greg" <ghv2(a)psu.edu> To: "galaxy-dev(a)lists.galaxyproject.org" <galaxy-dev(a)lists.galaxyproject.org> Subject: [galaxy-dev] Problems with the test tool shed? Message-ID: <9CCD9F8D-D91A-43AA-9F88-D7D777777AC9(a)mymail.psu.edu> Content-Type: text/plain; charset="utf-8" Hi all, I’m wondering if the TTS can be restarted. I’ve been seeing this of-and-on all afternoon. Thanks! Galaxy<http://galaxyproject.org/> The Test Tool Shed could not be reached You are seeing this message because a request to The Test Tool Shed timed out or was refused. This may be a temporary issue which could be resolved by retrying the operation you were performing. If you receive this message repeatedly or for an extended amount of time, please contact an administrator. -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171017/1…> ------------------------------ Message: 2 Date: Tue, 17 Oct 2017 18:56:28 +0000 From: Martin Čech <marten(a)bx.psu.edu> To: "Von Kuster, Greg" <ghv2(a)psu.edu>, "galaxy-dev(a)lists.galaxyproject.org" <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] Problems with the test tool shed? Message-ID: <CAHKBquHKS5zeCwc++8+BCvnqpRHtnowUTk0s62b9KTg6Et4iYQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Done, seems up now. Thanks for the report. M. On Tue, Oct 17, 2017 at 2:22 PM Von Kuster, Greg <ghv2(a)psu.edu> wrote: > Hi all, > > I’m wondering if the TTS can be restarted. I’ve been seeing this > of-and-on all afternoon. > > Thanks! > > Galaxy <http://galaxyproject.org/> > The Test Tool Shed could not be reached > > You are seeing this message because a request to The Test Tool Shed > timed out or was refused. This may be a temporary issue which could be > resolved by retrying the operation you were performing. If you receive > this message repeatedly or for an extended amount of time, please > contact an administrator. > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171017/f…> ------------------------------ Message: 3 Date: Wed, 18 Oct 2017 08:56:17 +0200 From: Hans-Rudolf Hotz <hrh(a)fmi.ch> To: Matthias Enders <m.enders(a)german-seed-alliance.de>, "galaxy-dev(a)lists.galaxyproject.org" <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8 Message-ID: <59E6FB11.4080900(a)fmi.ch> Content-Type: text/plain; charset="utf-8"; format=flowed On 10/17/2017 05:02 PM, Matthias Enders wrote: > Hi Hans, > > your right, I´ve checked this. The utils are free and the folder on > GITHub contains the tools needed. Perhaps it´s an idea to change the > link on the website (https://galaxyproject.org/visualization-setup/) > from here ("http://hgdownload.cse.ucsc.edu/admin/exe/") > to github? > ("https://github.com/ucscGenomeBrowser/kent/tree/master/src/utils") like the whole galaxy project, the Galaxy hub pages are a community effort. So feel free to improve the page yourself by making a adding the github page as a second resource for the faToTwoBit tool. Hans-Rudolf > > Mit freundlichen Grüßen > > Matthias Enders > ---------------------------------------------------------------------- > - > > > GERMAN SEED ALLIANCE GmbH > c/o Norddeutsche Pflanzenzucht > Hans-Georg Lembke KG > Hohenlieth, 24363 Holtsee > Tel.: +49 (0)4351/ 736-189 > Fax: + 49 (0)4351/ 736-271 > Mobil: +49 (0)151/ 14247360 > > Email: m.enders(a)german-seed-alliance.de > > Firmensitz Köln > Amtsgericht Köln, HRB 73844 > > -----Ursprüngliche Nachricht----- > Von: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] > Gesendet: Dienstag, 17. Oktober 2017 16:50 > An: Matthias Enders <m.enders(a)german-seed-alliance.de>; > galaxy-dev(a)lists.galaxyproject.org > Betreff: Re: AW: the future of trackster - was: galaxy-dev Digest, Vol > 136, Issue 8 > > Hi Matthias > > No, the twobit-files are not mandatory for trackster. They are only required if you want to zoom into the nucleotide level. > > Also, though, I am not sure, and I recommend to check this with your legal department, but I have been under the impression that the tool 'faToTwoBit' can be built from the "kent/src/utils" source code directory, which is freely available for all uses, isn't-it? > > > Regards, Hans-Rudolf > > > > > On 10/17/2017 04:29 PM, Matthias Enders wrote: >> Hi Hans, >> >> actually we are a company and the UCSC Genome Browser is not freely >> available for us. As you pinpointed me to the website: >> https://galaxyproject.org/visualization-setup/ >> >> There is an link to USCS utilities (for creating twobitfiles) >> (http://hgdownload.cse.ucsc.edu/admin/exe/) >> Actually this tools are also