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"Edit attributes" for interval dataset not consistent with documentation
by Peter Briggs 18 Jan '18

18 Jan '18

Dear Devs One of my local users has noticed that the "edit attributes" function for "interval"-type datasets is not consistent with the documentation at: https://galaxyproject.org/learn/datatypes/#interval This states that only CHROM, START, and END are required, with the implication that other fields are optional. However when editing the attributes for a dataset, if either of "Strand" or "Name" are not set to an explicit column number then "Save attributes" fails with the message: "Error occurred while saving. Please fill all the required fields and try again." This is true on both our local Galaxy running release_17.09 and also on Galaxy main. Is this a bug in the documentation, or the implementation? Thanks, Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

1 0

Error at the end of a BWA job
by SAPET, Frederic 18 Jan '18

18 Jan '18

Hello I've just installed BWA ((Galaxy Version 0.7.17.3) , Galaxy itself is On branch release_17.09). The first run is not a success. I can see that the BAM is created, but job is tagged as fail (Unable to finish job). It looks like close to this issue: https://github.com/galaxyproject/galaxy/issues/2083 I've checked, samtools is in the path. Do you have any ideas ? Thank you Fred Here is what I see in the log: galaxy.jobs.runners.drmaa DEBUG 2018-01-17 10:57:23,787 (7062/86331.universe) state change: job finished normally galaxy.model.metadata DEBUG 2018-01-17 10:57:23,993 setting metadata externally failed for HistoryDatasetAssociation 11537: 'invalidated' galaxy.jobs.runners ERROR 2018-01-17 10:57:24,108 (7062/86331.universe) Job wrapper finish method failed Traceback (most recent call last): File "/softs/bioinfo/galaxy-prod/lib/galaxy/jobs/runners/__init__.py", line 630, in finish_job job_state.job_wrapper.finish(stdout, stderr, exit_code) File "/softs/bioinfo/galaxy-prod/lib/galaxy/jobs/__init__.py", line 1287, in finish dataset.datatype.set_meta(dataset, overwrite=False) File "/softs/bioinfo/galaxy-prod/lib/galaxy/datatypes/binary.py", line 424, in set_meta exit_code = subprocess.call(args=command, stderr=open(stderr_name, 'wb')) File "/softs/add-ons/Python-2.7.12/lib/python2.7/subprocess.py", line 523, in call return Popen(*popenargs, **kwargs).wait() File "/softs/add-ons/Python-2.7.12/lib/python2.7/subprocess.py", line 711, in __init__ errread, errwrite) File "/softs/add-ons/Python-2.7.12/lib/python2.7/subprocess.py", line 1343, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory --- Frederic Sapet Bioinformatics Research Engineer BIOGEMMA - Upstream Genomics Group Centre de Recherche de Chappes CS 90126 63720 CHAPPES FRANCE Tel : +33 (0)4 73 67 88 54 Fax : +33 (0)4 73 67 88 99 E-mail : frederic.sapet(a)biogemma.com<mailto:frederic.sapet@biogemma.com>

