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41
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1 #!/usr/bin/env bash
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2
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3 # Migration path for old images that had the tool_deps under /export/galaxy-central/tool_deps/
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4
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5 if [ -d "/export/galaxy-central/tool_deps/" ] && [ ! -L "/export/galaxy-central/tool_deps/" ]; then
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6 mkdir -p /export/tool_deps/
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7 mv /export/galaxy-central/tool_deps /export/
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8 ln -s /export/tool_deps/ $GALAXY_ROOT/
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9 fi
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10
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11 # This is needed for Docker compose to have a unified alias for the main container.
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12 # Modifying /etc/hosts can only happen during runtime not during build-time
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13 echo "127.0.0.1 galaxy" >> /etc/hosts
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14
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15 # Set number of Galaxy handlers via GALAXY_HANDLER_NUMPROCS or default to 2
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16 ansible localhost -m ini_file -a "dest=/etc/supervisor/conf.d/galaxy.conf section=program:handler option=numprocs value=${GALAXY_HANDLER_NUMPROCS:-2}" &> /dev/null
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17
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18 # If the Galaxy config file is not in the expected place, copy from the sample
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19 # and hope for the best (that the admin has done all the setup through env vars.)
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20 if [ ! -f $GALAXY_CONFIG_FILE ]
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21 then
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22 # this should succesfully copy either .yml or .ini sample file to the expected location
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23 cp /export/config/galaxy${GALAXY_CONFIG_FILE: -4}.sample $GALAXY_CONFIG_FILE
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24 fi
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25
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26 # Configure proxy prefix filtering
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27 if [[ ! -z $PROXY_PREFIX ]]
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28 then
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29 if [ ${GALAXY_CONFIG_FILE: -4} == ".ini" ]
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30 then
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31 ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_FILE} section=filter:proxy-prefix option=prefix value=${PROXY_PREFIX}" &> /dev/null
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32 ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_FILE} section=app:main option=filter-with value=proxy-prefix" &> /dev/null
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33 else
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34 ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ module:' state=absent" &> /dev/null
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35 ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ socket:' state=absent" &> /dev/null
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36 ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ mount:' state=absent" &> /dev/null
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37 ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} regexp='^ manage-script-name:' state=absent" &> /dev/null
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38 ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' manage-script-name: true'" &> /dev/null
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39 ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' mount: ${PROXY_PREFIX}=galaxy.webapps.galaxy.buildapp:uwsgi_app()'" &> /dev/null
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40 ansible localhost -m lineinfile -a "path=${GALAXY_CONFIG_FILE} insertafter='^uwsgi:' line=' socket: unix:///srv/galaxy/var/uwsgi.sock'" &> /dev/null
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41
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42 # Also set SCRIPT_NAME. It's not always necessary due to manage-script-name: true in galaxy.yml, but it makes life easier in this container + it does no harm
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43 ansible localhost -m lineinfile -a "path=/etc/nginx/conf.d/uwsgi.conf regexp='^ uwsgi_param SCRIPT_NAME' state=absent" &> /dev/null
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44 ansible localhost -m lineinfile -a "path=/etc/nginx/conf.d/uwsgi.conf insertafter='^ include uwsgi_params' line=' uwsgi_param SCRIPT_NAME ${PROXY_PREFIX};'" &> /dev/null
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45 fi
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46
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47 ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_DIR}/reports_wsgi.ini section=filter:proxy-prefix option=prefix value=${PROXY_PREFIX}/reports" &> /dev/null
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48 ansible localhost -m ini_file -a "dest=${GALAXY_CONFIG_DIR}/reports_wsgi.ini section=app:main option=filter-with value=proxy-prefix" &> /dev/null
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49
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50 # Fix path to html assets
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51 ansible localhost -m replace -a "dest=$GALAXY_CONFIG_DIR/web/welcome.html regexp='(href=\"|\')[/\\w]*(/static)' replace='\\1${PROXY_PREFIX}\\2'" &> /dev/null
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52
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53 # Set some other vars based on that prefix
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54 if [ "x$GALAXY_CONFIG_COOKIE_PATH" == "x" ]
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55 then
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56 export GALAXY_CONFIG_COOKIE_PATH="$PROXY_PREFIX"
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57 fi
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58 if [ "x$GALAXY_CONFIG_DYNAMIC_PROXY_PREFIX" == "x" ]
