Quick Start
Installation
The first step is to install the tinybio-cli module. You can do this by opening a terminal or command prompt and running the following command:
pip install tiny-cli
Authentication
After installing the module, you need to authenticate your Google account with tinybio.cloud. To do this, go to https://api.tinybio.cloud/readme-docs/login and use your Google account to authenticate.
Once authenticated, you will be redirected to our api docs and receive a bearer token that you can use to start requests with.
Usage
Set environment variables and import Tiny Cli
import os
os.environ['TINYBIO_AUTH_TOKEN']='YOUR_TOKEN_HERE'
import tiny
We created a starter bench with samples when you signed up to help you get started. This is how you can see your active Workbenches
tiny.list_workbenches()
+----------------------------------------------+----------+----------------+
| Workbench Name | Size | Last Updated |
+==============================================+==========+================+
| tiny-26-starter-samples-20230501181335640599 | 161.7 GB | 2 day ago |
+----------------------------------------------+----------+----------------+
Initialize your starter Workbench or create a new one
workbench = tiny.Workbench('user-id-4-starter-samples-20230419172317820288')
or
workbench = tiny.create_workbench('foobar')
The foobar-20230410160630063331 workbench is now available.
Take a look at the files on the Workbench
workbench.ls()
tiny-26-starter-samples-20230501181335640599
├── input
│ ├──
│ │ └── input/ (0 Bytes)
│ ├── atac-seq
│ │ ├── SRR10261591_1.fastq.gz
│ │ │ └── input/atac-seq/SRR10261591_1.fastq.gz (592.4 MB)
│ │ ├── SRR10261591_2.fastq.gz
│ │ │ └── input/atac-seq/SRR10261591_2.fastq.gz (1.3 GB)
│ │ ├── SRR10261592_1.fastq.gz
│ │ │ └── input/atac-seq/SRR10261592_1.fastq.gz (1.9 GB)
│ │ ├── SRR10261592_2.fastq.gz
│ │ │ └── input/atac-seq/SRR10261592_2.fastq.gz (1.9 GB)
│ │ ├── SRR10261593_1.fastq.gz
│ │ │ └── input/atac-seq/SRR10261593_1.fastq.gz (1.4 GB)
│ │ ├── SRR10261593_2.fastq.gz
│ │ │ └── input/atac-seq/SRR10261593_2.fastq.gz (1.4 GB)
│ │ ├── SRR10261594_1.fastq.gz
│ │ │ └── input/atac-seq/SRR10261594_1.fastq.gz (1.6 GB)
│ │ ├── SRR10261594_2.fastq.gz
│ │ │ └── input/atac-seq/SRR10261594_2.fastq.gz (1.7 GB)
│ │ ├── SRR10261595_1.fastq.gz
│ │ │ └── input/atac-seq/SRR10261595_1.fastq.gz (1.3 GB)
│ │ ├── SRR10261595_2.fastq.gz
│ │ │ └── input/atac-seq/SRR10261595_2.fastq.gz (1.4 GB)
│ │ ├── SRR10261596_1.fastq.gz
│ │ │ └── input/atac-seq/SRR10261596_1.fastq.gz (1.3 GB)
│ │ ├── SRR10261596_2.fastq.gz
│ │ │ └── input/atac-seq/SRR10261596_2.fastq.gz (1.4 GB)
│ │ ├── ref_gen
│ │ │ ├── SC.amb
│ │ │ │ └── input/atac-seq/ref_gen/SC.amb (45 Bytes)
│ │ │ ├── SC.ann
│ │ │ │ └── input/atac-seq/ref_gen/SC.ann (515 Bytes)
│ │ │ ├── SC.bwt
│ │ │ │ └── input/atac-seq/ref_gen/SC.bwt (12.2 MB)
│ │ │ ├── SC.pac
