NCBI to Anndata

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy France
• Galaxy Main
• Galaxy Australia
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nGSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nGSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nGSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nGSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nGSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nGSM5353215_PA_AUG_PB_1B_S2_dge.txt"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nGSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nGSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\nGSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["ℹ️ Input Dataset\nGSM5353214_PA_AUG_PB_1A_S1_dge.txt"];
  style 9 stroke:#2c3143,stroke-width:4px;
  10["Import Anndata and loom"];
  0 -->|output| 10;
  11["Import Anndata and loom"];
  1 -->|output| 11;
  12["Import Anndata and loom"];
  2 -->|output| 12;
  13["Import Anndata and loom"];
  3 -->|output| 13;
  14["Import Anndata and loom"];
  4 -->|output| 14;
  15["Import Anndata and loom"];
  5 -->|output| 15;
  16["Import Anndata and loom"];
  6 -->|output| 16;
  17["Import Anndata and loom"];
  7 -->|output| 17;
  18["Import Anndata and loom"];
  8 -->|output| 18;
  19["Import Anndata and loom"];
  9 -->|output| 19;
  20["Manipulate AnnData"];
  10 -->|anndata| 20;
  21["Manipulate AnnData"];
  11 -->|anndata| 21;
  22["Manipulate AnnData"];
  12 -->|anndata| 22;
  23["Manipulate AnnData"];
  13 -->|anndata| 23;
  24["Manipulate AnnData"];
  14 -->|anndata| 24;
  25["Manipulate AnnData"];
  15 -->|anndata| 25;
  26["Manipulate AnnData"];
  16 -->|anndata| 26;
  27["Manipulate AnnData"];
  17 -->|anndata| 27;
  28["Manipulate AnnData"];
  18 -->|anndata| 28;
  29["Manipulate AnnData"];
  19 -->|anndata| 29;
  30["Manipulate AnnData"];
  29 -->|anndata| 30;
  23 -->|anndata| 30;
  24 -->|anndata| 30;
  21 -->|anndata| 30;
  25 -->|anndata| 30;
  22 -->|anndata| 30;
  27 -->|anndata| 30;
  28 -->|anndata| 30;
  26 -->|anndata| 30;
  20 -->|anndata| 30;
  31["Inspect AnnData"];
  30 -->|anndata| 31;
  32["Replace Text"];
  31 -->|obs| 32;
  33["Replace Text"];
  31 -->|obs| 33;
  34["Replace Text"];
  31 -->|obs| 34;
  35["Replace Text"];
  31 -->|obs| 35;
  36["Cut"];
  32 -->|outfile| 36;
  37["Cut"];
  33 -->|outfile| 37;
  38["Cut"];
  34 -->|outfile| 38;
  39["Cut"];
  35 -->|outfile| 39;
  40["Paste"];
  37 -->|out_file1| 40;
  36 -->|out_file1| 40;
  41["Paste"];
  40 -->|out_file1| 41;
  38 -->|out_file1| 41;
  42["Paste"];
  41 -->|out_file1| 42;
  39 -->|out_file1| 42;
  43["Manipulate AnnData"];
  30 -->|anndata| 43;
  42 -->|out_file1| 43;
  44["Scanpy FilterCells"];
  43 -->|anndata| 44;
  45["AnnData Operations"];
  44 -->|output_h5ad| 45;
  98fdc079-8b71-4841-a9aa-a3adda888616["Output\noutput_h5ad"];
  45 --> 98fdc079-8b71-4841-a9aa-a3adda888616;
  style 98fdc079-8b71-4841-a9aa-a3adda888616 stroke:#2c3143,stroke-width:4px;
  46["Inspect AnnData"];
  45 -->|output_h5ad| 46;
  e4df8425-3c1e-439c-abe5-42b705eed1b3["Output\nobs"];
  46 --> e4df8425-3c1e-439c-abe5-42b705eed1b3;
  style e4df8425-3c1e-439c-abe5-42b705eed1b3 stroke:#2c3143,stroke-width:4px;

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Hands-on: Importing a workflow

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• Provide your workflow
  • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
  • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
• Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-ncbi-anndata/workflows/NCBI_to_Anndata.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows