Package: tiny-cli
tinybio-cliTinybio is a python library for quickly running bioinformatics jobs on on a powerful cloud computer. The main feature of tinybio is being able to spin up and run bioinformatics commands on files that are stored on tinybio storage buckets that we’ll refer to as workbenches.Please visithttps://docs.tinybio.cloud/docs/for the full documentation.A full list of commands can be foundhttps://docs.tinybio.cloud/docs/tiny-cli-commandsQuick StartInstallationThe 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-cliAuthenticationAfter installing the module, you need to authenticate your Google account with tinybio.cloud. To do this, go tohttps://api.tinybio.cloud/readme-docs/loginand 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.UsageSet environment variables and import Tiny Cliimportosos.environ['TINYBIO_AUTH_TOKEN']='YOUR_TOKEN_HERE'importtinyWe created a starter bench with samples when you signed up to help you get started. This is how you can see your active Workbenchestiny.list_workbenches()+----------------------------------------------+----------+----------------+|WorkbenchName|Size|LastUpdated|+==============================================+==========+================+|tiny-26-starter-samples-20230501181335640599|161.7GB|2dayago|+----------------------------------------------+----------+----------------+Initialize your starter Workbench or create a new oneworkbench=tiny.Workbench('user-id-4-starter-samples-20230419172317820288')orworkbench=tiny.create_workbench('foobar')Thefoobar-20230410160630063331workbenchisnowavailable.Take a look at the files on the Workbenchworkbench.ls()tiny-26-starter-samples-20230501181335640599├──input│├──││└──input/(0Bytes)│├──atac-seq││├──SRR10261591_1.fastq.gz│││└──input/atac-seq/SRR10261591_1.fastq.gz(592.4MB)││├──SRR10261591_2.fastq.gz│││└──input/atac-seq/SRR10261591_2.fastq.gz(1.3GB)││├──SRR10261592_1.fastq.gz│││└──input/atac-seq/SRR10261592_1.fastq.gz(1.9GB)││├──SRR10261592_2.fastq.gz│││└──input/atac-seq/SRR10261592_2.fastq.gz(1.9GB)││├──SRR10261593_1.fastq.gz│││└──input/atac-seq/SRR10261593_1.fastq.gz(1.4GB)││├──SRR10261593_2.fastq.gz│││└──input/atac-seq/SRR10261593_2.fastq.gz(1.4GB)││├──SRR10261594_1.fastq.gz│││└──input/atac-seq/SRR10261594_1.fastq.gz(1.6GB)││├──SRR10261594_2.fastq.gz│││└──input/atac-seq/SRR10261594_2.fastq.gz(1.7GB)││├──SRR10261595_1.fastq.gz│││└──input/atac-seq/SRR10261595_1.fastq.gz(1.3GB)││├──SRR10261595_2.fastq.gz│││└──input/atac-seq/SRR10261595_2.fastq.gz(1.4GB)││├──SRR10261596_1.fastq.gz│││└──input/atac-seq/SRR10261596_1.fastq.gz(1.3GB)││├──SRR10261596_2.fastq.gz│││└──input/atac-seq/SRR10261596_2.fastq.gz(1.4GB)││├──ref_gen│││├──SC.amb││││└──input/atac-seq/ref_gen/SC.amb(45Bytes)│││├──SC.ann││││└──input/atac-seq/ref_gen/SC.ann(515Bytes)│││├──SC.bwt││││└──input/atac-seq/ref_gen/SC.bwt(12.2MB)│││├──SC.pac││││└──input/atac-seq/ref_gen/SC.pac(3.0MB)│││├──SC.sa││││└──input/atac-seq/ref_gen/SC.sa(6.1MB)│││├──S_cerevisiae_masked_rRNA.fasta││││└──input/atac-seq/ref_gen/S_cerevisiae_masked_rRNA.fasta(12.4MB)│││├──S_uvarum.fasta││││└──input/atac-seq/ref_gen/S_uvarum.fasta(11.6MB)│││├──Saccharomyces_cerevisiae.R64-1-1.106.gtf││││└──input/atac-seq/ref_gen/Saccharomyces_cerevisiae.R64-1-1.106.gtf(9.6MB)│││├──Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa││││└──input/atac-seq/ref_gen/