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59 then
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60 export GALAXY_CONFIG_DYNAMIC_PROXY_PREFIX="$PROXY_PREFIX/gie_proxy"
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61 fi
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62
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63 # Change the defaults nginx upload/x-accel paths
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64 if [ "$GALAXY_CONFIG_NGINX_UPLOAD_PATH" == "/_upload" ]
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65 then
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66 export GALAXY_CONFIG_NGINX_UPLOAD_PATH="${PROXY_PREFIX}${GALAXY_CONFIG_NGINX_UPLOAD_PATH}"
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67 fi
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68 fi
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69
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70 # Disable authentication of Galaxy reports
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71 if [[ ! -z $DISABLE_REPORTS_AUTH ]]
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72 then
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73 # disable authentification
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74 echo "Disable Galaxy reports authentification "
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75 echo "" > /etc/nginx/conf.d/reports_auth.conf
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76 else
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77 # enable authentification
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78 echo "Enable Galaxy reports authentification "
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79 cp /etc/nginx/conf.d/reports_auth.conf.source /etc/nginx/conf.d/reports_auth.conf
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80 fi
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81
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82 # Try to guess if we are running under --privileged mode
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83 if [[ ! -z $HOST_DOCKER_LEGACY ]]; then
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84 if mount | grep "/proc/kcore"; then
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85 PRIVILEGED=false
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86 else
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87 PRIVILEGED=true
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88 fi
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89 else
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90 # Taken from http://stackoverflow.com/questions/32144575/how-to-know-if-a-docker-container-is-running-in-privileged-mode
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91 ip link add dummy0 type dummy 2>/dev/null
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92 if [[ $? -eq 0 ]]; then
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93 PRIVILEGED=true
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94 # clean the dummy0 link
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95 ip link delete dummy0 2>/dev/null
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96 else
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97 PRIVILEGED=false
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98 fi
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99 fi
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100
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101 cd $GALAXY_ROOT
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102 . $GALAXY_VIRTUAL_ENV/bin/activate
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103
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104 if $PRIVILEGED; then
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105 umount /var/lib/docker
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106 fi
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107
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108 if [[ ! -z $STARTUP_EXPORT_USER_FILES ]]; then
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109 # If /export/ is mounted, export_user_files file moving all data to /export/
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110 # symlinks will point from the original location to the new path under /export/
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111 # If /export/ is not given, nothing will happen in that step
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112 echo "Checking /export..."
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113 python3 /usr/local/bin/export_user_files.py $PG_DATA_DIR_DEFAULT
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114 fi
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115
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116 # Delete compiled templates in case they are out of date
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117 if [[ ! -z $GALAXY_CONFIG_TEMPLATE_CACHE_PATH ]]; then
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118 rm -rf $GALAXY_CONFIG_TEMPLATE_CACHE_PATH/*
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119 fi
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120
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121 # Enable loading of dependencies on startup. Such as LDAP.
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122 # Adapted from galaxyproject/galaxy/scripts/common_startup.sh
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123 if [[ ! -z $LOAD_GALAXY_CONDITIONAL_DEPENDENCIES ]]
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124 then
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125 echo "Installing optional dependencies in galaxy virtual environment..."
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126 : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"}
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127 GALAXY_CONDITIONAL_DEPENDENCIES=$(PYTHONPATH=lib python -c "import galaxy.dependencies; print('\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE')))")
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128 [ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -q -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}"
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129 fi
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130
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131 if [[ ! -z $LOAD_GALAXY_CONDITIONAL_DEPENDENCIES ]] && [[ ! -z $LOAD_PYTHON_DEV_DEPENDENCIES ]]
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132 then
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133 echo "Installing development requirements in galaxy virtual environment..."
