(base) fgodoy@burgundy:~/downloads$ sudo bash -x browserSetup.sh install 2>&1 > install.log [sudo] password for fgodoy: + set -u -e -o pipefail + trap errorHandler ERR + APACHEDIR=/usr/local/apache + HTDOCDIR=/usr/local/apache/htdocs + CGIBINDIR=/usr/local/apache/cgi-bin + TRASHDIR=/usr/local/apache/trash + MYSQLDIR=/var/lib/mysql + MYSQLADMIN=mysqladmin + MYSQLUSER=mysql + MYSQL=mysql + SET_MYSQL_ROOT=0 + HGDOWNLOAD=hgdownload.soe.ucsc.edu + GBDBDIR=/gbdb + SEDINPLACE='sed -ri' + UDRURL=http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/udr + RSYNC=rsync + RSYNCOPTS= + COMPLETEFLAG=/usr/local/apache/cgiInstallComplete.flag + BUILDEXT=0 + BUILDKENT=0 + BINPKGURL=http://hgwdev.soe.ucsc.edu/~max/gbInstall/mysqlApacheOSX_10.7.tgz + CGIBINURL=http://hgwdev.soe.ucsc.edu/~max/gbInstall/kentCgi_OSX_10.7.tgz + MYSQLDBURL=http://hgwdev.soe.ucsc.edu/~max/gbInstall/mysql56Data.tgz + STARTSCRIPTURL=https://raw.githubusercontent.com/maximilianh/browserInstall/master/browserStartup.sh + ONLYGENOMES=0 + set +e + read -r -d '' APACHE_CONFIG_STR ++ errorHandler ++ echo The UCSC Genome Browser installation script exited with an error. ++ echo Please contact us at genome-mirror@soe.ucsc.edu and send us an output log ++ echo of the command prefixed with '"bash -x",' e.g. ++ echo 'bash -x browserSetup.sh install 2>&1 > install.log' + read -r -d '' HG_CONF_STR ++ errorHandler ++ echo The UCSC Genome Browser installation script exited with an error. ++ echo Please contact us at genome-mirror@soe.ucsc.edu and send us an output log ++ echo of the command prefixed with '"bash -x",' e.g. ++ echo 'bash -x browserSetup.sh install 2>&1 > install.log' + read -r -d '' HELP_STR ++ errorHandler ++ echo The UCSC Genome Browser installation script exited with an error. ++ echo Please contact us at genome-mirror@soe.ucsc.edu and send us an output log ++ echo of the command prefixed with '"bash -x",' e.g. ++ echo 'bash -x browserSetup.sh install 2>&1 > install.log' + set -e + [[ fgodoy != '' ]] + export HOME=/root + HOME=/root + trap errorHandler ERR + [[ 1 -eq 0 ]] + getopts :baeut:hof opt + shift 0 ++ uname + unameStr=Linux + DIST=none + [[ Linux == MINGW32_NT* ]] + [[ Linux == Darwin* ]] + [[ Linux == Linux* ]] + OS=linux + '[' -f /etc/debian_version ']' + DIST=debian ++ cat /etc/debian_version + VER=bullseye/sid + APACHECONF=/etc/apache2/sites-available/001-browser.conf + APACHEUSER=www-data + '[' debian == none ']' + lastArg=install + [[ 1 -gt 1 ]] + [[ i == \- ]] + uname -m + grep -vq _64 + [[ 0 != \0 ]] + '[' install == install ']' + installBrowser + '[' -f /usr/local/apache/cgiInstallComplete.flag ']' + echo -------------------------------- + echo UCSC Genome Browser installation + echo -------------------------------- + echo Detected OS: linux/debian, bullseye/sid + echo + echo This script will go through three steps: + echo '1 - setup apache and mysql, open port 80, deactivate SELinux' + echo '2 - copy CGI binaries into /usr/local/apache/cgi-bin, html files into /usr/local/apache/htdocs' + echo '3 - optional: download genome assembly databases into mysql and /gbdb' + echo + echo This script will now install and configure Mysql and Apache if they are not yet installed. + echo 'Your distribution'\''s package manager will be used for this.' + echo If Mysql is not installed yet, it will be installed, secured and a root password defined. + echo + echo This script will also deactivate SELinux if active and open port 80/http. + waitKey + echo2 + command echo '|' + echo '|' + echo2 Press any key to continue or CTRL-C to abort. + command echo '|' Press any key to continue or CTRL-C to abort. + echo '|' Press any key to continue or CTRL-C to abort. + read -n 1 + echo2 + command echo '|' + echo '|' + '[' '!' -f /usr/local/apache/cgiInstallComplete.flag ']' + [[ debian == \O\S\X ]] + [[ debian == \d\e\b\i\a\n ]] + installDebian + '[' '!' -f /tmp/browserInstall.aptGetUpdateDone ']' + echo2 Installing ghostscript and imagemagick + command echo '|' Installing ghostscript and imagemagick + echo '|' Installing ghostscript and imagemagick + waitKey + echo2 + command echo '|' + echo '|' + echo2 Press any key to continue or CTRL-C to abort. + command echo '|' Press any key to continue or CTRL-C to abort. + echo '|' Press any key to continue or CTRL-C to abort. + read -n 1 + echo2 + command echo '|' + echo '|' + apt-get --no-install-recommends --assume-yes install ghostscript imagemagick wget rsync r-base-core curl gsfonts + grep 'Candidate: .none.' + apt-cache policy python-mysqldb + echo2 The package python-mysqldb is not available anymore. Working around it + command echo '|' The package python-mysqldb is not available anymore. Working around it + echo '|' The package python-mysqldb is not available anymore. Working around it + echo2 by installing python2 and MySQL-python with pip2 + command echo '|' by installing python2 and MySQL-python with pip2 + echo '|' by