2 2

User Registration Error
by Thomas, Dallas 17 Jan '18

17 Jan '18

Help Please, So I am feeling a bit dumb right now. I have set-up another local Galaxy test server and have enabled all of the user authentication stuff in the galaxy.ini. I am using nginx for proxy however am not using the external authentication or remote. Every time a user clicks on the User->Register - there is the following error: Internal Server Error Galaxy was unable to successfully complete your request URL: http://10.115.0.65:8080/user/create Module galaxy.web.framework.middleware.error:149 in __call__ >> <http://10.115.0.65:8080/user/create> app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ >> <http://10.115.0.65:8080/user/create> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> <http://10.115.0.65:8080/user/create> return self.application(environ, start_response) Module galaxy.web.framework.base:133 in __call__ >> <http://10.115.0.65:8080/user/create> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:191 in handle_request >> <http://10.115.0.65:8080/user/create> body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.user:746 in create >> <http://10.115.0.65:8080/user/create> status=status ) Module galaxy.web.framework.webapp:810 in fill_template >> <http://10.115.0.65:8080/user/create> return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework.webapp:818 in fill_template_mako >> <http://10.115.0.65:8080/user/create> template = template_lookup.get_template( filename ) Module mako.lookup:218 in get_template >> <http://10.115.0.65:8080/user/create> return self._load(srcfile, uri) Module mako.lookup:283 in _load >> <http://10.115.0.65:8080/user/create> **self.template_args) Module mako.template:218 in __init__ >> <http://10.115.0.65:8080/user/create> module = self._compile_from_file(path, filename) Module mako.template:245 in _compile_from_file >> <http://10.115.0.65:8080/user/create> module = imp.load_source(self.module_id, path, open(path, 'rb')) IOError: [Errno 13] Permission denied: '/home/galaxy/galaxy_dist/database/compiled_templates/user/register.mako.py' extra data<http://10.115.0.65:8080/user/create#extra_data> full traceback<http://10.115.0.65:8080/user/create#full_traceback> text version<http://10.115.0.65:8080/user/create#text_version> This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. Any help would be very much appreciated. Sincerely Dallas Thomas