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134 : ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"}
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135 dev_requirements='./lib/galaxy/dependencies/dev-requirements.txt'
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136 [ -f $dev_requirements ] && pip install -q -r $dev_requirements --index-url "${GALAXY_WHEELS_INDEX_URL}"
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137 fi
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138
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139 # Enable Test Tool Shed
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140 if [[ ! -z $ENABLE_TTS_INSTALL ]]
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141 then
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142 echo "Enable installation from the Test Tool Shed."
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143 export GALAXY_CONFIG_TOOL_SHEDS_CONFIG_FILE=$GALAXY_HOME/tool_sheds_conf.xml
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144 fi
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145
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146 # Remove all default tools from Galaxy by default
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147 if [[ ! -z $BARE ]]
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148 then
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149 echo "Remove all tools from the tool_conf.xml file."
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150 export GALAXY_CONFIG_TOOL_CONFIG_FILE=config/shed_tool_conf.xml,$GALAXY_ROOT/test/functional/tools/upload_tool_conf.xml
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151 fi
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152
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153 # If auto installing conda envs, make sure bcftools is installed for __set_metadata__ tool
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154 if [[ ! -z $GALAXY_CONFIG_CONDA_AUTO_INSTALL ]]
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155 then
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156 if [ ! -d "/tool_deps/_conda/envs/__bcftools@1.5" ]; then
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157 su $GALAXY_USER -c "/tool_deps/_conda/bin/conda create -y --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name __bcftools@1.5 bcftools=1.5"
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158 su $GALAXY_USER -c "/tool_deps/_conda/bin/conda clean --tarballs --yes"
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159 fi
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160 fi
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161
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162 if [[ ! -z $GALAXY_EXTRAS_CONFIG_POSTGRES ]]; then
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163 if [[ $NONUSE != *"postgres"* ]]
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164 then
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165 # Backward compatibility for exported postgresql directories before version 15.08.
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166 # In previous versions postgres has the UID/GID of 102/106. We changed this in
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167 # https://github.com/bgruening/docker-galaxy-stable/pull/71 to GALAXY_POSTGRES_UID=1550 and
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168 # GALAXY_POSTGRES_GID=1550
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169 if [ -e /export/postgresql/ ];
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170 then
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171 if [ `stat -c %g /export/postgresql/` == "106" ];
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172 then
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173 chown -R postgres:postgres /export/postgresql/
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174 fi
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175 fi
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176 fi
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177 fi
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178
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179
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180 if [[ ! -z $GALAXY_EXTRAS_CONFIG_CONDOR ]]; then
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181 if [[ ! -z $ENABLE_CONDOR ]]
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182 then
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183 if [[ ! -z $CONDOR_HOST ]]
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184 then
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185 echo "Enabling Condor with external scheduler at $CONDOR_HOST"
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186 echo "# Config generated by startup.sh
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187 CONDOR_HOST = $CONDOR_HOST
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188 ALLOW_ADMINISTRATOR = *
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189 ALLOW_OWNER = *
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190 ALLOW_READ = *
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191 ALLOW_WRITE = *
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192 ALLOW_CLIENT = *
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193 ALLOW_NEGOTIATOR = *
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194 DAEMON_LIST = MASTER, SCHEDD
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195 UID_DOMAIN = galaxy
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196 DISCARD_SESSION_KEYRING_ON_STARTUP = False
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197 TRUST_UID_DOMAIN = true" > /etc/condor/condor_config.local
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198 fi
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199
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200 if [[ -e /export/condor_config ]]
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201 then
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202 echo "Replacing Condor config by locally supplied config from /export/condor_config"
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203 rm -f /etc/condor/condor_config
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204 ln -s /export/condor_config /etc/condor/condor_config
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205 fi
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206 fi
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207 fi
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208
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209
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210 # Copy or link the slurm/munge config files
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211 if [ -e /export/slurm.conf ]
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212 then
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213 rm -f /etc/slurm-llnl/slurm.conf
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214 ln -s /export/slurm.conf /etc/slurm-llnl/slurm.conf
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215 else
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216 # Configure SLURM with runtime hostname.
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217 # Use absolute path to python so virtualenv is not used.