under license agreements, that permits free commercial download or usage. >> >> If I understand it correctly the twobit-files are mandatory for trackster, implicating that we have to buy licenses for using UCSC Genome Browser and/or Trackster? >> >> If yes: Are there any attempts to build in or rebuild this utilities, so the full project with all parts "remains" compatible with AFL3 license? >> >> Mit freundlichen Grüßen >> >> Matthias Enders >> --------------------------------------------------------------------- >> - >> - >> >> >> GERMAN SEED ALLIANCE GmbH >> c/o Norddeutsche Pflanzenzucht >> Hans-Georg Lembke KG >> Hohenlieth, 24363 Holtsee >> Tel.: +49 (0)4351/ 736-189 >> Fax: + 49 (0)4351/ 736-271 >> Mobil: +49 (0)151/ 14247360 >> >> Email: m.enders(a)german-seed-alliance.de >> >> Firmensitz Köln >> Amtsgericht Köln, HRB 73844 >> >> -----Ursprüngliche Nachricht----- >> Von: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] >> Gesendet: Dienstag, 17. Oktober 2017 10:33 >> An: Matthias Enders <m.enders(a)german-seed-alliance.de>; >> galaxy-dev(a)lists.galaxyproject.org >> Betreff: the future of trackster - was: galaxy-dev Digest, Vol 136, >> Issue 8 >> >> Hi Matthias >> >> We had a Birds of a Feather session about (the future of) Trackster at the recent galaxy community conference in Montpellier. Though, as far as I know (I might be wrong), this didn't result in any no active development on the Trackster code. >> >> What kind of functionality do you miss? It might be worth rising an issue on github (https://github.com/galaxyproject/galaxy/issues) ? >> >> >> Personally, I consider Trackster and the option to display data at >> the UCSC genome browser as two different pairs of shoes: >> >> - Trackster is a easy option to look at your data quickly. It is >> particular useful, if you work with non-model organisms >> >> - the display of your data at UCSC is handy, if you want to >> visually compare it with all the available UCSC tracks. However, keep >> in mind, unless you are using a local copy of the UCSC gemome >> browser, the data will leave your local network. >> >> >> >> WRT tutorial: Have you seen these pages: >> >> https://galaxyproject.org/learn/visualization/ >> https://galaxyproject.org/visualization-setup/ >> >> >> Regards, Hans-Rudolf >> >> >> PS: I took the freedom to change the subject line for easier >> searching in the future >> >> >> >> >> >> >> On 10/16/2017 03:50 PM, Matthias Enders wrote: >>> Dear Galaxy Dev List, >>> >>> we currently searching for a good Genome Browser. As we run a local galaxy instance, we noticed the integrated GTB ("Galaxy Track Browser"). >>> >>> So my question is: Is there a roadmap for further support / development of the GTB? >>> >>> Or will it perhaps get replaced/deprecated in the near future (we read a lot of UCSC Genome Browser - Galaxy - Integration)? >>> >>> Another question would be on good sources/tutorials/manuals for configuring and setup for the GTB. >>> >>> Mit freundlichen Grüßen >>> >>> Matthias Enders >>> -------------------------------------------------------------------- >>> - >>> -- >>> >>> >>> GERMAN SEED ALLIANCE GmbH >>> c/o Norddeutsche Pflanzenzucht >>> Hans-Georg Lembke KG >>> Hohenlieth, 24363 Holtsee >>> Tel.: +49 (0)4351/ 736-189 >>> Fax: + 49 (0)4351/ 736-271 >>> Mobil: +49 (0)151/ 14247360 >>> >>> Email: m.enders(a)german-seed-alliance.de >>> >>> Firmensitz Köln >>> Amtsgericht Köln, HRB 73844 >>> ___________________________________________________________ >>> 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: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/ >>> ------------------------------ Message: 4 Date: Wed, 18 Oct 2017 15:46:25 +0000 From: Deepak Tanwar <dktanwar(a)hotmail.com> To: Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] MACS2 Error Message-ID: <DM5PR0201MB3622F9AECC91FB13134EBB11DF4D0(a)DM5PR0201MB3622.namprd02.prod.outlook.com> Content-Type: text/plain; charset="utf-8" Hello, I am still facing problem. I have tried to reinstall MACS2 but nothing helped. Thank you! Deepak On Oct 16, 2017, at 4:00 PM, Deepak Tanwar <dktanwar(a)hotmail.com<mailto:dktanwar@hotmail.com>> wrote: Hi all, There is some problem with MACS2: export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: line 25: macs2: command not found Fatal error: Exit code 127 () Tool installed: /shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2<http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2> Dependency Resolver Details Dependency Version