Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Switch to per-rfc example domain to use in ftp_upload_dir #396

Open
wants to merge 3 commits into
base: dev
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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 <YOUR FILE HERE>'
sftp -v -P 8022 -o User=admin@example.org localhost <<< $'put <YOUR FILE HERE>'
```


Expand Down Expand Up @@ -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"
```
Expand Down Expand Up @@ -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
```

Expand Down Expand Up @@ -718,7 +718,7 @@ In rare situations where you cannot share your tools but still want to include t

# Users & Passwords <a name="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.

Expand Down
8 changes: 4 additions & 4 deletions galaxy/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -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 \
Expand Down Expand Up @@ -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 \
Expand All @@ -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.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 \
Expand Down Expand Up @@ -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 && \
Expand Down