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218 /usr/bin/python /usr/sbin/configure_slurm.py
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219 fi
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220 if [ -e /export/munge.key ]
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221 then
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222 rm -f /etc/munge/munge.key
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223 ln -s /export/munge.key /etc/munge/munge.key
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224 chmod 400 /export/munge.key
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225 fi
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226
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227 # link the gridengine config file
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228 if [ -e /export/act_qmaster ]
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229 then
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230 rm -f /var/lib/gridengine/default/common/act_qmaster
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231 ln -s /export/act_qmaster /var/lib/gridengine/default/common/act_qmaster
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232 fi
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233
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234 # Waits until postgres is ready
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235 function wait_for_postgres {
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236 echo "Checking if database is up and running"
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237 until /usr/local/bin/check_database.py 2>&1 >/dev/null; do sleep 1; echo "Waiting for database"; done
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238 echo "Database connected"
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239 }
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240
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241 # $NONUSE can be set to include cron, proftp, reports or nodejs
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242 # if included we will _not_ start these services.
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243 function start_supervisor {
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244 supervisord -c /etc/supervisor/supervisord.conf
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245 sleep 5
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246
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247 if [[ ! -z $SUPERVISOR_MANAGE_POSTGRES && ! -z $SUPERVISOR_POSTGRES_AUTOSTART ]]; then
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248 if [[ $NONUSE != *"postgres"* ]]
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249 then
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250 echo "Starting postgres"
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251 supervisorctl start postgresql
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252 fi
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253 fi
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254
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255 wait_for_postgres
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256
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257 # Make sure the database is automatically updated
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258 if [[ ! -z $GALAXY_AUTO_UPDATE_DB ]]
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259 then
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260 echo "Updating Galaxy database"
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261 sh manage_db.sh -c /etc/galaxy/galaxy.yml upgrade
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262 fi
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263
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264 if [[ ! -z $SUPERVISOR_MANAGE_CRON ]]; then
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265 if [[ $NONUSE != *"cron"* ]]
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266 then
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267 echo "Starting cron"
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268 supervisorctl start cron
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269 fi
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270 fi
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271
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272 if [[ ! -z $SUPERVISOR_MANAGE_PROFTP ]]; then
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273 if [[ $NONUSE != *"proftp"* ]]
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274 then
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275 echo "Starting ProFTP"
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276 supervisorctl start proftpd
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277 fi
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278 fi
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279
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280 if [[ ! -z $SUPERVISOR_MANAGE_REPORTS ]]; then
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281 if [[ $NONUSE != *"reports"* ]]
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282 then
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283 echo "Starting Galaxy reports webapp"
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284 supervisorctl start reports
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285 fi
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286 fi
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287
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288 if [[ ! -z $SUPERVISOR_MANAGE_IE_PROXY ]]; then
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289 if [[ $NONUSE != *"nodejs"* ]]
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290 then
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291 echo "Starting nodejs"
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292 supervisorctl start galaxy:galaxy_nodejs_proxy
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293 fi
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294 fi
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295
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296 if [[ ! -z $SUPERVISOR_MANAGE_CONDOR ]]; then
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297 if [[ $NONUSE != *"condor"* ]]
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298 then
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299 echo "Starting condor"
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300 supervisorctl start condor
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301 fi
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302 fi
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303
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304 if [[ ! -z $SUPERVISOR_MANAGE_SLURM ]]; then
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305 if [[ $NONUSE != *"slurmctld"* ]]
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306 then
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307 echo "Starting slurmctld"
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308 supervisorctl start slurmctld
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|
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309 fi
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310 if [[ $NONUSE != *"slurmd"* ]]
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311 then
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312 echo "Starting slurmd"
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313 supervisorctl start slurmd
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|
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314 fi
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315 supervisorctl start munge
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|
|
316 else
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317 if [[ $NONUSE != *"slurmctld"* ]]
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318 then
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319 echo "Starting slurmctld"
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320 /usr/sbin/slurmctld -L $GALAXY_LOGS_DIR/slurmctld.log
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|
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321 fi
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322 if [[ $NONUSE != *"slurmd"* ]]
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323 then
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324 echo "Starting slurmd"
|
|
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325 /usr/sbin/slurmd -L $GALAXY_LOGS_DIR/slurmd.log
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|
|
326 fi
|
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327
|
|
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328 # We need to run munged regardless
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|
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329 mkdir -p /var/run/munge && /usr/sbin/munged -f
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|
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330 fi
|
|
|
331 }
|
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332
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|
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333 if [[ ! -z $SUPERVISOR_POSTGRES_AUTOSTART ]]; then
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|
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334 if [[ $NONUSE != *"postgres"* ]]
|
|
|
335 then
|
|
|
336 # Change the data_directory of postgresql in the main config file
|
|
|
337 ansible localhost -m lineinfile -a "line='data_directory = \'$PG_DATA_DIR_HOST\'' dest=$PG_CONF_DIR_DEFAULT/postgresql.conf backup=yes state=present regexp='data_directory'" &> /dev/null
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|
|
338 fi
|
|
|
339 fi
|
|
|
340
|
|
|
341 if $PRIVILEGED; then
|
|
|
342 echo "Enable Galaxy Interactive Environments."
