migrate from galaxy-central to "galaxy"

galaxy/Dockerfile

@@ -1,6 +1,6 @@
 # Galaxy - Stable
 #
-# VERSION       Galaxy-central
+# VERSION       Galaxy in Docker
 
 # TODO
 #
@@ -11,7 +11,7 @@
 
 FROM buildpack-deps:22.04 AS build_base
 
-ENV GALAXY_ROOT_DIR=/galaxy-central \
+ENV GALAXY_ROOT_DIR=/galaxy \
     GALAXY_VIRTUAL_ENV=/galaxy_venv \
     GALAXY_HOME=/home/galaxy \
     GALAXY_CONDA_PREFIX=/tool_deps/_conda \
@@ -63,7 +63,7 @@ RUN mkdir $GALAXY_ROOT_DIR $GALAXY_VIRTUAL_ENV \
 
 FROM ubuntu:22.04 AS galaxy_cluster_base
 
-ENV GALAXY_ROOT_DIR=/galaxy-central \
+ENV GALAXY_ROOT_DIR=/galaxy \
     GALAXY_VIRTUAL_ENV=/galaxy_venv \
     GALAXY_LOGS_DIR=/home/galaxy/logs \
     GALAXY_CONFIG_DIR=/etc/galaxy \

galaxy/ansible/templates/export_user_files.py.j2

@@ -6,11 +6,16 @@ import os
 import shutil
 import subprocess
 
+PG_VERSION = os.environ.get('PG_VERSION', '15')
+GALAXY_UID = int(os.environ['GALAXY_UID'])
+GALAXY_GID = int(os.environ['GALAXY_GID'])
+GALAXY_ROOT_DIR = os.environ.get('GALAXY_ROOT_DIR', '/galaxy/')
+
 if len( sys.argv ) == 2:
     PG_DATA_DIR_DEFAULT = sys.argv[1]
 else:
-    PG_DATA_DIR_DEFAULT = "/var/lib/postgresql/15/main"
-PG_DATA_DIR_HOST = os.environ.get("PG_DATA_DIR_HOST", "/export/postgresql/15/main/")
+    PG_DATA_DIR_DEFAULT = f"/var/lib/postgresql/{PG_VERSION}/main"
+PG_DATA_DIR_HOST = os.environ.get("PG_DATA_DIR_HOST", f"/export/postgresql/{PG_VERSION}/main/")
 
 def change_path( src ):
     """
@@ -25,8 +30,8 @@ def change_path( src ):
                 os.makedirs(dest_dir)
             shutil.move( src, dest )
             os.symlink( dest, src.rstrip('/') )
-            os.chown( src, int(os.environ['GALAXY_UID']), int(os.environ['GALAXY_GID']) )
-            subprocess.call( 'chown -R %s:%s %s' % ( os.environ['GALAXY_UID'], os.environ['GALAXY_GID'], dest ), shell=True )
+            os.chown( src, GALAXY_UID, GALAXY_GID )
+            subprocess.call( f'chown -R {GALAXY_UID}:{GALAXY_GID} {dest}', shell=True )
         # if destination exists (e.g. continuing a previous session), remove source and symlink
         else:
             if not os.path.realpath( src ) == os.path.realpath( dest ):
@@ -46,13 +51,13 @@ def copy_samples(src, dest):
                 distrib_file = os.path.join(src, filename)
                 export_file = os.path.join(dest, filename)
                 shutil.copy(distrib_file, export_file)
-                os.chown(export_file, int(os.environ['GALAXY_UID']), int(os.environ['GALAXY_GID']))
+                os.chown(export_file, GALAXY_UID, GALAXY_GID)
 
 
 def _makedir(path):
     if not os.path.exists( path ):
         os.makedirs( path )
-    os.chown( path, int(os.environ['GALAXY_UID']), int(os.environ['GALAXY_GID']) )
+    os.chown(path, GALAXY_UID, GALAXY_GID)
 
 
 def _ignore_static(dir, *patterns):
@@ -72,38 +77,35 @@ if __name__ == "__main__":
         If the user re-starts (with docker start) the container the file /.galaxy_save is found and the linking
         is aborted.
     """
-
-    galaxy_root_dir = os.environ.get('GALAXY_ROOT_DIR', '/galaxy-central/')
-
-    galaxy_distrib_paths = {'/galaxy-central/config/': '/export/.distribution_config',
-                            '/galaxy-central/lib': '/export/galaxy-central/lib',
-                            '/galaxy-central/tools': '/export/galaxy-central/tools'}
+    galaxy_distrib_paths = {os.path.join(GALAXY_ROOT_DIR, 'config'): '/export/.distribution_config',
+                            os.path.join(GALAXY_ROOT_DIR, 'lib'): '/export/galaxy/lib',
+                            os.path.join(GALAXY_ROOT_DIR, 'tools'): '/export/galaxy/tools'}
     for image_path, export_path in galaxy_distrib_paths.items():
         if os.path.exists(export_path):
             shutil.rmtree(export_path)
         # Ignore 2 dead symlinks in galaxy code: see https://github.com/galaxyproject/galaxy/issues/9847
-        shutil.copytree( image_path, export_path, ignore=_ignore_static('/galaxy-central/lib/galaxy/web/framework/static/style', 'question-octagon-frame.png', 'ok_small.png') )
+        shutil.copytree( image_path, export_path, ignore=_ignore_static(os.path.join(GALAXY_ROOT_DIR, '/lib/galaxy/web/framework/static/style'), 'question-octagon-frame.png', 'ok_small.png') )
 