│ │ │ │ └── input/atac-seq/ref_gen/SC.pac (3.0 MB)
│ │ │ ├── SC.sa
│ │ │ │ └── input/atac-seq/ref_gen/SC.sa (6.1 MB)
│ │ │ ├── S_cerevisiae_masked_rRNA.fasta
│ │ │ │ └── input/atac-seq/ref_gen/S_cerevisiae_masked_rRNA.fasta (12.4 MB)
│ │ │ ├── S_uvarum.fasta
│ │ │ │ └── input/atac-seq/ref_gen/S_uvarum.fasta (11.6 MB)
│ │ │ ├── Saccharomyces_cerevisiae.R64-1-1.106.gtf
│ │ │ │ └── input/atac-seq/ref_gen/Saccharomyces_cerevisiae.R64-1-1.106.gtf (9.6 MB)
│ │ │ ├── Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa
│ │ │ │ └── input/atac-seq/ref_gen/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa (12.4 MB)
│ │ │ ├── Sbay.ultrascaf
│ │ │ │ └── input/atac-seq/ref_gen/Sbay.ultrascaf (11.5 MB)
│ │ │ ├── Sbay.unplaced
│ │ │ │ └── input/atac-seq/ref_gen/Sbay.unplaced (118.3 kB)
│ │ │ ├── hybrid.amb
│ │ │ │ └── input/atac-seq/ref_gen/hybrid.amb (5.9 kB)
│ │ │ ├── hybrid.ann
│ │ │ │ └── input/atac-seq/ref_gen/hybrid.ann (7.3 kB)
│ │ │ ├── hybrid.bwt
│ │ │ │ └── input/atac-seq/ref_gen/hybrid.bwt (23.8 MB)
│ │ │ ├── hybrid.fasta
│ │ │ │ └── input/atac-seq/ref_gen/hybrid.fasta (24.0 MB)
│ │ │ ├── hybrid.pac
│ │ │ │ └── input/atac-seq/ref_gen/hybrid.pac (5.9 MB)
│ │ │ ├── hybrid.sa
│ │ │ │ └── input/atac-seq/ref_gen/hybrid.sa (11.9 MB)
│ │ │ └── mask_rRNA.bed
│ │ │ └── input/atac-seq/ref_gen/mask_rRNA.bed (36 Bytes)
│ │ └── rscript
│ │ ├── diffbind_qc.R
│ │ │ └── input/atac-seq/rscript/diffbind_qc.R (2.5 kB)
│ │ └── occupancy_and_diff_accessibility.R
│ │ └── input/atac-seq/rscript/occupancy_and_diff_accessibility.R (2.4 kB)
│ ├── rna-seq
│ │ ├── SRR1278968_1.fastq.gz
│ │ │ └── input/rna-seq/SRR1278968_1.fastq.gz (1.0 GB)
│ │ ├── SRR1278968_2.fastq.gz
│ │ │ └── input/rna-seq/SRR1278968_2.fastq.gz (1.1 GB)
│ │ ├── SRR1278969_1.fastq.gz
│ │ │ └── input/rna-seq/SRR1278969_1.fastq.gz (1.0 GB)
│ │ ├── SRR1278969_2.fastq.gz
│ │ │ └── input/rna-seq/SRR1278969_2.fastq.gz (1.1 GB)
│ │ ├── SRR1278970_1.fastq.gz
│ │ │ └── input/rna-seq/SRR1278970_1.fastq.gz (1.0 GB)
│ │ ├── SRR1278970_2.fastq.gz
│ │ │ └── input/rna-seq/SRR1278970_2.fastq.gz (1.1 GB)
│ │ ├── SRR1278971_1.fastq.gz
│ │ │ └── input/rna-seq/SRR1278971_1.fastq.gz (966.6 MB)
│ │ ├── SRR1278971_2.fastq.gz
│ │ │ └── input/rna-seq/SRR1278971_2.fastq.gz (961.4 MB)
│ │ ├── SRR1278972_1.fastq.gz
│ │ │ └── input/rna-seq/SRR1278972_1.fastq.gz (1.0 GB)
│ │ ├── SRR1278972_2.fastq.gz
│ │ │ └── input/rna-seq/SRR1278972_2.fastq.gz (1.0 GB)
│ │ ├── SRR1278973_1.fastq.gz
│ │ │ └── input/rna-seq/SRR1278973_1.fastq.gz (982.2 MB)
│ │ ├── SRR1278973_2.fastq.gz
│ │ │ └── input/rna-seq/SRR1278973_2.fastq.gz (983.3 MB)
│ │ ├── ref_gen
│ │ │ ├── C_parapsilosis_CDC317_current_chromosomes.fasta
│ │ │ │ └── input/rna-seq/ref_gen/C_parapsilosis_CDC317_current_chromosomes.fasta (13.2 MB)
│ │ │ └── C_parapsilosis_CDC317_current_features.gff
