From 741598ebfb9583692bd920c7a5ba47281129cb20 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 12 Nov 2024 22:03:33 +0100 Subject: [PATCH] fix some conversion --- README.md | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index ed2439c0..bfa2073b 100644 --- a/README.md +++ b/README.md @@ -592,23 +592,23 @@ In this example configuration the cluster file system has a directory `/cluster_ The container should be started with the following settings configured: ```bash -docker run -d -p 8080:80 -p 8021:21 \ --v /cluster_storage/galaxy_data/galaxy_export:/export \ # This makes sure all galaxy files are on the cluster filesystem --v /cluster_storage/galaxy_data:/cluster_storage/galaxy_data \ # This ensures the links within the docker container and on the cluster fs are the same +docker run -d -p 8080:80 -p 8021:21 +-v /cluster_storage/galaxy_data/galaxy_export:/export # This makes sure all galaxy files are on the cluster filesystem +-v /cluster_storage/galaxy_data:/cluster_storage/galaxy_data # This ensures the links within the docker container and on the cluster fs are the same # The following settings make sure that each job is configured with the paths on the cluster fs instead of /export --e GALAXY_CONFIG_TOOL_DEPENDENCY_DIR="/cluster_storage/galaxy_data/galaxy_export/tool_deps" \ --e GALAXY_CONFIG_TOOL_DEPENDENCY_CACHE_DIR="/cluster_storage/galaxy_data/galaxy_export/tool_deps/_cache" \ --e GALAXY_CONFIG_FILE_PATH="/cluster_storage/galaxy_data/galaxy_export/galaxy/database/files" \ --e GALAXY_CONFIG_TOOL_PATH="/cluster_storage/galaxy_data/galaxy_export/galaxy/tools" \ --e GALAXY_CONFIG_TOOL_DATA_PATH="/cluster_storage/galaxy_data/galaxy_export/galaxy/tool-data" \ --e GALAXY_CONFIG_SHED_TOOL_DATA_PATH="/cluster_storage/galaxy_data/galaxy_export/galaxy/tool-data" \ +-e GALAXY_CONFIG_TOOL_DEPENDENCY_DIR="/cluster_storage/galaxy_data/galaxy_export/tool_deps" +-e GALAXY_CONFIG_TOOL_DEPENDENCY_CACHE_DIR="/cluster_storage/galaxy_data/galaxy_export/tool_deps/_cache" +-e GALAXY_CONFIG_FILE_PATH="/cluster_storage/galaxy_data/galaxy_export/galaxy/database/files" +-e GALAXY_CONFIG_TOOL_PATH="/cluster_storage/galaxy_data/galaxy_export/galaxy/tools" +-e GALAXY_CONFIG_TOOL_DATA_PATH="/cluster_storage/galaxy_data/galaxy_export/galaxy/tool-data" +-e GALAXY_CONFIG_SHED_TOOL_DATA_PATH="/cluster_storage/galaxy_data/galaxy_export/galaxy/tool-data" # The following settings are for directories that can be anywhere on the cluster fs. --e GALAXY_CONFIG_JOB_WORKING_DIRECTORY="/cluster_storage/galaxy_data/galaxy_export/galaxy/database/job_working_directory" \ #IMPORTANT: needs to be created manually. Can also be placed elsewhere, but is originally located here --e GALAXY_CONFIG_NEW_FILE_PATH="/cluster_storage/galaxy_data/tmp" \ # IMPORTANT: needs to be created manually. This needs to be writable by UID=1450 and have its flippy bit set (chmod 1777 for world-writable with flippy bit) --e GALAXY_CONFIG_OUTPUTS_TO_WORKING_DIRECTORY=False \ # Writes Job scripts, stdout and stderr to job_working_directory. --e GALAXY_CONFIG_RETRY_JOB_OUTPUT_COLLECTION=5 \ #IF your cluster fs uses nfs this may introduce latency. You can set galaxy to retry if a job output is not yet created. +-e GALAXY_CONFIG_JOB_WORKING_DIRECTORY="/cluster_storage/galaxy_data/galaxy_export/galaxy/database/job_working_directory" #IMPORTANT: needs to be created manually. Can also be placed elsewhere, but is originally located here +-e GALAXY_CONFIG_NEW_FILE_PATH="/cluster_storage/galaxy_data/tmp" # IMPORTANT: needs to be created manually. This needs to be writable by UID=1450 and have its flippy bit set (chmod 1777 for world-writable with flippy bit) +-e GALAXY_CONFIG_OUTPUTS_TO_WORKING_DIRECTORY=False # Writes Job scripts, stdout and stderr to job_working_directory. +-e GALAXY_CONFIG_RETRY_JOB_OUTPUT_COLLECTION=5 #IF your cluster fs uses nfs this may introduce latency. You can set galaxy to retry if a job output is not yet created. # Conda settings. IMPORTANT! --e GALAXY_CONFIG_CONDA_PREFIX="/cluster_storage/galaxy_data/_conda" \ # Can be anywhere EXCEPT cluster_storage/galaxy/galaxy_export! +-e GALAXY_CONFIG_CONDA_PREFIX="/cluster_storage/galaxy_data/_conda" # Can be anywhere EXCEPT cluster_storage/galaxy/galaxy_export! # Conda uses $PWD to determine where the virtual environment is. If placed inside the export directory conda will determine $PWD to be a subirectory of the /export folder which does not exist on the cluster! -e GALAXY_CONFIG_CONDA_AUTO_INIT=True # When the necessary environment can not be found a new one will automatically be created ```