cmdcolin
commented
6 years ago Can you check out the setup.log file and paste it here? I am going to suspect that somehow it did not complete properly
Closed tiramisutes closed 6 years ago
cmdcolin
commented
6 years ago Can you check out the setup.log file and paste it here? I am going to suspect that somehow it did not complete properly
tiramisutes
commented
6 years ago This is some test content!
This message brought to you by the number \'+Math.round(Math.random()*100)+\'.
\';} ', 'action' => 'contentDialog', 'title' => 'function(track,feature,div) { return \'Random content snippet \'+Math.random()+\' title!\'; }', 'label' => 'Popup with content snippet from a function (feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'content' => 'This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.
', 'action' => 'contentDialog', 'title' => '{randomNumberTitle}', 'label' => 'Popup with content snippet from string (feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'action' => '{exampleFeatureClick}', 'label' => '{randomNumberLabel}' } ], 'hooks' => { 'modify' => 'function( track, feature, div ) { div.style.backgroundColor = [\'green\',\'blue\',\'red\',\'orange\',\'purple\'][Math.round(Math.random()*5)];}' }, 'key' => 'HTMLFeatures - Features with right-click menus', 'feature' => [ 'match' ], 'shortDescription' => 'Features with customized right-click menus', 'compress' => 0, 'metadata' => { 'category' => 'Miscellaneous', 'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.' } }; searching for features of type: match working on track Genes mergedTrackCfg: $VAR1 = { 'fmtDetailValue_Name' => 'function(name,feature) { if(feature.get(\'type\')==\'gene\') { return name + \' [NCBI custom link]\'; } else { return name; } }', 'fmtMetaDescription_Name' => 'function(name) { return \'[Custom description]\'; }', 'fmtMetaValue_Name' => 'function(name) { return name+\' [Track with custom callbacks for About track popup]\'; }', 'key' => 'CanvasFeatures - Protein-coding genes', 'onClick' => { 'action' => 'defaultDialog', 'title' => '{type} {name}', 'label' => 'This is some test content!
This message brought to you by the number \'+Math.round(Math.random()*100)+\'.
\';} ', 'action' => 'contentDialog', 'title' => 'function(track,feature,div) { return \'Random content snippet \'+Math.random()+\' title!\'; }', 'label' => 'Popup with content snippet from a function (feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'content' => 'This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.
', 'action' => 'contentDialog', 'title' => '{randomNumberTitle}', 'label' => 'Popup with content snippet from string (feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'action' => '{exampleFeatureClick}', 'label' => '{randomNumberLabel}' } ], 'hooks' => { 'modify' => 'function( track, feature, div ) { div.style.backgroundColor = [\'green\',\'blue\',\'red\',\'orange\',\'purple\'][Math.round(Math.random()*5)];}' }, 'key' => 'HTMLFeatures - Features with right-click menus', 'feature' => [ 'match' ], 'shortDescription' => 'Features with customized right-click menus', 'compress' => 0, 'metadata' => { 'category' => 'Miscellaneous', 'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.' } }; searching for features of type: match working on track Genes mergedTrackCfg: $VAR1 = { 'fmtDetailValue_Name' => 'function(name,feature) { if(feature.get(\'type\')==\'gene\') { return name + \' [NCBI custom link]\'; } else { return name; } }', 'fmtMetaDescription_Name' => 'function(name) { return \'[Custom description]\'; }', 'fmtMetaValue_Name' => 'function(name) { return name+\' [Track with custom callbacks for About track popup]\'; }', 'key' => 'CanvasFeatures - Protein-coding genes', 'onClick' => { 'action' => 'defaultDialog', 'title' => '{type} {name}', 'label' => 'cmdcolin
commented
6 years ago I think you are not running from the github clone, I can see in the setup.log that this is from JBrowse-1.15.1.zip or similar.
Are you using the github clone or the downloaded zip release files? I'm just wondering because it depends on what you're using for what instructions you need :)
tiramisutes
commented
6 years ago Yes, from downloading with JBrowse-1.15.1.zip. I don't knower It's different with git clone.
cmdcolin
commented
6 years ago There are actually three cases here
Otherwise just setup with Apache or nginx probably :)
cmdcolin
commented
6 years ago We will be rewriting the so called "quick start guide" and hopefully make this easier
tiramisutes
commented
6 years ago I try git clone from GitHub, but have same problem as show in picture ( jbrowse).
This is some test content!
This message brought to you by the number \'+Math.round(Math.random()*100)+\'.
\';} ', 'action' => 'contentDialog', 'title' => 'function(track,feature,div) { return \'Random content snippet \'+Math.random()+\' title!\'; }', 'label' => 'Popup with content snippet from a function (feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'content' => 'This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.
', 'action' => 'contentDialog', 'title' => '{randomNumberTitle}', 'label' => 'Popup with content snippet from string (feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'action' => '{exampleFeatureClick}', 'label' => '{randomNumberLabel}' } ], 'hooks' => { 'modify' => 'function( track, feature, div ) { div.style.backgroundColor = [\'green\',\'blue\',\'red\',\'orange\',\'purple\'][Math.round(Math.random()*5)];}' }, 'key' => 'HTMLFeatures - Features with right-click menus', 'feature' => [ 'match' ], 'shortDescription' => 'Features with customized right-click menus', 'compress' => 0, 'metadata' => { 'category' => 'Miscellaneous', 'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.' } }; searching for features of type: match working on track Genes mergedTrackCfg: $VAR1 = { 'fmtDetailValue_Name' => 'function(name,feature) { if(feature.get(\'type\')==\'gene\') { return name + \' [NCBI custom link]\'; } else { return name; } }', 'fmtMetaDescription_Name' => 'function(name) { return \'[Custom description]\'; }', 'fmtMetaValue_Name' => 'function(name) { return name+\' [Track with custom callbacks for About track popup]\'; }', 'key' => 'CanvasFeatures - Protein-coding genes', 'onClick' => { 'action' => 'defaultDialog', 'title' => '{type} {name}', 'label' => 'This is some test content!
