CloudNeo Manual¶
Getting Started¶
Register for an account¶
Register for a account with the Seven Bridges Cloud Platform.
Create a Project¶
Login to the account and create a project to do your analysis. Projects act as a container to store your data, apps, and workflows. You can create a project by clicking on ‘Create a Project’ button, as highlighted in the below screenshot.
See also
More information on how to create a project is available here.
Accessing the CloudNeo App¶
After creating the account and the project, please contact the author Dr. Chuang for access to the CloudNeo app. Workflows and Tools are called Apps on Seven Bridges CGC platfrom. There are two ways we could provide access to the app:
- You can add one of the authors as a temporary team member to your project. The team member would then copy the app to the project.
- We could also add you as a temporary member to one of our projects. You will be able to access and copy the app to your own project.
See also
More information on adding a member to the project.
Running the CloudNeo App¶
Creating a draft task¶
Once the App has been copied to your project, it will be available in the ‘Apps’ tab as shown below in the example screenshot.
Next, click on the ‘Run’ button (highlighted in the screenshots) to create a draft task.
See also
More information on how to create a draft task.
Select input files¶
Add the files that you would like to analyze to the project. The files must be in the project to select it as input. All the inputs are required for the CloudNeo app.
See also
More information on uploading the files to the project.
Define app settings¶
The Seven Bridges CGC interface allows you to change the app’s setting before you submit the task. Click on the ‘App Settings’ tab to change any parameters. This is an optional step and the CloudNeo pipeline has a set of defaults that can be used.
Run the Analysis/Task¶
Click on the ‘Run’ button (green button - shown below) to submit the task.
See also
More information on how to submit a task.
View submitted Tasks¶
The tasks submitted can be viewed in the ‘Tasks’ tabs as shown below.
See also
More information on how to view tasks.
Finding apps on CGC¶
The public apps developed by Seven Bridges can be accessed directly on the platform. Click on the ‘Public Apps’ tabs on the CGC platfrom as shown below. The URL can be directly accessed at: https://cgc.sbgenomics.com/public/apps.
You can search for the apps/tools on the same page. The below screenshot shows the search result for VCftools.
See also
More information on how to search for a tool or app.
See also
More information on how to bring your own tool to Seven Bridges Genomics Platform.
Note
The entire documentation about the Seven Bridges Genomics Platfrom is here, along with the tutorials.
CloudNeo App¶
Inputs¶
Input Details¶
| ID | Label | Type | Required | Format |
|---|---|---|---|---|
| input_bam | input_bam | File | Yes | BAM |
| input_reference_file | input_reference_file | File | Yes | TAR.GZ |
| input_file | input_file | File | Yes | VCF TXT |
| input_database_file | input_database_file | File | Yes | FASTA |
| input_allele_database | input_allele_database | File | Yes | fasta |
| input_gtf | input_gtf_1 | File | Yes | GTF |
| input_csv | input_csv_1 | File | Yes | CSV |
- input_bam
- Input BAM file to call neoepitopes
- input_reference_file
- This is the Variant Effect Predictor reference file. This can be downloaded from the following link. homo_sapiens_vep_83_GRCh37.tar.gz
- input_file
- Input VCF file to call neoepitopes
- input_database_file
- This is the IMGT hla_prot.fasta file for input to netmhcpan. The input file must be formatted as below:
# The header in this file must be formated and renamed as netmhcpan-3.0.imgt.fasta
cat hla_prot.fasta | perl -ne 'chomp;if(/\>\S+\s+(\S+)/){print ">$1\n";}else{print "$_\n";}' > netmhcpan-3.0.imgt.fasta
- input_allele_database
This is the Hlaminer/IMGT database file, which can be downloaded from the following link: HLAminer Database. The index files can be obtained from the same link.
- RNA-Seq data analysis
- All files starting with HLA-I_II_CDS.* must be copied for RNA-seq analysis. The HLA-I_II_CDS.fasta comprises all IMGT/HLA HLA CDS (including class I and II).
- DNA-Seq data analysis
- All files starting with HLA-I_II_GEN.* must be copied for DNA-seq analysis. The HLA-I_II_GEN.fasta comprises all IMGT/HLA HLA genomic sequences (including class I and II).
Note
instructions to build the IMGT/HLA database are here on hlaminer github repository.
If you would like to update the coding sequences database(HLA-I_II_CDS.fasta), the instructions are provided here on the HLAminer github repository.
If you would like to update the genomics sequences database(HLA-I_II_GEN.fasta), the instructions are provided here on the HLAminer github repository.
- input_gtf
- Input Homo sapiens GTF file from Ensembl: Homo_sapiens.GRCh37.75.gtf.gz.
- input_csv
- Human Proteins (GRCh37.75) file: HumanProteins.GRCh37.75.csv.
App Settings¶
Settings Defaults¶
| ID | Label | Type | Required | Prefix | Default |
|---|---|---|---|---|---|
| num_gap_extensions | maximum number of gap extensions | int | No | -e | 0 |
| maximum_number_of_gap_opens | maximum number or fraction of gap opens | int | No | -o | 0 |
| vcf | Output as VCF file | boolean | No | –vcf | TRUE |
| html | HTML | boolean | No | –html | TRUE |
| filter_common | Filter common | boolean | No | TRUE | |
| minimum_score | enum | No | -s | 500 | |
| label_run_name | string | No | -l | ||
| bool_single_end_reads_used | bool | int | No | -e | 1 |
| peptide_length | peptide_length | int | No | 9 | |
| kmer_peptide_length | kmer peptide length | int | No | 17 |
Outputs¶
| ID | Label | Type | Format |
|---|---|---|---|
| predictions_file | predictions_file | File | TXT |
| html_summary | html_summary | File | HTML |
| html_output | html_output | File | HTML |
| vep_output | vep_output | File | TEXT, JSON, VCF, GVF |
| output_vcf_file | output_vcf_file | File | VCF |
| netmhcpan_outputs_xls | netmhcpan_outputs_xls | File array | XLS |
| netmhcpan_outputs_txt | netmhcpan_outputs_txt | File array | TXT |
| output_xls | output_xls | File | XLS |
| control_fasta | control_fasta | File | FASTA |
| tumor_fasta | tumor_fasta | File | FASTA |
Outputs Details¶
- predictions_file
- the output file from HLAminer
- html_summary
- The HTML output summary file from Variant Effect Predictor
- vep_output
- The VEP annotated output VCF file
- output_vcf_file
- Formatted VCF file as input to netmhcpan
- netmhcpan_outputs_xls
- netmhcpan outputs in XLS format
- netmhcpan_outputs_txt
- netmhcpan outputs in TXT format
- output_xls
- Intermediary file from protein translator
- control_fasta
- control file without the mutation (control Proteome)
- tumor_fasta
- Fasta file with the mutation (tumor proteome)
Contribute¶
- Issue Tracker: https://github.com/TheJacksonLaboratory/CloudNeo/issues
- Source Code: https://github.com/TheJacksonLaboratory/CloudNeo