Galaxy

Introduction

For support contact: scinet_vrsc@usda.gov

First, a quick note on the terms “Ceres” and “SCINet”: “SCINet” is the network through which you access the high-performance computer named “Ceres”. Generally, we will refer to Ceres accounts in this tutorial because most people think of having an account on a computer, but the account is, more broadly, a network account on SCINet.

There are a few compelling reasons why we think you’re going to like using Galaxy on Ceres:

1. It is a great bioinformatics alternative for those who prefer a graphical user interface.
2. You don’t have to worry with defining queues and number of nodes in a batch command file. We have tried hard to establish appropriate default parameters to take advantage of Ceres’s parallel processing power.
3. FTP transfer is tightly integrated in the Ceres Galaxy framework, so file transfer is intuitive, and you don’t run into data limit bottlenecks as quickly.
4. Galaxy makes it easy to share your analysis with bioinformatic support should the need arise. In addition, you can share with collaborators assuming that they have a Ceres account.
5. There is plenty of external documentation covering almost all conventional bioinformatic analyses. In fact, many workflows (see below) probably already exist that you can use directly on your data.
6. If you don’t see a tool in the current interface, it probably is in the Toolshed (see below). You can then request that an administrator install it.

In order to use SCINet Galaxy, you need an account on Ceres. Sign up for a SCINet account to start that process. New accounts will automatically get a Galaxy user name and directory. The user name should match the email you used when registering for your Ceres account and the password will match your Ceres password.

NOTE: All uploaded and output files are removed after 90 Days so it is recommended users save their data outside of galaxy.

Logging On

Ceres Galaxy is public facing, so to access it you just type or paste “https://galaxy.scinet.usda.gov” into the address bar of a web browser. We recommend Firefox, Chrome, or Safari. MAKE SURE TO TYPE THE “https://” prefix and note the “s”.

You will be presented with the following login screen:

Click on “Sign in with Keycloak” and follow yubikey/lincpass login. After logging in, the standard Galaxy home screen should appear:

The “Tools” bar in the left window frame is where you can load, manipulate, and analyze data. The central window frame is where you will see options and parameters programs that you will be running. The right “History” frame shows all the imported files and programs you have run. In order to begin, you need to upload data. Often data of general interest, such a genome sequences or annotations, are already available in Galaxy under the “Get Data” tab. More commonly, you will be using data that you have generated.

You will import files into Galaxy by clicking on the “Tools” sub-heading “Get Data” and then “Upload File” under “Get Data”. The following download/upload screen should appear:

Galaxy offers a method to import data directly from your computer as “Choose local file” button. Feel free to experiment with this direct method, but we find it can be slower and fickler than FTP transfer. To that end, we will mainly focus on uploading files using a file transfer program, such as Globus or Filezilla. If you click on “Choose FTP file”, Galaxy will look in your FTP upload folder on Ceres (/galaxy/upload/ceres_email_ID) for files you have uploaded, so you must first upload your data to that folder.

Galaxy KeyCloak Instructions

Going forward, Keycloak is the only supported login method. Legacy auth will be discontinued, users who logged in via legacy auth have to manually transition by following the instructions below.

The following instructions will aid with migrating your Galaxy/SCINet Authenticator to KeyCloak

1. Log in to Galaxy through your SCINet email and Password+GoogleAuthenticator (For example: Username: john.smith Password: FruitPunch789!123456) Please wait patiently at this step as it may take about 20 seconds to login.
2. Once Logged in, click on the “User” Tab on the top of your homepage
3. Under the User tab banner click on Preferences
4. Under the User preferences click on Manage Third Party Identities
5. In Manage Third Party Identities click on Sign in with keycloak
6. You will then be prompted to sign in to your SCINet account. Login using your preferred method
7. After successful login, your galaxy account should be migrated. If you go to the Manage Third Party Identities again, you should see Keycloak under Connected External identities.
8. Further logins should only be done via keycloak. The legacy login will no longer work.

Import data to Ceres Galaxy

You need to move or copy your data files to the Galaxy folder in your home directory on Ceres to make them “visible” to Galaxy. Then, you will be able to upload/import the files using Galaxy. Remember, the default quota in SCINet galaxy is only 100 GB. Please contact us to increase your default quota.

We recommend using Globus to move files to your Galaxy folder on Ceres. For instructions please see the Transferring Files Guide.

NOTE: If you already have data on Ceres, simply copy files into your Galaxy folder on Ceres either via command-line (cp command) or by using a Filezilla-like tool. These files will appear as if you had uploaded them via FTP and can be imported using the approach described below.

IMPORTANT NOTE: Make sure when transfering files to consider how the files are being transfered, i.e. using cp or mv. Moving (mv) instead of copying(cp) will REMOVE the original files so it is recommended to use cp or review how you want your files to be handled before moving.