3 2

Problem with dependencies: Conda/freebayes
by Matthias Enders 15 Jan '18

15 Jan '18

Following the suggestion from Devon Ryan @ https://biostar.usegalaxy.org/p/26197/ Our IT-people re-do the installation several times, until it works out. So it works on occasion.. 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: Donnerstag, 11. Januar 2018 18:00 An: galaxy-dev(a)lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 139, Issue 4 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. Re: Problem with dependencies: Conda/freebayes (Björn Grüning) 2. Re: Problem with dependencies: Conda/freebayes (Devon Ryan) 3. Re: Problems installing conda dependencies for seq2hla tool (Peter Briggs) 4. Re: Problem with dependencies: Conda/freebayes (Jennifer Hillman-Jackson) ---------------------------------------------------------------------- Message: 1 Date: Thu, 11 Jan 2018 09:44:10 +0100 From: Björn Grüning <bjoern.gruening(a)gmail.com> To: Matthias Enders <m.enders(a)german-seed-alliance.de>, "galaxy-dev(a)lists.galaxyproject.org" <galaxy-dev(a)lists.galaxyproject.org> Cc: Fabian Kaiser <f.kaiser(a)npz-innovation.de> Subject: Re: [galaxy-dev] Problem with dependencies: Conda/freebayes Message-ID: <2b047e78-2a48-02e2-b413-8c597d0d5a89(a)gmail.com> Content-Type: text/plain; charset=utf-8; format=flowed Hi Matthias, sorry for answering so late! Do you have any error message from the logs during installation? What means it is not recognised by Galaxy? Do you see the conda environment in /tool_deps/_conda/ ? Is freebayes crashing? Ciao, Bjoern > Dear Galaxy Dev Mailing List, > > We encountered a problem while installing freebayes and its via Tool > Shed. > > Galaxy installed correctly freebayes (1.1.0.46); samtools (0.1.19); > gawk (4.1.3) (all have the Current Installation Status "Installed > through Conda") but then failed on the last dependency "parallel". > (Status: "Not Installed") > > The strange thing is: parallel was installed correctly. Its callable > from the command line, (e.g. parallel --help works fine) and installed > with the latest version. But it's not recognized by Galaxy. > > We are using the Galaxy - Docker image in Version 17.09. > > Can you please assist us in resolving this? > > 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: Donnerstag, 21. > Dezember 2017 18:00 An: galaxy-dev(a)lists.galaxyproject.org Betreff: > galaxy-dev Digest, Vol 138, Issue 9 > > 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. Re: Galaxy v17.09 impersonation doesn't work (Ping Luo) > > > ---------------------------------------------------------------------- > > Message: 1 Date: Wed, 20 Dec 2017 13:52:45 -0600 From: Ping Luo > <luop0812(a)gmail.com> To: Hans-Rudolf Hotz <hrh(a)fmi.ch> Cc: galaxy-dev > <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] Galaxy > v17.09 impersonation doesn't work Message-ID: > <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=ADoyw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hans-Rudolf, > > I just started a brand new galaxy with the default internal database. > I did the minimal change to galaxy.ini so that I could use CAS > authentication. Still, impersonation failed. > > > Ping > > On Wed, Dec 20, 2017 at 3:02 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch> > wrote: > >> Hi Ping >> >> >> Does it work with a fresh installation ( v17.09) staring with an >> empty PostgrSQL database? >> >> >> Hans-Rudolf >> >> On 12/19/2017 03:41 PM, Ping Luo wrote: >> >>> Hans-Rudolf, >>> >>> Yes, I have set the flag to be true >>> >>> # Allow administrators to log in as other users (useful for >>> debugging) allow_user_impersonation = True >>> >>> We use CAS authentication and our database is Postgresql. Our >>> current Galaxy is v15.07 and impersonation works well. I have tried >>> v16.10 before and impersonation didn't work either. >>> >>> Thanks, >>> >>> Ping >>> >>> On Tue, Dec 19, 2017 at 5:12 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch >>> <mailto:hrh@fmi.ch>> wrote: >>> >>> Hi Ping >>> >>> The 'impersonate a user' function works for me with v17.09. >>> >>> >>> I assume, you have set: "allow_user_impersonation = True" in the >>> galaxy.ini file? >>> >>> >>> Do you encounter this problem, for the first time, i.e did it work >>> before using (v17.05 or earlier) and you only have the issues after >>> upgrading? >>> >>> What database do you use? >>> >>> Do you use external authentication? >>> >>> >>> Regards, Hans-Rudolf >>> >>> >>> >>> >>> >>> >>> On 12/18/2017 05:22 PM, Ping Luo wrote: >>> >>> The impersonation feature in Galaxy v17.09 doesn't work as expected. >>> >>> After clicking the person to impersonate, the webpage shows "you >>> have now logged in as xxx, return to home page', where 'xxx' is the >>> name of the person I want to impersonate. So far so good. But after >>> I click home, and check the login information, the login name is >>> still myself. >>> >>> Is