Resolver Exact version Current Installation Status macs2 2.1.1.20160309 Conda True [http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png] gawk 4.1.3 Conda True [http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png] Thank you, Deepak -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171018/1…> ------------------------------ Message: 5 Date: Wed, 18 Oct 2017 17:51:48 +0200 From: Devon Ryan <dpryan79(a)gmail.com> To: Deepak Tanwar <dktanwar(a)hotmail.com>, Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] MACS2 Error Message-ID: <5592e574-694c-fe3a-ce13-5e340e73627e(a)gmail.com> Content-Type: text/plain; charset="windows-1252"; Format="flowed" Assuming you don't have galaxy set to clean up job working directories upon failure, have a look at the tool_script.sh in that directory and see if you can discern the issue. Also check the conda activation log file (under working/ I think) in that directory to see if it has anything useful. Devon On 10/18/2017 05:46 PM, Deepak Tanwar wrote: > Hello, > > I am still facing problem. I have tried to reinstall MACS2 but nothing > helped. > > Thank you! > Deepak > > >> On Oct 16, 2017, at 4:00 PM, Deepak Tanwar <dktanwar(a)hotmail.com >> <mailto:dktanwar@hotmail.com>> wrote: >> >> Hi all, >> >> There is some problem with MACS2: >> >> export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: >> line 25: macs2: command not found Fatal error: Exit code 127 () Tool >> installed: >> /shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2 >> <http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2> >> >> Dependency Resolver Details >> Dependency Version Resolver Exact version Current Installation >> Status >> macs2 2.1.1.20160309 Conda True >> gawk 4.1.3 Conda True >> >> >> >> Thank you, >> Deepak > > > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ -- Devon Ryan, PhD Bioinformatician / Data manager Bioinformatics Core Facility Max Planck Institute for Immunobiology and Epigenetics Email: dpryan79(a)gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171018/c…> ------------------------------ Message: 6 Date: Wed, 18 Oct 2017 07:02:44 +0000 From: Enders Matthias <m.enders(a)npz-innovation.de> To: "galaxy-dev(a)lists.galaxyproject.org" <galaxy-dev(a)lists.galaxyproject.org> Subject: [galaxy-dev] Problems with BlastDB.loc Message-ID: <61B3F546DFD52B46B25883C23E2FF9DA294048BC(a)MAIL.npz.local> Content-Type: text/plain; charset="iso-8859-1" Dear Galaxy Dev List, we currently facing a problem with integrating new Blast Databases in our Galaxy instance. We added a the new DB to the file: /galaxy-central/tool-data/blastdb.loc But the new Database didn't show up in the respective tools, this situation remains also after restarting the galaxy instance and reloading the tool config (blasn for example). As we included several databases before (which worked fine) we tried to find the error an excluded (out-commented) an existing Db, but this database stayed in the tools. So the blastdb.loc file seems to be ignored by galaxy. (This is consistent for multiple users and browser, so we are sure this is not a client-sided Browser-Cache issue) So my questions are: Is there any kind of internal Cache in Galaxy which could explain this behavior? How can we track down / solve the issue? Our Galaxy Version is 17.05 Thanks a lot in advance! Mit freundlichen Grüßen i.A. Matthias Enders ********************************** [cid:image002.png@01CF9B54.EBA59810] NPZ Innovation GmbH Hohenlieth-Hof, D-24363 Holtsee Tel. +49-4351-736 189<tel:%2B49-4351-736%20189> Fax +49-4351-736 271<tel:%2B49-4351-736%20271> Mobil: +49-151-14247360<tel:%2B49-0151-14247360> Mail: m.enders(a)npz-innovation.de<mailto:m.enders@npz-innovation.de> Web: www.npz-innovation.de<http://www.npz-innovation.de/> Firmensitz Hohenlieth, Holtsee Amtsgericht Kiel, HRB 15342 Kl Geschäftsführer: Dr. Gunhild Leckband, Thorsten Pommer -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171018/5…> -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 6168 bytes Desc: image001.png URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171018/5…> ------------------------------ Subject: Digest Footer _______________________________________________ galaxy-dev mailing list galaxy-dev(a)lists.galaxyproject.org https://lists.galaxyproject.org/listinfo/galaxy-dev To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ------------------------------ End of galaxy-dev Digest, Vol 136, Issue 11 *******************************************

