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charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi I followed https://github.com/phnmnl/phenomenal-h2020/wiki/QuickStart-Insta= llation-for-Local-PhenoMeNal-Workflow with Older Galaxy chart to deploy loc= al galaxy-k8s instance with minikube on Windows 10. The following message c= ame from the logs of my pod. I can't connect to my local instance. Can you = please give me some advice to debug it and make it work? Thank you very muc= h. kubectl logs galaxy-k8s-tr6fc [ run_galaxy_config.sh ] -- Galaxy sqlite directory created since we are no= t using postgresql [ run_galaxy_config.sh ] -- Replaced galaxy ini for the user's injected one debconf: unable to initialize frontend: Dialog debconf: (Dialog frontend will not work on a dumb terminal, an emacs shell = buffer, or without a controlling terminal.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype dpkg-preconfigure: unable to re-open stdin: [WARNING]: It is unneccessary to use '{{' in loops, leave variables in loo= p expressions bare. [ run_galaxy_config.sh ] -- Playbook for galaxy config run. [ run_galaxy_config.sh ] -- Set k8s pull policy to use with Galaxy to IfNot= Present on job_conf.xml [ run_galaxy_config.sh ] -- Need to set up galaxy database for admin user s= etup... /galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ss= l_.py:369: SNIMissingWarning: An HTTPS request has been made, but the SNI (= Server Name Indication) extension to TLS is not available on this platform.= This may cause the server to present an incorrect TLS certificate, which c= an cause validation failures. You can upgrade to a newer version of Python = to solve this. For more information, see https://urllib3.readthedocs.io/en/= latest/advanced-usage.html#ssl-warnings SNIMissingWarning /galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/urllib3/util/ss= l_.py:160: InsecurePlatformWarning: A true SSLContext object is not availab= le. This prevents urllib3 from configuring SSL appropriately and may cause = certain SSL connections to fail. You can upgrade to a newer version of Pyth= on to solve this. For more information, see https://urllib3.readthedocs.io/= en/latest/advanced-usage.html#ssl-warnings InsecurePlatformWarning galaxy.tools.deps WARNING 2019-08-16 19:20:48,175 Path './database/dependen= cies' does not exist, ignoring galaxy.tools.deps WARNING 2019-08-16 19:20:48,175 Path './database/dependen= cies' is not directory, ignoring galaxy.tools.deps.installable WARNING 2019-08-16 19:20:48,190 Conda not ins= talled and auto-installation disabled. galaxy.tools.deps.installable WARNING 2019-08-16 19:20:48,190 Conda not ins= talled and auto-installation disabled. tail: unrecognized file system type 0x794c7630 for 'paster.log'. please rep= ort this to bug-coreutils@gnu.org. reverting to polling Best wishes, Jianliang --_000_AM0PR06MB6131D077931EA62DB98F2E19CCAF0AM0PR06MB6131eurp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi 


I followed https://github.com/phnmnl/phenomenal-h2020/wiki/QuickStart-Inst= allation-for-Local-PhenoMeNal-Workflow with Older Galaxy chart to deploy local galaxy-k8s instance with minikube on Wi= ndows 10. The following message came from the logs of my pod. I can't conne= ct to my local instance. Can you please give me some advice to debug it and= make it work? Thank you very much.


kubectl logs galaxy-k8s-tr6fc<= br>
[ run_galaxy_config.sh ] -- Galaxy sqlite directory created since we a= re not using postgresql
[ run_galaxy_config.sh ] -- Replaced galaxy ini for the user's injecte= d one
debconf: unable to initialize frontend: Dialog
debconf: (Dialog frontend will not work on a dumb terminal, an emacs s= hell buffer, or without a controlling terminal.)
debconf: falling back to frontend: Readline
debconf: unable to initialize frontend: Readline
debconf: (This frontend requires a controlling tty.)
debconf: falling back to frontend: Teletype
dpkg-preconfigure: unable to re-open stdin:
 [WARNING]: It is unneccessary to use '{{' in loops, leave variab= les in loop
expressions bare.