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa(12.4MB)│││├──Sbay.ultrascaf││││└──input/atac-seq/ref_gen/Sbay.ultrascaf(11.5MB)│││├──Sbay.unplaced││││└──input/atac-seq/ref_gen/Sbay.unplaced(118.3kB)│││├──hybrid.amb││││└──input/atac-seq/ref_gen/hybrid.amb(5.9kB)│││├──hybrid.ann││││└──input/atac-seq/ref_gen/hybrid.ann(7.3kB)│││├──hybrid.bwt││││└──input/atac-seq/ref_gen/hybrid.bwt(23.8MB)│││├──hybrid.fasta││││└──input/atac-seq/ref_gen/hybrid.fasta(24.0MB)│││├──hybrid.pac││││└──input/atac-seq/ref_gen/hybrid.pac(5.9MB)│││├──hybrid.sa││││└──input/atac-seq/ref_gen/hybrid.sa(11.9MB)│││└──mask_rRNA.bed│││└──input/atac-seq/ref_gen/mask_rRNA.bed(36Bytes)││└──rscript││├──diffbind_qc.R│││└──input/atac-seq/rscript/diffbind_qc.R(2.5kB)││└──occupancy_and_diff_accessibility.R││└──input/atac-seq/rscript/occupancy_and_diff_accessibility.R(2.4kB)│├──rna-seq││├──SRR1278968_1.fastq.gz│││└──input/rna-seq/SRR1278968_1.fastq.gz(1.0GB)││├──SRR1278968_2.fastq.gz│││└──input/rna-seq/SRR1278968_2.fastq.gz(1.1GB)││├──SRR1278969_1.fastq.gz│││└──input/rna-seq/SRR1278969_1.fastq.gz(1.0GB)││├──SRR1278969_2.fastq.gz│││└──input/rna-seq/SRR1278969_2.fastq.gz(1.1GB)││├──SRR1278970_1.fastq.gz│││└──input/rna-seq/SRR1278970_1.fastq.gz(1.0GB)││├──SRR1278970_2.fastq.gz│││└──input/rna-seq/SRR1278970_2.fastq.gz(1.1GB)││├──SRR1278971_1.fastq.gz│││└──input/rna-seq/SRR1278971_1.fastq.gz(966.6MB)││├──SRR1278971_2.fastq.gz│││└──input/rna-seq/SRR1278971_2.fastq.gz(961.4MB)││├──SRR1278972_1.fastq.gz│││└──input/rna-seq/SRR1278972_1.fastq.gz(1.0GB)││├──SRR1278972_2.fastq.gz│││└──input/rna-seq/SRR1278972_2.fastq.gz(1.0GB)││├──SRR1278973_1.fastq.gz│││└──input/rna-seq/SRR1278973_1.fastq.gz(982.2MB)││├──SRR1278973_2.fastq.gz│││└──input/rna-seq/SRR1278973_2.fastq.gz(983.3MB)││├──ref_gen│││├──C_parapsilosis_CDC317_current_chromosomes.fasta││││└──input/rna-seq/ref_gen/C_parapsilosis_CDC317_current_chromosomes.fasta(13.2MB)│││└──C_parapsilosis_CDC317_current_features.gff│││└──input/rna-seq/ref_gen/C_parapsilosis_CDC317_current_features.gff(5.8MB)││└──rscript││├──DE.R│││└──input/rna-seq/rscript/DE.R(2.3kB)││└──GO.R││└──input/rna-seq/rscript/GO.R(1.9kB)│└──variants-calling│├──SRR15498471_1.fastq.gz││└──input/variants-calling/SRR15498471_1.fastq.gz(1.4GB)│├──SRR15498471_2.fastq.gz││└──input/variants-calling/SRR15498471_2.fastq.gz(1.5GB)│└──ref_gen│├──C_glabrata_CBS138_current_chromosomes.fasta││└──input/variants-calling/ref_gen/C_glabrata_CBS138_current_chromosomes.fasta(13.0MB)│└──C_glabrata_CBS138_current_features.gff│└──input/variants-calling/ref_gen/C_glabrata_CBS138_current_features.gff(5.3MB)├──output│├──││└──output/(0Bytes)│├──atac-seq││└──││└──output/atac-seq/(0Bytes)│├──rna-seq││└──││└──output/rna-seq/(0Bytes)│└──variants-calling│└──│└──output/variants-calling/(0Bytes)└──working└──└──working/(0Bytes)Start using the tools available on TinyBioworkbench.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 sessionworkbench.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 :notebook-with-decorative-cover: to discover more on what Tinybio can doATAC-Seq Colab NotebookVariants Calling Colab NotebookRNA-Seq Colab NotebookSee a full list of supported tools by using our APIcurl-X'GET'\'https://api.tinybio.cloud/available-tools'\-H'accept: application/json'Distribute package to PIP# bump version in setup.pypythonsetup.pysdist
twineuploaddist/tiny-cli-{version}.tar.gz