there anything I missed in the configuration file? >>> >>> Thanks, >>> >>> Ping >>> >>> >>> ___________________________________________________________ >>> 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/ <https://lists.galaxyproject.o rg/> >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/ <http://galaxyproject.org/sear ch/> >>> >>> >>> > -------------- next part -------------- An HTML attachment was > scrubbed... URL: > <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/2017 > 1220/a562a405/attachment-0001.html> > > ------------------------------ > > 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 138, Issue 9 > ****************************************** > ___________________________________________________________ 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: 2 Date: Thu, 11 Jan 2018 09:47:42 +0100 From: Devon Ryan <dpryan(a)dpryan.com> To: Björn Grüning <bjoern.gruening(a)gmail.com> Cc: Fabian Kaiser <f.kaiser(a)npz-innovation.de>, "galaxy-dev(a)lists.galaxyproject.org" <galaxy-dev(a)lists.galaxyproject.org>, Matthias Enders <m.enders(a)german-seed-alliance.de> Subject: Re: [galaxy-dev] Problem with dependencies: Conda/freebayes Message-ID: <CADus9os+Adb=ciHgQaCaDqejn7tbe2ns5dS45TGjPv2iDa1taQ(a)mail.gmail.com> Content-Type: text/plain; charset="UTF-8" This is presumably the same question elsewhere: https://biostar.usegalaxy.org/p/26197/ -- 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, Jan 11, 2018 at 9:44 AM, Björn Grüning <bjoern.gruening(a)gmail.com> wrote: > Hi Matthias, > > sorry for answering so late! > > Do you have any error message from the logs during installation? > > What means it is not recognised by Galaxy? > Do you see the conda environment in /tool_deps/_conda/ ? > > Is freebayes crashing? > > Ciao, > Bjoern > > >> Dear Galaxy Dev Mailing List, >> >> We encountered a problem while installing freebayes and its via Tool >> Shed. >> >> Galaxy installed correctly freebayes (1.1.0.46); samtools (0.1.19); >> gawk (4.1.3) (all have the Current Installation Status "Installed >> through Conda") but then failed on the last dependency "parallel". >> (Status: "Not Installed") >> >> The strange thing is: parallel was installed correctly. Its callable >> from the command line, (e.g. parallel --help works fine) and >> installed with the latest version. But it's not recognized by Galaxy. >> >> We are using the Galaxy - Docker image in Version 17.09. >> >> Can you please assist us in resolving this? >> >> 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: Donnerstag, 21. >> Dezember 2017 18:00 An: galaxy-dev(a)lists.galaxyproject.org Betreff: >> galaxy-dev Digest, Vol 138, Issue 9 >> >> 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. Re: Galaxy v17.09 impersonation doesn't work (Ping Luo) >> >> >> --------------------------------------------------------------------- >> - >> >> Message: 1 Date: Wed, 20 Dec 2017 13:52:45 -0600 From: Ping Luo >> <luop0812(a)gmail.com> To: Hans-Rudolf Hotz <hrh(a)fmi.ch> Cc: galaxy-dev >> <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] Galaxy >> v17.09 impersonation doesn't work Message-ID: >> <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=ADoyw(a)mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hans-Rudolf, >> >> I just started a brand new galaxy with the default internal database. >> I did the minimal change to galaxy.ini so that I could use CAS >> authentication. Still, impersonation failed. >> >> >> Ping >> >> On Wed, Dec 20, 2017 at 3:02 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch> >> wrote: >> >>> Hi Ping >>> >>> >>> Does it work with a fresh installation ( v17.09) staring with an >>> empty PostgrSQL database? >>> >>> >>> Hans-Rudolf >>> >>> On 12/19/2017 03:41 PM, Ping Luo wrote: >>> >>>> Hans-Rudolf, >>>> >>>> Yes, I have set the flag to be true >>>> >>>> # Allow administrators to log in as other users (useful for >>>> debugging) allow_user_impersonation = True >>>> >>>> We use CAS authentication and our database is Postgresql. Our >>>> current Galaxy is v15.07 and impersonation works well. I have tried >>>> v16.10 before and impersonation didn't work either. >>>> >>>> Thanks, >>>> >>>> Ping >>>> >>>> On Tue, Dec 19, 2017 at 5:12 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch >>>> <mailto:hrh@fmi.ch>> wrote: >>>> >>>> Hi Ping >>>> >>>> The 'impersonate a user' function works for me with v17.09. >>>> >>>> >>>> I assume, you have set: "allow_user_impersonation = True" in the >>>> galaxy.ini file? >>>> >>>> >>>> Do you encounter this problem, for the first time, i.e did it work >>>> before using (v17.05 or earlier) and you only have the issues after >>>> upgrading? >>>> >>>> What database do you use? >>>> >>>> Do you use external authentication? >>>> >>>> >>>> Regards, Hans-Rudolf >>>> >>>> >>>> >>>> >>>> >>>> >>>> On 12/18/2017 05:22 PM, Ping Luo wrote: >>>> >>>> The impersonation feature