Once your data files are in your Galaxy folder in your home directory on Ceres, go back to the “Upload File” screen and click “Choose FTP site”. You will see the download/upload screen with a list of your files:

Select the file you want to import and hit “Start”.

NOTE: Importing the data into galaxy will REMOVE the file that you moved via FTP. NOTE: Uploading directly from disk is slower than the other methods of tranfering.

You can close this window and the file will appear in the History pane on the right of your home screen:

This is a generic way to import files and can be used regardless of file format. You are now ready to process your data.

Using Galaxy

We have tried to focus on aspects of using Galaxy that are specific to USDA-ARS’s Ceres installation. There are hundreds of tutorials and videos to introduce you to the Galaxy framework, which is essentially the same no matter where it is installed. We suggest that you start at https://galaxyproject.org/learn/. A nice interactive introduction is also available at Help > Interactive Tours, or https://galaxy.scinet.usda.gov/tours.

A common initial hang-up is getting your uploaded data in the right format. For sequencing data, you usually need to make clear what quality-scale you are using. For illumina reads, review the following link: https://galaxyproject.org/support/fastqsanger/. In addition, it is common for sample data from sequencing centers to be spread across multiple lanes. If you only have a few samples, you can concatenate these in Galaxy using Concatenate – Text Manipulation tool. If you have many samples, it will probably be best to concatenate those files prior to uploading using the commandline function cat.

For example, for files ‘samp1_L1_R1.fq’, ‘samp1_L2_R1.fq’ use

[jane.user@sn-cn-18-0 ~]$ cat *R1.fq >sample1_R1.fq

Also note, .gz compressed files can be concatenated using the same approach without having to uncompress them first.

You will usually want to structure your data into Collections for batch processing and downstream analysis. See https://galaxyproject.org/tutorials/collections/ or, for a worked example, https://depot.galaxyproject.org/hub/attachments/documents/presentations/gcc2014/Chilton.pdf. Alternatively, most tools will allow you to run the same process on multiple datasets of the same format without combining them as Collections.

Some links to common analyses are given below. Many of these analyses already exist as published workflows and can be used directly. See https://usegalaxy.org/workflow/list_published for a searchable list. To use, download the workflow of interest, click on the “Workflow” tab at the top of your main screen, and then import the workflow according to the instructions. An example of usage is available here: http://sepsis-omics.github.io/tutorials/modules/workflows/. For those wanting to develop their own worflows, a graphic editor is available, as described here: https://galaxyproject.org/tutorials/g101/#opening-workflow-editor.

RNA-seq – general overview (https://galaxyproject.org/tutorials/rb_rnaseq/) and galaxy specific pipeline (https://galaxyproject.org/tutorials/nt_rnaseq). Also check out https://sites.google.com/site/princetonhtseq/tutorials/rna-seq.

SNP-calling – https://galaxyproject.org/tutorials/var_dip/ for diploid genomes and https://galaxyproject.org/tutorials/var_hap/ for haploid genomes.

IMPORTANT: If you receive the job error “This job was terminated because it ran longer than the maximum allowed job run time” it means that the tool has not been appropriately configured to run on Ceres using the scale of data that you have provided. Please contact scinet_vrsc@usda.gov and we can optimize these parameters for you and for future users.

Sharing Your Data and Analysis

If you need some consultation on your results or on parameter settings, it can be very useful to share your analysis with someone so that you can both be viewing the same thing. To that end, we will give this aspect special emphasis. You can see a short introduction to this option at https://galaxyproject.org/learn/share.

Briefly, if you are in the appropriate history, follow the clicks on the History pane indicated in red (select Settings gear icon, then select “Share or Publish” on the settings menu):

You will see the “Share or Publsish History Galaxy_Walkthru” screem:

You can manually enter the user name you wish to share with in the drop-down space. Be careful that the user-name is exact and appropriate capitalization is observed.

After you have gone through these steps, the person you have shared your history with will need to go to the same gear icon used above but instead click on “Histories Shared With Me”. The shared history should be present on the resultant interface.

Can’t Find a Tool You Need?

We have loaded a core subset of all tools that are available on the public Galaxy server (https://usegalaxy.org). If you do not see a tool you need and cannot use a good alternative, you should search in the Toolshed (https://toolshed.g2.bx.psu.edu). After identifying the relevant tool, email a Ceres Galaxy administrator: scinet_vrsc@usda.gov. If there are multiple options, we encourage the use of tools developed by either “devteam” or “iuc”. Depending on the nature of the tool you are requesting, we may ask you to supply a sample dataset for testing purposes, so anticipate having that data available.

Additionally, there is an option for galaxy install as well on the application to request software installation by the VRSC. Select the Galaxy checkbox in the “Type of Application” section: