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Re: [Gmod-ajax] Problems installing jbrowse1
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From: Hans Vasquez-G. <hav...@uc...> - 2021-03-11 22:24:13
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Hi Colin, I just tried installing from the latest dev branch. Everything went smoothly this time. Thank you! Best, -Hans On Thu, Mar 11, 2021 at 1:38 PM Colin <col...@gm...> wrote: > I just pushed a fix to the "dev" branch of jbrowse with a possible fix for > the "Commit hash required" message I saw in your log file > > > If you are able to test it out, and see if you can run setup.sh on the dev > branch, let me know > > Try > > > git clone https://github.com/GMOD/jbrowse > cd jbrowse > git checkout dev > ./setup.sh > > We could then make a quick new release with that if it works > > > -Colin > > On Thu, Mar 11, 2021 at 12:30 PM Hans Vasquez-Gross < > hav...@uc...> wrote: > >> Hi Robert, >> >> No I haven't. In my previous lab, I had extended viroblast PHP code to >> keep track of source BLAST databases and pull up the specific genome >> reference in JBrowse using URL encoded tracks. However, this was all very >> specific to that lab. >> >> In the new lab I joined, I was going to use SequenceServer to connect the >> BLAST service to different JBrowse genome projects. Right now, It doesn't >> sound like there is an easy way to integrate SequenceServer with JB2. Thank >> you for your suggestion though. >> >> Colin: thank you for the issue report. I'll try the workaround. >> >> Best, >> -Hans >> >> On Thu, Mar 11, 2021 at 11:05 AM Robert Buels <rb...@gm...> wrote: >> >>> Regarding url encoded tracks, the currently best “jbrowse 2 way” of >>> creating tracks and injecting them into the browser is to directly embed a >>> jb2 embedded linear genome view in your application that you can fully >>> control. Have you considered going in that direction? >>> >>> >>> On Wed, Mar 10, 2021 at 6:22 PM Colin <col...@gm...> wrote: >>> >>>> Interesting... I think this error was also noted here >>>> https://github.com/GMOD/jbrowse/issues/1555 >>>> >>>> >>>> Probably we should remove our dependency in jbrowse 1 from installing a >>>> package directly from GitHub to properly fix, I think it is the jszlib >>>> dependency that we use >>>> >>>> >>>> -Colin >>>> >>>> On Wed, Mar 10, 2021, 6:39 PM Hans Vasquez-Gross via Gmod-ajax < >>>> gmo...@li...> wrote: >>>> >>>>> Hello, >>>>> >>>>> I recently installed jbrowse2 on a new system, but some of the >>>>> functionality that was in jbrowse1 is missing in jbrowse2 (URL encoded >>>>> tracks). Today, I tried installing jbrowse1, but am running into some >>>>> nodejs issues. >>>>> >>>>> When I try loading up the page, I can see my main.bundle.js is missing >>>>> (404 error) which I think is related to the nodejs problems. >>>>> >>>>> Please see setup log below. >>>>> >>>>> Any advice would be greatly appreciated. >>>>> >>>>> Thank you, >>>>> -Hans >>>>> >>>>> >>>>> > bash setup.sh >>>>> Gathering system information ...done. >>>>> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been >>>>> removed from setup. Their functionality has been superseded by >>>>> add-bam-track.pl and add-bw-track.pl. If you require the old >>>>> versions, please use JBrowse 1.12.3 or earlier. >>>>> Installing node.js dependencies and building with webpack ... failed. >>>>> See setup.log file for error messages. >>>>> setup cannot continue, aborting. >>>>> >>>>> Gathering system information ... >>>>> ============== System information ==== >>>>> + lsb_release -a >>>>> No LSB modules are available. >>>>> Distributor ID: Ubuntu >>>>> Description: Ubuntu 20.04.1 LTS >>>>> Release: 20.04 >>>>> Codename: focal >>>>> + uname -a >>>>> Linux borlaug 5.8.0-36-generic #40~20.04.1-Ubuntu SMP Wed Jan 6 >>>>> 10:15:55 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux >>>>> + sw_vers >>>>> setup.sh: line 89: sw_vers: command not found >>>>> + grep MemTotal /proc/meminfo >>>>> MemTotal: 65733500 kB >>>>> + echo >>>>> >>>>> + echo >>>>> >>>>> >>>>> done. >>>>> >>>>> >>>>> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been >>>>> removed from setup. Their functionality has been superseded by >>>>> add-bam-track.pl and add-bw-track.pl. If you require the old >>>>> versions, please use JBrowse 1.12.3 or earlier. >>>>> >>>>> >>>>> Installing node.js dependencies and building with webpack ... >>>>> Node v15.11.0 installed at /usr/bin/node with npm 7.6.0 >>>>> npm WARN deprecated ini@1.3.5: Please update to ini >=1.3.6 to avoid >>>>> a prototype pollution issue >>>>> npm WARN deprecated urix@0.1.0: Please see >>>>> https://github.com/lydell/urix#deprecated >>>>> npm WARN deprecated sprintf@0.1.5: The sprintf package is deprecated >>>>> in favor of sprintf-js. >>>>> npm WARN deprecated har-validator@5.1.3: this library is no longer >>>>> supported >>>>> npm WARN deprecated mkdirp@0.5.3: Legacy versions of mkdirp are no >>>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface >>>>> has changed to use Promises in 1.x.) >>>>> npm WARN deprecated resolve-url@0.2.1: >>>>> https://github.com/lydell/resolve-url#deprecated >>>>> npm WARN deprecated chokidar@1.7.0: Chokidar 2 will break on node >>>>> v14+. Upgrade to chokidar 3 with 15x less dependencies. >>>>> npm WARN deprecated circular-json@0.3.3: CircularJSON is in >>>>> maintenance only, flatted is its successor. >>>>> npm WARN deprecated xmldom@0.1.31: Deprecated due to CVE-2021-21366 >>>>> resolved in 0.5.0 >>>>> npm WARN deprecated filesaver.js@0.2.0: Unmaintained namespace. >>>>> Please use the file-saver package: >>>>> https://www.npmjs.com/package/file-saver >>>>> npm WARN deprecated debug@3.2.6: Debug versions >=3.2.0 <3.2.7 || >=4 >>>>> <4.3.1 have a low-severity ReDos regression when used in a Node.js >>>>> environment. It is recommended you upgrade to 3.2.7 or 4.3.1. ( >>>>> https://github.com/visionmedia/debug/issues/797) >>>>> npm WARN deprecated chokidar@2.1.8: Chokidar 2 will break on node >>>>> v14+. Upgrade to chokidar 3 with 15x less dependencies. >>>>> WARN deprecated debug@4.1.1: Debug versions >=3.2.0 <3.2.7 || >=4 >>>>> <4.3.1 have a low-severity ReDos regression when used in a Node.js >>>>> environment. It is recommended you upgrade to 3.2.7 or 4.3.1. ( >>>>> https://github.com/visionmedia/debug/issues/797) >>>>> npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no >>>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface >>>>> has changed to use Promises in 1.x.) >>>>> npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no >>>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface >>>>> has changed to use Promises in 1.x.) >>>>> npm WARN deprecated babel-eslint@8.2.6: babel-eslint is now >>>>> @babel/eslint-parser. This package will no longer receive updates. >>>>> npm WARN deprecated mkdirp@0.5.1: Legacy versions of mkdirp are no >>>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface >>>>> has changed to use Promises in 1.x.) >>>>> npm WARN deprecated request@2.88.2: request has been deprecated, see >>>>> https://github.com/request/request/issues/3142 >>>>> npm WARN deprecated uglify-es@3.3.9: support for ECMAScript is >>>>> superseded by `uglify-js` as of v3.13.0 >>>>> npm WARN deprecated webdriverio@4.14.4: outdated version, please use >>>>> @next >>>>> npm WARN deprecated core-js@2.6.11: core-js@<3 is no longer >>>>> maintained and not recommended for usage due to the number of issues. >>>>> Please, upgrade your dependencies to the actual version of core-js@3. >>>>> >>>>> added 1500 packages, and audited 1501 packages in 3m >>>>> >>>>> 24 packages are looking for funding >>>>> run `npm fund` for details >>>>> >>>>> 35 vulnerabilities (21 low, 3 moderate, 11 high) >>>>> >>>>> To address issues that do not require attention, run: >>>>> npm audit fix >>>>> >>>>> To address all issues possible (including breaking changes), run: >>>>> npm audit fix --force >>>>> >>>>> Some issues need review, and may require choosing >>>>> a different dependency. >>>>> >>>>> Run `npm audit` for details. >>>>> yarn install v1.22.4 >>>>> warning package-lock.json found. Your project contains lock files >>>>> generated by tools other than Yarn. It is advised not to mix package >>>>> managers in order to avoid resolution inconsistencies caused by >>>>> unsynchronized lock files. To clear this warning, remove package-lock.json. >>>>> [1/4] Resolving packages... >>>>> warning ava > chokidar > fsevents@1.2.13: fsevents 1 will break on >>>>> node v14+ and could be using insecure binaries. Upgrade to fsevents 2. >>>>> warning webpack > watchpack > chokidar > fsevents@1.2.13: fsevents 1 >>>>> will break on node v14+ and could be using insecure binaries. Upgrade to >>>>> fsevents 2. >>>>> [2/4] Fetching packages... >>>>> error An unexpected error occurred: "Commit hash required". >>>>> info If you think this is a bug, please open a bug report with the >>>>> information provided in >>>>> "/var/www/html/jbrowse-1.16.10-release/yarn-error.log". >>>>> info Visit https://yarnpkg.com/en/docs/cli/install for documentation >>>>> about this command. >>>>> >>>>> >>>>> Formatting Volvox example data ...done. >>>>> To see the volvox example data, browse to >>>>> http://your.jbrowse.root/index.html?data=sample_data/json/volvox. >>>>> >>>>> Formatting Yeast example data ...done. >>>>> To see the yeast example data, browse to >>>>> http://your.jbrowse.root/index.html?data=sample_data/json/yeast. >>>>> _______________________________________________ >>>>> Gmod-ajax mailing list >>>>> Gmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>> >>>> _______________________________________________ >>>> Gmod-ajax mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>> >>> >> >> -- >> Hans Vasquez-Gross >> <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> >> PhD Candidate >> Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ >> Department of Plant Science >> University of California at Davis >> Email: hav...@uc... >> Skype: hansvg.ucd >> > -- Hans Vasquez-Gross <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> PhD Candidate Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ Department of Plant Science University of California at Davis Email: hav...@uc... Skype: hansvg.ucd |
