JBrowser missing and Menu Buttons disappears
First of all congrats for your impressive contribution to the community.
I have detected three problems to report. I think i have found the solution to a) and c) but b) looks very weird. My installation is using docker approach.
a) During Docker Image build process it reports the following errors: --2019-02-28 07:49:53-- http://jbrowse.org/releases/JBrowse-1.12.5/JBrowse-1.12.5.zip Resolving jbrowse.org (jbrowse.org)... 184.72.219.192 Connecting to jbrowse.org (jbrowse.org)|184.72.219.192|:80... connected. HTTP request sent, awaiting response... 404 Not Found 2019-02-28 07:49:54 ERROR 404: Not Found.
unzip: cannot find or open JBrowse-1.12.5.zip, JBrowse-1.12.5.zip.zip or JBrowse-1.12.5.zip.ZIP. rm: cannot remove 'jbrowse': No such file or directory ./install_jbrowse-1.12.5.sh: line 8: cd:/var/www/myGenomeBrowser/bin/int/../..//bin/ext/jbrowse: No such file or directory ./install_jbrowse-1.12.5.sh: line 9: ./setup.sh: No such file or directory ./install_jbrowse-1.12.5.sh: line 12: cd:/var/www/myGenomeBrowser/bin/int/../..//bin/ext/jbrowse/src/perl5/: No such file or directory mv: cannot stat 'GenomeDB.pm': No such file or directory ./install_jbrowse-1.12.5.sh: line 15: cd:/var/www/myGenomeBrowser/bin/int/../..//web/jbrowse/plugins: No such file or directory Cloning into 'MultiVariantViewer'... ./install_jbrowse-1.12.5.sh: line 17: cd:/var/www/myGenomeBrowser/bin/int/../..//web/jbrowse/plugins: No such file or directory Cloning into 'MultiBigWig'... ./install_jbrowse-1.12.5.sh: line 19: cd:/var/www/myGenomeBrowser/bin/int/../..//web/jbrowse/plugins: No such file or directory Cloning into 'StrandedPlotPlugin'... ./install_jbrowse-1.12.5.sh: line 21: cd:/var/www/myGenomeBrowser/bin/int/../..//web/jbrowse/plugins: No such file or directory Cloning into 'HierarchicalCheckboxPlugin'... ./install_jbrowse-1.12.5.sh: line 23: cd:/var/www/myGenomeBrowser/bin/int/../..//web/jbrowse/plugins: No such file or directory Cloning into 'TrackScorePlugin'... ./install_jbrowse-1.12.5.sh: line 26:/var/www/myGenomeBrowser/bin/int/../..//web/jbrowse/jbrowse.conf: No such file or directory ./install_jbrowse-1.12.5.sh: line 28:/var/www/myGenomeBrowser/bin/int/../..//web/jbrowse/jbrowse.conf: No such file or directory ./install_jbrowse-1.12.5.sh: line 30:/var/www/myGenomeBrowser/bin/int/../..//web/jbrowse/jbrowse.conf: No such file or directory ./install_jbrowse-1.12.5.sh: line 32:/var/www/myGenomeBrowser/bin/int/../..//web/jbrowse/jbrowse.conf: No such file or directory ./install_jbrowse-1.12.5.sh: line 34:/var/www/myGenomeBrowser/bin/int/../..//web/jbrowse/jbrowse.conf: No such file or directory ./install_jbrowse-1.12.5.sh: line 36:/var/www/myGenomeBrowser/bin/int/../..//web/jbrowse/jbrowse.conf: No such file or directory ./install_jbrowse-1.12.5.sh: line 39:/var/www/myGenomeBrowser/bin/int/../..//web/jbrowse/jbrowse.conf: No such file or directory ./install_jbrowse-1.12.5.sh: line 42:/var/www/myGenomeBrowser/bin/int/../..//web/jbrowse/jbrowse.conf: No such file or directory
b) When pressing buttons on the main menu eg. "Browse" and then pressing it again the option "Browse" disappears from the menu!! The same happens with the rest of the buttons
c) When trying to monitor a genome with jbrowser from Option Browse->ID it reports the following: Forbidden, You don't have permission to access /myGenomeBrowser/web/jbrowse/index.html on this server.
problem seems to be solved executing the following (the following commands must be executed inside the running Container):
cd /var/www/myGenomeBrowser/bin/ext
ls -al
check and see where jbrowse symbol link redirects eg. JBrowse-1.12.5. then download via git latest version of jbrowser in the previous folder
git clone https://github.com/GMOD/jbrowse JBrowse-1.12.5
cd JBrowse-1.12.5
apt-get install curl
curl -sL https://deb.nodesource.com/setup_11.x | bash -
apt-get install -y nodejs
./setup.sh
Thank you for your work