-    shutil.copy('/galaxy-central/requirements.txt','/export/galaxy-central/requirements.txt')
+    shutil.copy(os.path.join(GALAXY_ROOT_DIR, 'requirements.txt'), '/export/galaxy/requirements.txt')
 
-    _makedir('/export/galaxy-central/')
+    _makedir('/export/galaxy/')
     _makedir('/export/ftp/')
 
-    change_path( os.path.join(galaxy_root_dir, 'config') )
+    change_path( os.path.join(GALAXY_ROOT_DIR, 'config') )
 
     # Copy all sample config files to config dir
     # TODO find a way to update plugins/ without breaking user customizations
-    config_src = os.path.join(galaxy_root_dir, 'config')
-    config_dest = os.path.join('/export/', galaxy_root_dir, 'config')
+    config_src = os.path.join(GALAXY_ROOT_DIR, 'config')
+    config_dest = os.path.join('/export/', GALAXY_ROOT_DIR, 'config')
     copy_samples(config_src, config_dest)
 
     # Copy all sample files to tool-data dir
     # TODO find a way to update shared/ without breaking user customizations
-    tool_data_src = os.path.join(galaxy_root_dir, 'tool-data')
-    tool_data_dest = os.path.join('/export/', galaxy_root_dir, 'tool-data')
+    tool_data_src = os.path.join(GALAXY_ROOT_DIR, 'tool-data')
+    tool_data_dest = os.path.join('/export/', GALAXY_ROOT_DIR, 'tool-data')
     copy_samples(tool_data_src, tool_data_dest)
 
-    # TODO find a way to update /export/galaxy-central/display_applications/ without breaking user customizations
+    # TODO find a way to update /export/galaxy/display_applications/ without breaking user customizations
 
     # Copy all files starting with "welcome"
     # This enables a flexible start page design.
@@ -112,15 +114,15 @@ if __name__ == "__main__":
             export_file = os.path.join( '/export/', filename)
             image_file = os.path.join('/etc/galaxy/web/', filename)
             shutil.copy(export_file, image_file)
-            os.chown( image_file, int(os.environ['GALAXY_UID']), int(os.environ['GALAXY_GID']) )
+            os.chown( image_file, GALAXY_UID, GALAXY_GID )
 
     # copy image defaults to config/<file>.docker_sample to base derivatives on,
     # and if there is a realized version of these files in the export directory
     # replace Galaxy's copy with these. Use symbolic link instead of copying so
     # deployer can update and reload Galaxy and changes will be reflected.
     for config in [ 'galaxy.yml', 'gravity.yml' ,'job_conf.xml' ]:
         image_config = os.path.join('/etc/galaxy/', config)
-        export_config = os.path.join( '/export/galaxy-central/config', config )
+        export_config = os.path.join( '/export/galaxy/config', config )
         export_sample = export_config + ".docker_sample"
         shutil.copy(image_config, export_sample)
         if os.path.exists(export_config):
@@ -136,12 +138,12 @@ if __name__ == "__main__":
                     shutil.rmtree(os.path.join(dest_conda, subdir))
                 subprocess.call('cp -p --preserve -R %s %s' % (os.path.join(src_conda, subdir), os.path.join(dest_conda, subdir)), shell=True)
 
-    change_path( os.path.join(galaxy_root_dir, 'tools.yaml') )
-    change_path( os.path.join(galaxy_root_dir, 'integrated_tool_panel.xml') )
-    change_path( os.path.join(galaxy_root_dir, 'display_applications') )
+    change_path( os.path.join(GALAXY_ROOT_DIR, 'tools.yaml') )
+    change_path( os.path.join(GALAXY_ROOT_DIR, 'integrated_tool_panel.xml') )
+    change_path( os.path.join(GALAXY_ROOT_DIR, 'display_applications') )
     change_path( os.path.join('/tool_deps') )
-    change_path( os.path.join(galaxy_root_dir, 'tool-data') )
-    change_path( os.path.join(galaxy_root_dir, 'database') )
+    change_path( os.path.join(GALAXY_ROOT_DIR, 'tool-data') )
+    change_path( os.path.join(GALAXY_ROOT_DIR, 'database') )
 
     if os.path.exists('/export/common_htpasswd'):
         shutil.copy('/export/common_htpasswd', '/etc/nginx/htpasswd')

galaxy/startup.sh

@@ -1,13 +1,5 @@
 #!/usr/bin/env bash
 
-# Migration path for old images that had the tool_deps under /export/galaxy-central/tool_deps/
-
-if [ -d "/export/galaxy-central/tool_deps/" ] && [ ! -L "/export/galaxy-central/tool_deps/" ]; then
-    mkdir -p /export/tool_deps/
-    mv /export/galaxy-central/tool_deps /export/
-    ln -s /export/tool_deps/ $GALAXY_ROOT_DIR/
-fi
-
 # This is needed for Docker compose to have a unified alias for the main container.
 # Modifying /etc/hosts can only happen during runtime not during build-time
 echo "127.0.0.1      galaxy" >> /etc/hosts