|
|
|
343 export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY="config/plugins/interactive_environments"
|
|
|
344 if [ x$DOCKER_PARENT == "x" ]; then
|
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345 #build the docker in docker environment
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346 bash /root/cgroupfs_mount.sh
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347 start_supervisor
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348 supervisorctl start docker
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349 else
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350 #inheriting /var/run/docker.sock from parent, assume that you need to
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351 #run docker with sudo to validate
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352 echo "$GALAXY_USER ALL = NOPASSWD : ALL" >> /etc/sudoers
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353 start_supervisor
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354 fi
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355 if [[ ! -z $PULL_IE_IMAGES ]]; then
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356 echo "About to pull IE images. Depending on the size, this may take a while!"
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357
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358 for ie in {JUPYTER,RSTUDIO,ETHERCALC,PHINCH,NEO}; do
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359 enabled_var_name="GALAXY_EXTRAS_IE_FETCH_${ie}";
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360 if [[ ${!enabled_var_name} ]]; then
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361 # Store name in a var
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362 image_var_name="GALAXY_EXTRAS_${ie}_IMAGE"
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363 # And then read from that var
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364 docker pull "${!image_var_name}"
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365 fi
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366 done
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367 fi
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368
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369 # in privileged mode autofs and CVMFS is available
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370 # install autofs
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371 echo "Installing autofs to enable automatic CVMFS mounts"
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372 apt-get install autofs --no-install-recommends -y
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373 apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/*
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374 else
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375 echo "Disable Galaxy Interactive Environments. Start with --privileged to enable IE's."
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376 export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY=""
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377 start_supervisor
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378 fi
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379
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380 if [ "$USE_HTTPS_LETSENCRYPT" != "False" ]
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381 then
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382 echo "Settting up letsencrypt"
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383 ansible-playbook -c local /ansible/provision.yml \
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384 --extra-vars gather_facts=False \
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385 --extra-vars galaxy_extras_config_ssl=True \
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386 --extra-vars galaxy_extras_config_ssl_method=letsencrypt \
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387 --extra-vars galaxy_extras_galaxy_domain="GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL" \
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388 --extra-vars galaxy_extras_config_nginx_upload=False \
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389 --tags https
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390 fi
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391 if [ "$USE_HTTPS" != "False" ]
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392 then
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393 if [ -f /export/server.key -a -f /export/server.crt ]
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394 then
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395 echo "Copying SSL keys"
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396 ansible-playbook -c local /ansible/provision.yml \
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|
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397 --extra-vars gather_facts=False \
|
|
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398 --extra-vars galaxy_extras_config_ssl=True \
|
|
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399 --extra-vars galaxy_extras_config_ssl_method=own \
|
|
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400 --extra-vars src_nginx_ssl_certificate_key=/export/server.key \
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|
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401 --extra-vars src_nginx_ssl_certificate=/export/server.crt \
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402 --extra-vars galaxy_extras_config_nginx_upload=False \
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|
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403 --tags https
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|
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404 else
|
|
|
405 echo "Setting up self-signed SSL keys"
|
|
|
406 ansible-playbook -c local /ansible/provision.yml \
|
|
|
407 --extra-vars gather_facts=False \
|
|
|
408 --extra-vars galaxy_extras_config_ssl=True \
|
|
|
409 --extra-vars galaxy_extras_config_ssl_method=self-signed \
|
|
|
410 --extra-vars galaxy_extras_config_nginx_upload=False \
|
|
|
411 --tags https
|
|
|
412 fi
|
|
|
413 fi
|
|
|
414
|
|
|
415 # In case the user wants the default admin to be created, do so.