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error despite success
by Matthias Bernt 18 Oct '17

18 Oct '17

Dear list, today I got an erroneous result (red) despite the output of the tool to be seems fine. Seemingly there was an error during setting the metadata. ``` Fatal error: An error occured during execution, see stderr and stdout for more information Reading reference gene model /gpfs1/data/galaxy_server/galaxy-dev/database/files/002/dataset_2992.dat ... Done Loading SAM/BAM file ... Finished Total 62188 usable reads were sampled Traceback (most recent call last): File "/gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/001/1858/set_metadata_Ad6q_v.py", line 1, in from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy_ext/metadata/set_metadata.py", line 85, in set_metadata datatypes_registry.load_datatypes(root_dir=galaxy_root, config=datatypes_config) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/datatypes/registry.py", line 109, in load_datatypes tree = galaxy.util.parse_xml(config) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/util/__init__.py", line 214, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/xml/etree/ElementTree.py", line 647, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: '/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp_uHZbW' ``` Are there any suggestions how to continue with such a behavior. The file system on our cluster seems to be slow at the moment, could this be the cause? Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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Problems with BlastDB.loc
by Enders Matthias 18 Oct '17

18 Oct '17

Dear Galaxy Dev List, we currently facing a problem with integrating new Blast Databases in our Galaxy instance. We added a the new DB to the file: /galaxy-central/tool-data/blastdb.loc But the new Database didn't show up in the respective tools, this situation remains also after restarting the galaxy instance and reloading the tool config (blasn for example). As we included several databases before (which worked fine) we tried to find the error an excluded (out-commented) an existing Db, but this database stayed in the tools. So the blastdb.loc file seems to be ignored by galaxy. (This is consistent for multiple users and browser, so we are sure this is not a client-sided Browser-Cache issue) So my questions are: Is there any kind of internal Cache in Galaxy which could explain this behavior? How can we track down / solve the issue? Our Galaxy Version is 17.05 Thanks a lot in advance! Mit freundlichen Grüßen i.A. Matthias Enders ********************************** [cid:image002.png@01CF9B54.EBA59810] NPZ Innovation GmbH Hohenlieth-Hof, D-24363 Holtsee Tel. +49-4351-736 189<tel:%2B49-4351-736%20189> Fax +49-4351-736 271<tel:%2B49-4351-736%20271> Mobil: +49-151-14247360<tel:%2B49-0151-14247360> Mail: m.enders(a)npz-innovation.de<mailto:m.enders@npz-innovation.de> Web: www.npz-innovation.de<http://www.npz-innovation.de/> Firmensitz Hohenlieth, Holtsee Amtsgericht Kiel, HRB 15342 Kl Geschäftsführer: Dr. Gunhild Leckband, Thorsten Pommer

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Re: [galaxy-dev] galaxy-dev Digest, Vol 136, Issue 8
by Matthias Enders 18 Oct '17

18 Oct '17

Dear Galaxy Dev List, we currently searching for a good Genome Browser. As we run a local galaxy instance, we noticed the integrated GTB ("Galaxy Track Browser"). So my question is: Is there a roadmap for further support / development of the GTB? Or will it perhaps get replaced/deprecated in the near future (we read a lot of UCSC Genome Browser - Galaxy - Integration)? Another question would be on good sources/tutorials/manuals for configuring and setup for the GTB. Mit freundlichen Grüßen Matthias Enders ----------------------------------------------------------------------- GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.enders(a)german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844

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Problems with the test tool shed?
by Von Kuster, Greg 17 Oct '17

17 Oct '17

Hi all, I’m wondering if the TTS can be restarted. I’ve been seeing this of-and-on all afternoon. Thanks! Galaxy<http://galaxyproject.org/> The Test Tool Shed could not be reached You are seeing this message because a request to The Test Tool Shed timed out or was refused. This may be a temporary issue which could be resolved by retrying the operation you were performing. If you receive this message repeatedly or for an extended amount of time, please contact an administrator.