This message brought to you by the number \'+Math.round(Math.random()*100)+\'.
\';} ', 'action' => 'contentDialog', 'title' => 'function(track,feature,div) { return \'Random content snippet \'+Math.random()+\' title!\'; }', 'label' => 'Popup with content snippet from a function (feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'content' => 'This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.
', 'action' => 'contentDialog', 'title' => '{randomNumberTitle}', 'label' => 'Popup with content snippet from string (feature {name})' }, { 'iconClass' => 'dijitIconDatabase', 'action' => '{exampleFeatureClick}', 'label' => '{randomNumberLabel}' } ], 'hooks' => { 'modify' => 'function( track, feature, div ) { div.style.backgroundColor = [\'green\',\'blue\',\'red\',\'orange\',\'purple\'][Math.round(Math.random()*5)];}' }, 'key' => 'HTMLFeatures - Features with right-click menus', 'feature' => [ 'match' ], 'shortDescription' => 'Features with customized right-click menus', 'compress' => 0, 'metadata' => { 'category' => 'Miscellaneous', 'Description' => 'Features with extensively customized right-click menus, and with their colors set at random by a JavaScript callback.' } }; searching for features of type: match working on track Genes mergedTrackCfg: $VAR1 = { 'fmtDetailValue_Name' => 'function(name,feature) { if(feature.get(\'type\')==\'gene\') { return name + \' [NCBI custom link]\'; } else { return name; } }', 'fmtMetaDescription_Name' => 'function(name) { return \'[Custom description]\'; }', 'fmtMetaValue_Name' => 'function(name) { return name+\' [Track with custom callbacks for About track popup]\'; }', 'key' => 'CanvasFeatures - Protein-coding genes', 'onClick' => { 'action' => 'defaultDialog', 'title' => '{type} {name}', 'label' => 'cmdcolin
commented
6 years ago Do you have any output from the javascript console? It does appear to have successfully compiled via setup.sh!
tiramisutes
commented
6 years ago Just a blank page with Loading... (picture)
cmdcolin
commented
6 years ago I am looking for info in this thing called the "console log", here are some instructions to open it
https://developer.mozilla.org/en-US/docs/Tools/Browser_Console
Thanks for your patience :)
tiramisutes
commented
6 years ago Yes, I check the Browser Console and find some error.
Failed to load native module at path '/usr/lib64/firefox/components/libxpcomsample.so': (80004005) /usr/lib64/firefox/components/libxpcomsample.so: cannot open shared object file: No such file or directory
Could not read chrome manifest 'file:///usr/lib64/firefox/browser/extensions/%7B972ce4c6-7e08-4474-a285-3208198ce6fd%7D/chrome.manifest'.
The character encoding of the HTML document was not declared. The document will render with garbled text in some browser configurations if the document contains characters from outside the US-ASCII range. The character encoding of the page must be declared in the document or in the transfer protocol. index.html
Content Security Policy: Couldn't process unknown directive 'worker-src' <unknown>
Content Security Policy: Couldn't process unknown directive 'block-all-mixed-content' <unknown>
Key event not available on some keyboard layouts: key="r" modifiers="accel,alt" browser.xul
Key event not available on some keyboard layouts: key="c" modifiers="accel,alt" browser.xul
calling a builtin ArrayBuffer constructor without new is deprecated and will be forbidden in ES6 main.bundle.js:3306:4
calling a builtin typed array constructor without new is deprecated and will be forbidden in ES6 main.bundle.js:1540:6
SyntaxError: missing } after property list 0.bundle.js:40373:25
Error: Loading chunk 0 failed.
Stack trace:
onScriptComplete@http://localhost:3000/dist/main.bundle.js:99:24
main.bundle.js:142:51
"Unhandled promise rejection" Error: Loading chunk 0 failed.
Stack trace:
onScriptComplete@http://localhost:3000/dist/main.bundle.js:99:24
main.bundle.js:8873:10
reflow: 3.59ms function fillInPageTooltip, popup.xml line 618Thanks for checking. It looks like somehow the JavaScript had a syntax error. This seems unlikely because webpack would have caught basic syntax errors so it seems like corruption
To fix you could
(a) check out a stable release tag if you are using git e g. git checkout 1.15.0-release or git checkout master (b) remove package-lock.json, and maybe the entire node_modules folder, because I see in the setup.log file that it didn't like file existing (c) re-run setup.sh
cmdcolin
commented
6 years ago Another thing to add to that list is clear cache in browser
cmdcolin
commented
6 years ago Are there any updates @tiramisutes ? I may close this for now as it is likely a weird setup bug and probably not a true issue with jbrowse itself. Potentially more error handling could be done for chunk loading failures but it's a little tricky
cmdcolin
commented
6 years ago Feel free to post back here if you have any continued issues with the setup, I am just triaging issues :)
Dear, I want to install the jbrowse software with no root privilege. I clone it and install in my home as follows
and run with
./utils/jb_run.js -p 3000, But when I open thehttp://localhost:3000/using firefox, it just rests on Loading... page.