installing python2 and MySQL-python with pip2 + apt-get install --assume-yes python2 libmysqlclient-dev python2-dev wget gcc + curl https://bootstrap.pypa.io/pip/2.7/get-pip.py --output /tmp/get-pip.py % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1863k 100 1863k 0 0 1776k 0 0:00:01 0:00:01 --:--:-- 1776k + python2 /tmp/get-pip.py DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality. + '[' -f /usr/include/mysql/my_config.h ']' + echo my_config.h found + pip2 install MySQL-python DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality. + '[' '!' -f /etc/apache2/sites-available/001-browser.conf ']' + [[ ! -f /usr/sbin/mysqld ]] + [[ 0 == \1 ]] + checkCanConnectMysql + mysql -e 'SHOW DATABASES;' + true + disableSelinux + commandExists selinuxenabled + type selinuxenabled + checkDownloadUdr + [[ ! -f /usr/local/bin/udr ]] + '[' '!' -f /usr/local/apache/cgiInstallComplete.flag ']' + '[' -f /usr/local/apache ']' + '[' -d /usr/local/apache -a linux '!=' OSX ']' + mysqlDbSetup + mysqlAllowOldPasswords + echo2 'Checking for Mysql version >= 8' + command echo '|' 'Checking for Mysql version >= 8' + echo '|' 'Checking for Mysql version >= 8' ++ mysql -e 'SHOW VARIABLES LIKE "version";' -NB ++ cut -f2 ++ cut -d. -f1 + MYSQLMAJ=8 + '[' 8 -ge 8 ']' + echo2 'Mysql >= 8 found, checking if default-authentication allows native passwords' + command echo '|' 'Mysql >= 8 found, checking if default-authentication allows native passwords' + echo '|' 'Mysql >= 8 found, checking if default-authentication allows native passwords' + grep -q default-authentication /etc/mysql/my.cnf + echo2 'default-authentication already set in /etc/mysql/my.cnf' + command echo '|' 'default-authentication already set in /etc/mysql/my.cnf' + echo '|' 'default-authentication already set in /etc/mysql/my.cnf' + echo2 + command echo '|' + echo '|' + echo2 Creating Mysql databases customTrash, hgTemp and hgcentral + command echo '|' Creating Mysql databases customTrash, hgTemp and hgcentral + echo '|' Creating Mysql databases customTrash, hgTemp and hgcentral + waitKey + echo2 + command echo '|' + echo '|' + echo2 Press any key to continue or CTRL-C to abort. + command echo '|' Press any key to continue or CTRL-C to abort. + echo '|' Press any key to continue or CTRL-C to abort. + read -n 1 + echo2 + command echo '|' + echo '|' + mysql -e 'CREATE DATABASE IF NOT EXISTS customTrash;' + mysql -e 'CREATE DATABASE IF NOT EXISTS hgcentral;' + mysql -e 'CREATE DATABASE IF NOT EXISTS hgTemp;' + mysql -e 'CREATE DATABASE IF NOT EXISTS hgFixed;' + updateBlatServers + echo2 Creating or updating the BLAT servers table + command echo '|' Creating or updating the BLAT servers table + echo '|' Creating or updating the BLAT servers table + downloadFile http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql + url=http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql + mysql hgcentral + which wget + wget -nv http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql -O - 2021-07-29 10:45:34 URL:http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql [745228/745228] -> "-" [1] + mysql hgcentral -e 'UPDATE blatServers SET host=CONCAT(host,".soe.ucsc.edu");' + echo2 + command echo '|' + echo '|' + echo2 'Will now grant permissions to browser database access users:' + command echo '|' 'Will now grant permissions to browser database access users:' + echo '|' 'Will now grant permissions to browser database access users:' + echo2 'User: '\''browser'\'', password: '\''genome'\'' - full database access permissions' + command echo '|' 'User: '\''browser'\'', password: '\''genome'\'' - full database access permissions' + echo '|' 'User: '\''browser'\'', password: '\''genome'\'' - full database access permissions' + echo2 'User: '\''readonly'\'', password: '\''access'\'' - read only access for CGI binaries' + command echo '|' 'User: '\''readonly'\'', password: '\''access'\'' - read only access for CGI binaries' + echo '|' 'User: '\''readonly'\'', password: '\''access'\'' - read only access for CGI binaries' + echo2 'User: '\''readwrite'\'', password: '\''update'\'' - readwrite access for hgcentral DB' + command echo '|' 'User: '\''readwrite'\'', password: '\''update'\'' - readwrite access for hgcentral DB' + echo '|' 'User: '\''readwrite'\'', password: '\''update'\'' - readwrite access for hgcentral DB' + waitKey + echo2 + command echo '|' + echo '|' + echo2 Press any key to continue or CTRL-C to abort. + command echo '|' Press any key to continue or CTRL-C to abort. + echo '|' Press any key to continue or CTRL-C to abort. + read -n 1 + echo2 + command echo '|' + echo '|' + mysql -e 'GRANT SELECT, INSERT, UPDATE, DELETE, FILE, CREATE, DROP, ALTER, CREATE TEMPORARY TABLES on *.* TO browser@localhost IDENTIFIED BY '\''genome'\'';' ERROR 1064 (42000) at line 1: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'IDENTIFIED BY 'genome'' at line 1 (base) fgodoy@burgundy:~/downloads$