│ │ │ └── input/rna-seq/ref_gen/C_parapsilosis_CDC317_current_features.gff (5.8 MB)
│ │ └── rscript
│ │ ├── DE.R
│ │ │ └── input/rna-seq/rscript/DE.R (2.3 kB)
│ │ └── GO.R
│ │ └── input/rna-seq/rscript/GO.R (1.9 kB)
│ └── variants-calling
│ ├── SRR15498471_1.fastq.gz
│ │ └── input/variants-calling/SRR15498471_1.fastq.gz (1.4 GB)
│ ├── SRR15498471_2.fastq.gz
│ │ └── input/variants-calling/SRR15498471_2.fastq.gz (1.5 GB)
│ └── ref_gen
│ ├── C_glabrata_CBS138_current_chromosomes.fasta
│ │ └── input/variants-calling/ref_gen/C_glabrata_CBS138_current_chromosomes.fasta (13.0 MB)
│ └── C_glabrata_CBS138_current_features.gff
│ └── input/variants-calling/ref_gen/C_glabrata_CBS138_current_features.gff (5.3 MB)
├── output
│ ├──
│ │ └── output/ (0 Bytes)
│ ├── atac-seq
│ │ └──
│ │ └── output/atac-seq/ (0 Bytes)
│ ├── rna-seq
│ │ └──
│ │ └── output/rna-seq/ (0 Bytes)
│ └── variants-calling
│ └──
│ └── output/variants-calling/ (0 Bytes)
└── working
└──
└── working/ (0 Bytes)
Start using the tools available on TinyBio
workbench.run(
tool="fastqc",
full_command="fastqc -t 10 /input/atac-seq/*gz -o /output/atac-seq/fastqc_initial"
)
+------------------+--------+-----------+----------+-------------------------------------------+----------------------------------------------------------------------+
| Job ID | Tool | Version | Status | Get Logs | Full Command |
+==================+========+===========+==========+===========================================+======================================================================+
| fastqc85b9ac7494 | fastqc | 0.11.8 | Queued | workbench.jobs('fastqc85b9ac7494').logs() | fastqc -t 10 /input/atac-seq/*.gz -o /output/atac-seq/fastqc_initial |
+------------------+--------+-----------+----------+-------------------------------------------+----------------------------------------------------------------------+
View status of Jobs on your Workbench session
workbench.jobs()
+------------------+--------+-----------+----------+-------------------------------------------+----------------------------------------------------------------------+
| Job ID | Tool | Version | Status | Get Logs | Full Command |
+==================+========+===========+==========+===========================================+======================================================================+
| fastqc85b9ac7494 | fastqc | 0.11.8 | Running | workbench.jobs('fastqc85b9ac7494').logs() | fastqc -t 10 /input/atac-seq/*.gz -o /output/atac-seq/fastqc_initial |
+------------------+--------+-----------+----------+-------------------------------------------+----------------------------------------------------------------------+
Congratulations! You have successfully set up and used TinyBio to run a basic bioinformatic pipeline! 
Guides
Check out one of our existing Google Colab notebooks 
to discover more on what Tinybio can do
Updated 4 months ago