in Galaxy v17.09 doesn't work as expected. >>>> >>>> After clicking the person to impersonate, the webpage shows "you >>>> have now logged in as xxx, return to home page', where 'xxx' is the >>>> name of the person I want to impersonate. So far so good. But after >>>> I click home, and check the login information, the login name is >>>> still myself. >>>> >>>> Is there anything I missed in the configuration file? >>>> >>>> Thanks, >>>> >>>> Ping >>>> >>>> >>>> ___________________________________________________________ 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/ <https://lists.galaxyproject.o >>>> rg/> >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/ <http://galaxyproject.org/sear >>>> ch/> >>>> >>>> >>>> >> -------------- next part -------------- An HTML attachment was >> scrubbed... URL: >> >> <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/201 >> 71220/a562a405/attachment-0001.html> >> >> ------------------------------ >> >> 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 138, Issue 9 >> ****************************************** >> ___________________________________________________________ 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/ >> > ___________________________________________________________ > 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: 3 Date: Thu, 11 Jan 2018 10:19:46 +0000 From: Peter Briggs <peter.briggs(a)manchester.ac.uk> To: "galaxy-dev(a)lists.galaxyproject.org" <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] Problems installing conda dependencies for seq2hla tool Message-ID: <E20AB71CD352854B9E24B5830826BC43C8564673(a)MBXP13.ds.man.ac.uk> Content-Type: text/plain; charset="us-ascii" Just to follow up on my own question, in case it's helpful to anyone else: Re the specific problem with not being able to install the seq2HLA 2.2 dependency via conda: in the end I build my own version and made it available to Galaxy as "Galaxy package" (https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html#ga…) which seemed to work okay. Re updating to conda 4.3.24: after the update this gave me problems with at least one dependency, due to the "--offline bug" described here: https://github.com/galaxyproject/galaxy/issues/5187 I applied Norbert Eichner's fix in PR #5233 (https://github.com/galaxyproject/galaxy/pull/5233) and reinstalled the conda dependency via "Manage Tool Dependencies" in the "Admin" interface, which seemed to fix that problem. It's not clear to me yet whether other conda dependencies might need to be reinstalled, or if applying the patch is sufficient. Best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ________________________________________ From: galaxy-dev [galaxy-dev-bounces(a)lists.galaxyproject.org] on behalf of Peter Briggs [peter.briggs(a)manchester.ac.uk] Sent: Friday, January 05, 2018 12:06 PM To: galaxy-dev(a)lists.galaxyproject.org Subject: [galaxy-dev] Problems installing conda dependencies for seq2hla tool Dear Devs I've been having problems installing the jjohnson/seq2hla tool from the toolshed on our production instance (running release_17.09). Specifically Galaxy has been unable to successfully install the seq2HLA 2.2 dependency via conda. However it seems to work fine when installing into a clean local instance. Initially the problem seemed to be that our version of conda was too old (we had 4.2.13), so while the __seq2HLA(a)2.2 env was being created, the 'seq2hla' package couldn't be installed into it (so Galaxy thought that the requirement was satifsfied but essentially it was broken). I updated conda to 4.3.24 and checked that our "ensure_conda_channels" setting matched the one in 'galaxy.ini.sample'. Now when I try to reinstall the seq2hla tool, the dependency cannot be installed at all - there seems to be an issue with the R 3.1.2-2 conda package which this needs to pull in: ERROR conda.core.link:_execute_actions(337): An error occurred while installing package 'defaults::r-3.1.2-2'. PaddingError: Placeholder of length '80' too short in package /XXXXXXXXX/galaxy/production/tool_dependencies/_conda/envs/__seq2HLA(a)2.2/bin/Rscript. The package must be rebuilt with conda-build > 2.0. XXXX... above is the path to the Galaxy installation directory, and the full path does exceed 80 characters. Presumably this worked okay on the local Galaxy install because there the path is shorter than the 80 character limit. Is there any workaround or fix that I can use to get this working on our production instance? Also, is it generally safe to update the Galaxy conda installation as I have done? Is there a recommended conda version for Galaxy? Thanks for your help, best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ 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: Thu, 11 Jan 2018 08:40:25 -0800 From: Jennifer Hillman-Jackson <jen(a)galaxyproject.org> To: Matthias Enders <m.enders(a)german-seed-alliance.de> Cc: Fabian