-
This is your personal workspace. The "pd" folder represents your
- persistent drive:
+
This is your personal workspace. No one else can access the data or files here.
+
You can learn more about using the BRH Workspace in the
+ BRH Documentation.
+
+
The /pd folder (find it in the panel on the left) is your persistent drive:
+
- - The files you save here will still be available when you come back
- after terminating your workspace session.
-
- Any personal files outside of this folder will be lost.
+
- Use this folder to store files (notebooks, data files, etc) that you want to use again later.
+ The files you save here will still be available when you come back after terminating your workspace session.
+ - Any files you create or add outside of this folder will be lost if they are not moved to the
/pd
+ before your workspace session terminates.
+ - The Nextflow image
/pd has a storage capacity limit of 10Gi
-
-
If you are new to Nextflow, visit nextflow.io for detailed information.
+
The folder /brh.data-commons.org in the /data folder will host any data files you have
+ downloaded to the workspace through the BRH Discovery Page.
+ Move these files to the /pd directory if you want to access them again after you terminate your workspace session.
+
+
+
Open a new "Launcher" tab by clicking the + next to nextflow-welcome.html tab at the
+ top of this document.
+
+
From the Launcher tab, you can open: a new, empty Jupyter notebook; open a new code console or terminal window; or,
+ create several types of files (text, Markdown, Python). For notebooks or files - remember to move the file into the
+ /pd drive if you want to access them in a later workspace session.
+
+
You can learn how to download data files
+ through the BRH discovery page in our documentation.
+
+
Install software tools by using pip install (Python) or CRAN (R).
+ If you have a requirements text, you can install them with pip install -r requirements.txt.
+ You can view all pre-installed software packages by opening a terminal window and using the command pip list
+
+
There are some Nextflow examples that can be run without external containers in the
+ BRH documentation.
+ Find other examples of analyses that can be done in the BRH Workspace on the
+ BRH Example Analyses page.
+
+
If the locally-stored files you wish to analyze are large in number and/or size, you may need to zip them before
+ uploading to a workspace. Once in a workspace, files can be unzipped using the python library
+ zipfile.
+
+
+
+
Note: The Nextflow CPU image is currently sized for smaller analyses and testing.
+ The maximum storage in the /pd (including any notebooks or tools installed) is 10Gi.
+ If you need a larger image for your analyses, please reach out to the BRH support team at
+ brhsupport@gen3.org to discuss the possibility of a larger image.
+
+
If you are new to Nextflow, visit nextflow.io for detailed information.
You can also learn more about using Nextflow in BRH Workspace in the BRH Documentation.
+ href=https://uc-cdis.github.io/BRH-documentation/01-home>BRH Documentation.
+
+
This workspace is set up to run Nextflow workflows in AWS Batch.
+ Your Nextflow configuration must include:
+
+
+ - the Batch queue (in your config file,
process.queue),
+ - IAM role ARN (
aws.batch.jobRole), and
+ - work directory (
workDir)
+
+
These were created for you automatically, and the sample config file is already configured with these settings.
+ It will allow you to run simple workflows and can be adapted to your needs.
-
This workspace is set up to run Nextflow workflows in AWS Batch. Your
- Nextflow configuration must include the Batch queue (in your config file,
- process.queue), IAM role ARN (aws.batch.jobRole), and work
- directory (workDir) that were created for you automatically. The sample config
- file is already configured with these settings. It will allow you to run simple workflows and can be adapted to your
- needs. To get started:
+
To get started:
- - If you want your
nextflow.config file to persist, first double-click on the "pd" folder.
- - Open a new "Launcher" tab by clicking the + next to
nextflow-welcome.html
- - Scroll down until you see the option for terminal. Click to open a terminal.
-
- You can find your sample configuration file in the "data" directory.
- Copy it to a new "nextflow.config" file by running this command in the
- terminal:
cp
- ../data/sample-nextflow-config.txt ./nextflow.config
- - Launch a Hello World workflow by running this command in the terminal:
-
nextflow run hello
+ - If you want your
nextflow.config file to persist, first double-click on the /pd folder.
+ - Open a new "Launcher" tab by clicking the
+ next to nextflow-welcome.html
+ - Scroll down until you see the option for terminal. Click to open a terminal.
+ - You can find your sample configuration file in the
/data directory.
+ Copy it to a new nextflow.config file by running this command in the terminal:
+ cp ../data/sample-nextflow-config.txt ./nextflow.config.
+ Because you opened the /pd folder before you ran the command, it will save your config in the /pd.
+ - Launch a
Hello World workflow by running this command in the terminal:
+ nextflow run hello