From f49613cb2eef4e692173d000399d35ad58d668e7 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Mon, 6 Nov 2017 20:45:51 +0000 Subject: [PATCH 1/3] switch to per-rfc domain to use in examples Instead of an uncontrolled domain that may have users uploading data to the wrong place. --- galaxy/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/galaxy/Dockerfile b/galaxy/Dockerfile index 68ca45352..46e07f7a5 100644 --- a/galaxy/Dockerfile +++ b/galaxy/Dockerfile @@ -164,7 +164,7 @@ GALAXY_CONFIG_TEMPLATE_CACHE_PATH=$EXPORT_DIR/galaxy-central/database/compiled_t GALAXY_CONFIG_CITATION_CACHE_DATA_DIR=$EXPORT_DIR/galaxy-central/database/citations/data \ GALAXY_CONFIG_CLUSTER_FILES_DIRECTORY=$EXPORT_DIR/galaxy-central/database/pbs \ GALAXY_CONFIG_FTP_UPLOAD_DIR=$EXPORT_DIR/ftp \ -GALAXY_CONFIG_FTP_UPLOAD_SITE=galaxy.docker.org \ +GALAXY_CONFIG_FTP_UPLOAD_SITE=example.com \ GALAXY_CONFIG_USE_PBKDF2=False \ GALAXY_CONFIG_NGINX_X_ACCEL_REDIRECT_BASE=/_x_accel_redirect \ GALAXY_CONFIG_NGINX_X_ARCHIVE_FILES_BASE=/_x_accel_redirect \ From aa0306a68b17a500f7e682c3deb2ec5c69dd40b5 Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Mon, 6 Nov 2017 20:51:46 +0000 Subject: [PATCH 2/3] Be less commercial + switch to admin@example.org --- galaxy/Dockerfile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/galaxy/Dockerfile b/galaxy/Dockerfile index 46e07f7a5..0687eca3a 100644 --- a/galaxy/Dockerfile +++ b/galaxy/Dockerfile @@ -30,7 +30,7 @@ GALAXY_POSTGRES_UID=1550 \ GALAXY_POSTGRES_GID=1550 \ GALAXY_HOME=/home/galaxy \ GALAXY_LOGS_DIR=/home/galaxy/logs \ -GALAXY_DEFAULT_ADMIN_USER=admin@galaxy.org \ +GALAXY_DEFAULT_ADMIN_USER=admin@example.org \ GALAXY_DEFAULT_ADMIN_PASSWORD=admin \ GALAXY_DEFAULT_ADMIN_KEY=admin \ GALAXY_DESTINATIONS_DEFAULT=slurm_cluster \ @@ -153,7 +153,7 @@ WORKDIR $GALAXY_ROOT #RUN export GALAXY=$GALAXY_ROOT && sh ./cron/updateucsc.sh.sample ENV GALAXY_CONFIG_DATABASE_CONNECTION=postgresql://galaxy:galaxy@localhost:5432/galaxy?client_encoding=utf8 \ -GALAXY_CONFIG_ADMIN_USERS=admin@galaxy.org \ +GALAXY_CONFIG_ADMIN_USERS=admin@example.org \ GALAXY_CONFIG_MASTER_API_KEY=HSNiugRFvgT574F43jZ7N9F3 \ GALAXY_CONFIG_BRAND="Galaxy Docker Build" \ GALAXY_CONFIG_STATIC_ENABLED=False \ @@ -164,7 +164,7 @@ GALAXY_CONFIG_TEMPLATE_CACHE_PATH=$EXPORT_DIR/galaxy-central/database/compiled_t GALAXY_CONFIG_CITATION_CACHE_DATA_DIR=$EXPORT_DIR/galaxy-central/database/citations/data \ GALAXY_CONFIG_CLUSTER_FILES_DIRECTORY=$EXPORT_DIR/galaxy-central/database/pbs \ GALAXY_CONFIG_FTP_UPLOAD_DIR=$EXPORT_DIR/ftp \ -GALAXY_CONFIG_FTP_UPLOAD_SITE=example.com \ +GALAXY_CONFIG_FTP_UPLOAD_SITE=example.org \ GALAXY_CONFIG_USE_PBKDF2=False \ GALAXY_CONFIG_NGINX_X_ACCEL_REDIRECT_BASE=/_x_accel_redirect \ GALAXY_CONFIG_NGINX_X_ARCHIVE_FILES_BASE=/_x_accel_redirect \ @@ -203,7 +203,7 @@ ADD ./setup_postgresql.py /usr/local/bin/setup_postgresql.py # Configure PostgreSQL # 1. Remove all old configuration # 2. Create DB-user 'galaxy' with password 'galaxy' in database 'galaxy' -# 3. Create Galaxy Admin User 'admin@galaxy.org' with password 'admin' and API key 'admin' +# 3. Create Galaxy Admin User 'admin@example.org' with password 'admin' and API key 'admin' RUN rm $PG_DATA_DIR_DEFAULT -rf && \ python /usr/local/bin/setup_postgresql.py --dbuser galaxy --dbpassword galaxy --db-name galaxy --dbpath $PG_DATA_DIR_DEFAULT && \ From 26865dbcf9a0734c62cb3b47f7c68732512c86bc Mon Sep 17 00:00:00 2001 From: Eric Rasche Date: Mon, 6 Nov 2017 20:54:29 +0000 Subject: [PATCH 3/3] Also correct readme --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index cddc223ba..195ad8715 100644 --- a/README.md +++ b/README.md @@ -246,7 +246,7 @@ docker run -i -t -p 8080:80 -p 8022:22 \ And use for example [Filezilla](https://filezilla-project.org/) or the `sftp` program to transfer data: ```sh -sftp -v -P 8022 -o User=admin@galaxy.org localhost <<< $'put ' +sftp -v -P 8022 -o User=admin@example.org localhost <<< $'put ' ``` @@ -283,7 +283,7 @@ For example, you can set the Galaxy session timeout to 5 minutes by adding `-e " *by default* the `admin_users`, `master_api_key` and the `brand` variable it set to: ``` -GALAXY_CONFIG_ADMIN_USERS=admin@galaxy.org +GALAXY_CONFIG_ADMIN_USERS=admin@example.org GALAXY_CONFIG_MASTER_API_KEY=HSNiugRFvgT574F43jZ7N9F3 GALAXY_CONFIG_BRAND="Galaxy Docker Build" ``` @@ -664,7 +664,7 @@ Where all Galaxy workflows needs to be in one directory, here the `$GALAXY_HOME/ - running Galaxy data-managers to create indices or download data ```bash - run-data-managers -u admin@galaxy.org -p admin -g http://localhost:8080 + run-data-managers -u admin@example.org -p admin -g http://localhost:8080 --config data_manager_rna_seq.yaml ``` @@ -718,7 +718,7 @@ In rare situations where you cannot share your tools but still want to include t # Users & Passwords [[toc]](#toc) -The Galaxy Admin User has the username `admin@galaxy.org` and the password `admin`. +The Galaxy Admin User has the username `admin@example.org` and the password `admin`. The PostgreSQL username is `galaxy`, the password is `galaxy` and the database name is `galaxy` (I know I was really creative ;)). If you want to create new users, please make sure to use the `/export/` volume. Otherwise your user will be removed after your docker session is finished.