Kaiser <f.kaiser(a)npz-innovation.de>, "galaxy-dev(a)lists.galaxyproject.org" <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] Problem with dependencies: Conda/freebayes Message-ID: <CAJ_ABepjC4w7ayYu2Hhj3SnoZ+NkAMiE4EH3=iSfM5UTCSQ1RQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello, Did the suggested help from Biostars help? https://biostar.usegalaxy.org/p/26197/ Thanks! Jen -- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org On Wed, Jan 3, 2018 at 6:01 AM, Matthias Enders < m.enders(a)german-seed-alliance.de> wrote: > Dear Galaxy Dev Mailing List, > > We encountered a problem while installing freebayes and its via Tool Shed. > > Galaxy installed correctly freebayes (1.1.0.46); samtools (0.1.19); > gawk > (4.1.3) (all have the Current Installation Status "Installed through > Conda") but then failed on the last dependency "parallel". (Status: > "Not > Installed") > > The strange thing is: parallel was installed correctly. Its callable > from the command line, (e.g. parallel --help works fine) and installed > with the latest version. But it's not recognized by Galaxy. > > We are using the Galaxy - Docker image in Version 17.09. > > Can you please assist us in resolving this? > > 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: Donnerstag, 21. Dezember 2017 18:00 > An: galaxy-dev(a)lists.galaxyproject.org > Betreff: galaxy-dev Digest, Vol 138, Issue 9 > > 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. Re: Galaxy v17.09 impersonation doesn't work (Ping Luo) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 20 Dec 2017 13:52:45 -0600 > From: Ping Luo <luop0812(a)gmail.com> > To: Hans-Rudolf Hotz <hrh(a)fmi.ch> > Cc: galaxy-dev <galaxy-dev(a)lists.galaxyproject.org> > Subject: Re: [galaxy-dev] Galaxy v17.09 impersonation doesn't work > Message-ID: > <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=ADoyw@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hans-Rudolf, > > I just started a brand new galaxy with the default internal database. > I did the minimal change to galaxy.ini so that I could use CAS authentication. > Still, impersonation failed. > > > Ping > > On Wed, Dec 20, 2017 at 3:02 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch> wrote: > > > Hi Ping > > > > > > Does it work with a fresh installation ( v17.09) staring with an > > empty PostgrSQL database? > > > > > > Hans-Rudolf > > > > On 12/19/2017 03:41 PM, Ping Luo wrote: > > > >> Hans-Rudolf, > >> > >> Yes, I have set the flag to be true > >> > >> # Allow administrators to log in as other users (useful for > >> debugging) > >> allow_user_impersonation = True > >> > >> We use CAS authentication and our database is Postgresql. Our > >> current Galaxy is v15.07 and impersonation works well. I have tried > >> v16.10 before and impersonation didn't work either. > >> > >> Thanks, > >> > >> Ping > >> > >> On Tue, Dec 19, 2017 at 5:12 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch > >> <mailto:hrh@fmi.ch>> wrote: > >> > >> Hi Ping > >> > >> The 'impersonate a user' function works for me with v17.09. > >> > >> > >> I assume, you have set: "allow_user_impersonation = True" in the > >> galaxy.ini file? > >> > >> > >> Do you encounter this problem, for the first time, i.e did it work > >> before using (v17.05 or earlier) and you only have the issues after > >> upgrading? > >> > >> What database do you use? > >> > >> Do you use external authentication? > >> > >> > >> Regards, Hans-Rudolf > >> > >> > >> > >> > >> > >> > >> On 12/18/2017 05:22 PM, Ping Luo wrote: > >> > >> The impersonation feature in Galaxy v17.09 doesn't work as > >> expected. > >> > >> After clicking the person to impersonate, the webpage shows "you > >> have > >> now logged in as xxx, return to home page', where 'xxx' is the > >> name of > >> the person I want to impersonate. So far so good. But after > >> I click > >> home, and check the login information, the login name is still > >> myself. > >> > >> Is there anything I missed in the configuration file? > >> > >> Thanks, > >> > >> Ping > >> > >> > >> ___________________________________________________________ > >> 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/ > >> <https://lists.galaxyproject.o rg/> > >> > >> To search Galaxy mailing lists use the unified search at: > >> http://galaxyproject.org/search/ > >> <http://galaxyproject.org/sear ch/> > >> > >> > >> > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/ > attachments/20171220/a562a405/attachment-0001.html> > > ------------------------------ > > 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 138, Issue 9 > ****************************************** > ___________________________________________________________ > 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/20180111/f…> ------------------------------ 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 139, Issue 4 ******************************************