[ run_galaxy_config.sh ] -- Playbook for galaxy config run.
[ run_galaxy_config.sh ] -- Set k8s pull policy to use with Galaxy to = IfNotPresent on job_conf.xml
[ run_galaxy_config.sh ] -- Need to set up galaxy database for admin u= ser setup...
/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/urllib3/ut= il/ssl_.py:369: SNIMissingWarning: An HTTPS request has been made, but the = SNI (Server Name Indication) extension to TLS is not available on this plat= form. This may cause the server to present an incorrect TLS certificate, which can cause validation failur= es. You can upgrade to a newer version of Python to solve this. For more in= formation, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html= #ssl-warnings
  SNIMissingWarning
/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/urllib3/ut= il/ssl_.py:160: InsecurePlatformWarning: A true SSLContext object is not av= ailable. This prevents urllib3 from configuring SSL appropriately and may c= ause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more= information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.h= tml#ssl-warnings
  InsecurePlatformWarning
galaxy.tools.deps WARNING 2019-08-16 19:20:48,175 Path './database/dep= endencies' does not exist, ignoring
galaxy.tools.deps WARNING 2019-08-16 19:20:48,175 Path './database/dep= endencies' is not directory, ignoring
galaxy.tools.deps.installable WARNING 2019-08-16 19:20:48,190 Conda no= t installed and auto-installation disabled.
galaxy.tools.deps.installable WARNING 2019-08-16 19:20:48,190 Conda no= t installed and auto-installation disabled.
tail: unrecognized file system type 0x794c7630 for 'paster.log'. pleas= e report this to bug-coreutils@gnu.org. reverting to polling