|
|
|
416 if [[ ! -z $GALAXY_DEFAULT_ADMIN_USER ]]
|
|
|
417 then
|
|
|
418 echo "Creating admin user $GALAXY_DEFAULT_ADMIN_USER with key $GALAXY_DEFAULT_ADMIN_KEY and password $GALAXY_DEFAULT_ADMIN_PASSWORD if not existing"
|
|
|
419 python /usr/local/bin/create_galaxy_user.py --user "$GALAXY_DEFAULT_ADMIN_EMAIL" --password "$GALAXY_DEFAULT_ADMIN_PASSWORD" \
|
|
|
420 -c "$GALAXY_CONFIG_FILE" --username "$GALAXY_DEFAULT_ADMIN_USER" --key "$GALAXY_DEFAULT_ADMIN_KEY"
|
|
|
421 fi
|
|
|
422 # If there is a need to execute actions that would require a live galaxy instance, such as adding workflows, setting quotas, adding more users, etc.
|
|
|
423 # then place a file with that logic named post-start-actions.sh on the /export/ directory, it should have access to all environment variables
|
|
|
424 # visible here.
|
|
|
425 # The file needs to be executable (chmod a+x post-start-actions.sh)
|
|
|
426 # uses ephemeris, present in docker-galaxy-stable, to wait for the local instance
|
|
|
427
|
|
|
428 if [[ -f /export/post-start-actions.sh ]]
|
|
|
429 then
|
|
|
430 /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > $GALAXY_LOGS_DIR/post-start-actions.log
|
|
|
431 /export/post-start-actions.sh >> $GALAXY_LOGS_DIR/post-start-actions.log &
|
|
|
432 else
|
|
|
433 echo "No /export/post-start-actions.sh found or not executable so not running" >> $GALAXY_LOGS_DIR/post-start-actions.log
|
|
|
434 fi
|
|
|
435
|
|
|
436
|
|
|
437 # Reinstall tools if the user want to
|
|
|
438 if [[ ! -z $GALAXY_AUTO_UPDATE_TOOLS ]]
|
|
|
439 then
|
|
|
440 /tool_deps/_conda/bin/galaxy-wait -g http://127.0.0.1 -v --timeout 120 > /home/galaxy/logs/post-start-actions.log &&
|
|
|
441 OLDIFS=$IFS
|
|
|
442 IFS=','
|
|
|
443 for TOOL_YML in `echo "$GALAXY_AUTO_UPDATE_TOOLS"`
|
|
|
444 do
|
|
|
445 echo "Installing tools from $TOOL_YML"
|
|
|
446 /tool_deps/_conda/bin/shed-tools install -g "http://127.0.0.1" -a "$GALAXY_DEFAULT_ADMIN_KEY" -t "$TOOL_YML"
|
|
|
447 /tool_deps/_conda/bin/conda clean --tarballs --yes
|
|
|
448 done
|
|
|
449 IFS=$OLDIFS
|
|
|
450 fi
|
|
|
451
|
|
|
452 # migrate custom IEs or Visualisations (Galaxy plugins)
|
|
|
453 # this is needed for by the new client build system
|
|
|
454 python3 ${GALAXY_ROOT}/scripts/plugin_staging.py
|
|
|
455
|
|
|
456 # Enable verbose output
|
|
|
457 if [ `echo ${GALAXY_LOGGING:-'no'} | tr [:upper:] [:lower:]` = "full" ]
|
|
|
458 then
|
|
|
459 tail -f /var/log/supervisor/* /var/log/nginx/* $GALAXY_LOGS_DIR/*.log
|
|
|
460 else
|
|
|
461 tail -f $GALAXY_LOGS_DIR/*.log
|
|
|
462 fi
|