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Problem with dependencies: Conda/freebayes
by Matthias Enders 12 Jan '18

12 Jan '18

Dear Galaxy Dev Mailing List, We encountered a problem while installing freebayes and its via Tool Shed. Galaxy installed correctly freebayes (1.1.0.46); samtools (0.1.19); gawk (4.1.3) (all have the Current Installation Status "Installed through Conda") but then failed on the last dependency "parallel". (Status: "Not Installed") The strange thing is: parallel was installed correctly. Its callable from the command line, (e.g. parallel --help works fine) and installed with the latest version. But it's not recognized by Galaxy. We are using the Galaxy - Docker image in Version 17.09. Can you please assist us in resolving this? 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: Donnerstag, 21. Dezember 2017 18:00 An: galaxy-dev(a)lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 138, Issue 9 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. Re: Galaxy v17.09 impersonation doesn't work (Ping Luo) ---------------------------------------------------------------------- Message: 1 Date: Wed, 20 Dec 2017 13:52:45 -0600 From: Ping Luo <luop0812(a)gmail.com> To: Hans-Rudolf Hotz <hrh(a)fmi.ch> Cc: galaxy-dev <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] Galaxy v17.09 impersonation doesn't work Message-ID: <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=ADoyw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hans-Rudolf, I just started a brand new galaxy with the default internal database. I did the minimal change to galaxy.ini so that I could use CAS authentication. Still, impersonation failed. Ping On Wed, Dec 20, 2017 at 3:02 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch> wrote: > Hi Ping > > > Does it work with a fresh installation ( v17.09) staring with an empty > PostgrSQL database? > > > Hans-Rudolf > > On 12/19/2017 03:41 PM, Ping Luo wrote: > >> Hans-Rudolf, >> >> Yes, I have set the flag to be true >> >> # Allow administrators to log in as other users (useful for >> debugging) >> allow_user_impersonation = True >> >> We use CAS authentication and our database is Postgresql. Our current >> Galaxy is v15.07 and impersonation works well. I have tried v16.10 >> before and impersonation didn't work either. >> >> Thanks, >> >> Ping >> >> On Tue, Dec 19, 2017 at 5:12 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch >> <mailto:hrh@fmi.ch>> wrote: >> >> Hi Ping >> >> The 'impersonate a user' function works for me with v17.09. >> >> >> I assume, you have set: "allow_user_impersonation = True" in the >> galaxy.ini file? >> >> >> Do you encounter this problem, for the first time, i.e did it work >> before using (v17.05 or earlier) and you only have the issues after >> upgrading? >> >> What database do you use? >> >> Do you use external authentication? >> >> >> Regards, Hans-Rudolf >> >> >> >> >> >> >> On 12/18/2017 05:22 PM, Ping Luo wrote: >> >> The impersonation feature in Galaxy v17.09 doesn't work as >> expected. >> >> After clicking the person to impersonate, the webpage shows "you >> have >> now logged in as xxx, return to home page', where 'xxx' is the >> name of >> the person I want to impersonate. So far so good. But after I >> click >> home, and check the login information, the login name is still >> myself. >> >> Is there anything I missed in the configuration file? >> >> Thanks, >> >> Ping >> >> >> ___________________________________________________________ >> 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/ >> <https://lists.galaxyproject.o rg/> >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/ >> <http://galaxyproject.org/sear ch/> >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20171220/a…> ------------------------------ 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 138, Issue 9 ******************************************