   Best wishes,

Jianliang


--_000_AM0PR06MB6131D077931EA62DB98F2E19CCAF0AM0PR06MB6131eurp_-- From unknown Thu Sep 11 08:44:09 2025 X-Loop: help-debbugs@gnu.org Subject: bug#37058: Error message with local deployment of Galaxy-k8s Resent-From: Assaf Gordon Original-Sender: "Debbugs-submit" Resent-CC: bug-coreutils@gnu.org Resent-Date: Fri, 16 Aug 2019 21:46:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 37058 X-GNU-PR-Package: coreutils X-GNU-PR-Keywords: To: "Gao, Jianliang" , 37058@debbugs.gnu.org Received: via spool by 37058-submit@debbugs.gnu.org id=B37058.15659919451547 (code B ref 37058); Fri, 16 Aug 2019 21:46:02 +0000 Received: (at 37058) by debbugs.gnu.org; 16 Aug 2019 21:45:45 +0000 Received: from localhost ([127.0.0.1]:55113 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hyk2b-0000OQ-5G for submit@debbugs.gnu.org; Fri, 16 Aug 2019 17:45:45 -0400 Received: from mail-pg1-f173.google.com ([209.85.215.173]:41456) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1hyk2Y-0000G2-Nw; Fri, 16 Aug 2019 17:45:43 -0400 Received: by mail-pg1-f173.google.com with SMTP id x15so3557220pgg.8; Fri, 16 Aug 2019 14:45:42 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=subject:to:references:from:message-id:date:user-agent:mime-version :in-reply-to:content-language:content-transfer-encoding; bh=WV59GJYyxl2E9eMvNo9ZhzynVVvIFCK+iA32InFdGDw=; b=oUJi/U+Gb06g2pKdCFZR1JkXdesf2KRY+erbkyCIdYuIxer42ABhJpZFzpTj1VMQ3j Dmc6L7kkylf/gOvwWriNoSW68LHyUysobNxEaNaMGj8/IYFWF6dgbc/eqPoqvfBNj7U2 qS4VETi2CQXJDE2XUvCEirHI3gA769ZWJY97PoNu1LOpmXls0JV+pkgazm47j14/z3Qk Hn+krTpbvq1e76ZPpvToz4HTE+ymQMrpSqv6yyoaYIXwXOun1CMze/2T3zi+SBe7hP6B wlJ9rBxop9wDEbqGAO5SNHr3xu6FhI76XgCzomAFLk2ko4tHzMA8y+FN9si3fIxcJpkj 4QIw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:subject:to:references:from:message-id:date :user-agent:mime-version:in-reply-to:content-language :content-transfer-encoding; bh=WV59GJYyxl2E9eMvNo9ZhzynVVvIFCK+iA32InFdGDw=; b=YoYdWLONBQX/rcGsTvljwWNt71gNAcIDSZVdCg8o+vaNZVPyhJ7TmcNGQ6DK6gPhzn jfjIxA3w0kmExaz8YBg3IEq7WjzQ8KHK0w04bxxlu6IM4Jj1Pj1BtJ8/XcCQ4q3FTanD 6xx6LWPRo/UXeILpkfC+ciGo5qOesVoGRMlYdz9uQrcYkcKm6vAI7KOSRBsDXszs2E25 XFFbBoDtxvxCK5FgbIFZodsHf4CORuoucaIrBgFw37qus18pWT2FBUL2UPOD3GJVKvOe +Jh/7rwqmWgLlKU7AQH7LuohIIPpamz7BHoW9m74sZDIWINY1jO0eb0ypTi1U5dI8AyM VlyQ== X-Gm-Message-State: APjAAAUhEvtWIidVTF9JZ315JIlgfoceQea9Aldh6LFyYEZ0tzx3wjYX piwVIOqRJyi3P3KZcvHOao2Y6lL3 X-Google-Smtp-Source: APXvYqyucHdzoVHfI/gUjjujjTK3bElbqnsyq7wWR0M3G7KbJrpBTTNaDxuyfvL4R/4NZ1+knbCGtg== X-Received: by 2002:aa7:9799:: with SMTP id o25mr12871987pfp.74.1565991935778; Fri, 16 Aug 2019 14:45:35 -0700 (PDT) Received: from tomato.moose.housegordon.com (moose.housegordon.com. [184.68.105.38]) by smtp.googlemail.com with ESMTPSA id h11sm5631042pgv.5.2019.08.16.14.45.34 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Fri, 16 Aug 2019 14:45:34 -0700 (PDT) References: From: Assaf Gordon Message-ID: <8a903988-5ee3-923b-ce26-3dd429ebe8bf@gmail.com> Date: Fri, 16 Aug 2019 15:45:33 -0600 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:60.0) Gecko/20100101 Thunderbird/60.8.0 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8; format=flowed Content-Language: en-US Content-Transfer-Encoding: 7bit X-Spam-Score: -0.3 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.3 (-) tag 37058 notabug close 37058 stop Hello, Two issues are mixed here. First: On 2019-08-16 2:17 p.m., Gao, Jianliang wrote: > I followed https://github.com/phnmnl/phenomenal-h2020/wiki/QuickStart-Installation-for-Local-PhenoMeNal-Workflow with Older Galaxy chart to deploy local galaxy-k8s instance with minikube on Windows 10. The following message came from the logs of my pod. I can't connect to my local instance. [...] > kubectl logs galaxy-k8s-tr6fc > [ run_galaxy_config.sh ] -- Galaxy sqlite directory created since we are not using postgresql > [ run_galaxy_config.sh ] -- Replaced galaxy ini for the user's injected one [...] > dpkg-preconfigure: unable to re-open stdin: > [WARNING]: It is unneccessary to use '{{' in loops, leave variables in loop > expressions bare. [...] > galaxy.tools.deps WARNING 2019-08-16 19:20:48,175 Path './database/dependencies' does not exist, ignoring > galaxy.tools.deps WARNING 2019-08-16 19:20:48,175 Path './database/dependencies' is not directory, ignoring > galaxy.tools.deps.installable WARNING 2019-08-16 19:20:48,190 Conda not installed and auto-installation disabled. > galaxy.tools.deps.installable WARNING 2019-08-16 19:20:48,190 Conda not installed and auto-installation disabled. These are issues related your Galaxy setup. (for other readers: "Galaxy" in this context is a web-based framework for bioinformatics analysis, see https://galaxyproject.org/ and https://usegalaxy.org ). Such issues are best asked in their support forums: https://galaxyproject.org/support/ https://help.galaxyproject.org This includes problems in underlying layers, such as the 'dpkg' errors above that result from deploying Galaxy VMs or instances or kubernetes or containers etc. > tail: unrecognized file system type 0x794c7630 for 'paster.log'. please report this to bug-coreutils@gnu.org. reverting to polling This warning indeed comes from coreutils program 'tail', however it is harmless in your situation. For more details, see here: https://www.gnu.org/software/coreutils/filesystems.html --- A cursory look at the error logs makes it seem like "bug-coreutils@gnu.org" is the place to ask General questions about "Galaxy" server (because it is the last thing mentioned), but that is not the case. We can only help with coreutils programs (e.g. 'tail'). Please contact the Galaxy team for galaxy-related issues. Hope this helps. regards, - assaf