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primer blast tool
by Jochen Bick 13 Oct '17

13 Oct '17

Hi all, has anyone yet worked on wrapping primer-blast? https://www.ncbi.nlm.nih.gov/tools/primer-blast/ Cheers Jochen -- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 Office: Tannenstrasse 1 / TAN D 6.2 8092 Zurich, Switzerland Phone +41 44 632 28 25 jochen.bick(a)usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch

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Call for presentations at GMOD workshop at PAG
by Scott Cain 13 Oct '17

13 Oct '17

Hi all, This January in San Diego is the annual Plant and Animal Genomes (PAG) meeting (http://www.intlpag.org). As in previous PAGs, there will be several opportunities to present content related to GMOD projects. If you are interested in attending PAG and giving a talk at the GMOD workshop on Wednesday, January 17, please let me know. Your talk can either be about new developments/functionality in existing GMOD software, about how your organization is using the suite of GMOD software to good effect, or about technologies that you think the GMOD community would be interested in hearing about. Please email me directly with a title, an abstract or a vague idea of what you'd like to talk about. Also, if you'd really like to come but are having a hard time coming up with travel funds, please let me know, I might be able to help you with that too (up to a limit of one person anyway). Cheers, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

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Show history structure : Error 'Undefined' object is not callable
by julie dubois 12 Oct '17

12 Oct '17

Hi all, I'm on 17.05 galaxy version and display it on firefox. I'm trying to use "show structure" functionnality on my histories (I've never tried before this version) and I obtain this error : URL: http://192.168.100.98:8080/galaxy/history/display_structured File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/weberror/evalexception.py', line 431 in respond app_iter = self.application(environ, detect_start_response) File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/data/galaxy-dist/lib/galaxy/web/framework/base.py', line 135 in __call__ return self.handle_request( environ, start_response ) File '/data/galaxy-dist/lib/galaxy/web/framework/base.py', line 214 in handle_request body = method( trans, **kwargs ) File '/data/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/history.py', line 571 in display_structured return trans.fill_template( "history/display_structured.mako", items=items, history=history ) File '/data/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 891 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/data/galaxy-dist/lib/galaxy/web/framework/webapp.py', line 905 in fill_template_mako return template.render( **data ) File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/template.py', line 445 in render return runtime._render(self, self.callable_, args, data) File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 829 in _render **_kwargs_for_callable(callable_, data)) File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 864 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/data/galaxy-dist/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 890 in _exec_template callable_(context, *args, **kwargs) File '/data/galaxy-dist/database/compiled_templates/base.mako.py', line 63 in render_body __M_writer(unicode(next.body())) File '/data/galaxy-dist/database/compiled_templates/history/display_structured.mako.py', line 50 in render_body __M_writer(unicode(render_item( entity, children ))) File '/data/galaxy-dist/database/compiled_templates/history/display_structured.mako.py', line 35 in render_item return render_render_item(context._locals(__M_locals),entity,children) File '/data/galaxy-dist/database/compiled_templates/history/display_structured.mako.py', line 191 in render_render_item render_item_job( entity, children ) File '/data/galaxy-dist/database/compiled_templates/history/display_structured.mako.py', line 183 in render_item_job return render_render_item_job(context,job,children) File '/data/galaxy-dist/database/compiled_templates/history/display_structured.mako.py', line 239 in render_render_item_job __M_writer(unicode( show_params.inputs_recursive( tool.inputs, params_object, depth=1 ) )) File '/data/galaxy-dist/database/compiled_templates/show_params.mako.py', line 293 in render_inputs_recursive for i, element in enumerate(listify(param_values[input.name])): TypeError: 'Undefined' object is not callable Is it a problem with this history (I've tested with a full green history and with history containing red jobs without difference in error message) or with my galaxy configuration may be ? Thanks. Julie

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another conda problem
by Matthias Bernt 12 Oct '17

12 Oct '17

Dear list, thanks for giving me a workaround for yesterdays conda problem. Today I got a new one: I tried to install RSeQC which installs (including the dependencies) without reporting an error in the galaxy admin UI. But actually the package is not installed, e.g. infer_experiment.py can not be found in the environment. When I check the galaxy logs I find the following: `Installing conda-forge::wheel-0.30.0-py_1 requires a minimum conda version of 4.3.` Can I safely update conda to version 4.3? Galaxy's conda FAQ https://docs.galaxyproject.org/en/master/admin/conda_faq.html suggests 4.2.13? Is the successful reporting of the installation a bug? Cheers, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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galaxy-dev October 2017