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Problems installing conda dependencies for seq2hla tool
by Peter Briggs 11 Jan '18

11 Jan '18

Dear Devs I've been having problems installing the jjohnson/seq2hla tool from the toolshed on our production instance (running release_17.09). Specifically Galaxy has been unable to successfully install the seq2HLA 2.2 dependency via conda. However it seems to work fine when installing into a clean local instance. Initially the problem seemed to be that our version of conda was too old (we had 4.2.13), so while the __seq2HLA(a)2.2 env was being created, the 'seq2hla' package couldn't be installed into it (so Galaxy thought that the requirement was satifsfied but essentially it was broken). I updated conda to 4.3.24 and checked that our "ensure_conda_channels" setting matched the one in 'galaxy.ini.sample'. Now when I try to reinstall the seq2hla tool, the dependency cannot be installed at all - there seems to be an issue with the R 3.1.2-2 conda package which this needs to pull in: ERROR conda.core.link:_execute_actions(337): An error occurred while installing package 'defaults::r-3.1.2-2'. PaddingError: Placeholder of length '80' too short in package /XXXXXXXXX/galaxy/production/tool_dependencies/_conda/envs/__seq2HLA(a)2.2/bin/Rscript. The package must be rebuilt with conda-build > 2.0. XXXX... above is the path to the Galaxy installation directory, and the full path does exceed 80 characters. Presumably this worked okay on the local Galaxy install because there the path is shorter than the 80 character limit. Is there any workaround or fix that I can use to get this working on our production instance? Also, is it generally safe to update the Galaxy conda installation as I have done? Is there a recommended conda version for Galaxy? Thanks for your help, best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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January Galactic News
by Dave Clements 06 Jan '18

06 Jan '18

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Galaxy v17.09 impersonation doesn't work
by Ping Luo 21 Dec '17

21 Dec '17

The impersonation feature in Galaxy v17.09 doesn't work as expected. After clicking the person to impersonate, the webpage shows "you have now logged in as xxx, return to home page', where 'xxx' is the name of the person I want to impersonate. So far so good. But after I click home, and check the login information, the login name is still myself. Is there anything I missed in the configuration file? Thanks, Ping

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tool publishing
by Matthias Bernt 18 Dec '17

18 Dec '17

Dear dev-list, I'm just trying to publish my first tool to the testtoolshed via planemo. I got some problem during the process. Maybe someone can kickstart me (I guess I just forgot something). I followed http://planemo.readthedocs.io/en/latest/publishing.html The step `planemo shed_create --shed_target testtoolshed` ``` Repository created cd '/home/berntm/projects/mb-galaxy-tools/fasta_regex_finder' && git rev-parse HEAD cd '/home/berntm/projects/mb-galaxy-tools/fasta_regex_finder' && git diff --quiet Repository [fasta_regex_finder] does not exist in the targeted Tool Shed. ``` When I check online the repository is there but no changeset seems available. Retrying fails (expected): `planemo shed_create --shed_target testtoolshed` ``` Unexpected HTTP status code: 400: {"err_msg": "You already own a repository named <b>fasta_regex_finder<\/b>, please choose a different name.", "err_code": 400008} ```` Also shed_diff fails `fasta_regex_finder git:(master) ✗ planemo shed_diff --shed_target testtoolshed` ``` shed_diff: Repository [fasta_regex_finder] does not exist in the targeted Tool Shed. ``` Any idea? 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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intended behaviour for multiple data sets
by Matthias Bernt 18 Dec '17

18 Dec '17

Dear list, In addition to single datasets tool file inputs allow to choose between - multiple dataset - dataset collection - some tools use repeat tags for multiple inputs I would like to know what the intended behavior of galaxy is for the three options considering multiple datasets? Is this described somewhere? Is it that the tool is applied to each of the multiple inputs separately or at once. For some tools one case makes more sense than the other. 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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