About stencil-galaxy_tools

This repository contains galaxy tools for preprocessing and posting static and interactive plots and tables from Galaxy to Stencil. Preprocessing tools are mainly developed for deseq2, a popular RNA-seq analysis tool. The Post tools are generic and can be used for different static and interactive plots to Stencil Website.

preprocess tools:

RNA-seq pipeline tools:

1- deseq2_to_ma_plot_nivo_json" tool generates MA plot in nivo standard json format.

2- deseq2_to_bar_plot_nivo_json" tool generates Bar plot in nivo standard json format.

3- "deseq2_to_heatmap_plot_nivo_json" generates heatmap of distance between samples based on r-log normalized counts of reads per gene, in nivo standard json format.

4- "deseq2_to_pca_plot_nivo_json" generates a PCA plot from the rlog-normalized counts of read per gene data coming out of deseq2 tool

5- "deseq2_to_table_with_gene_name_nivo_json" gets the output of deseq2 in tabular format and gene annotation file in gf format. Adds a gene_name column to the table based on gene_id, finally convert the results to nivo JSON format.

ChIP-exo pipeline tools:

1- "tagpileup_tabular_to_nivo_json" tool generates Lineplot in nivo standard json format for two groups of sense strand reads and antisense strand reads.

POST tools to Stencil:

1- "post_static_plot_stencil" POSTs static images in png format to Stencil

2- "post_nivo_table_and_plot_stencil" POSTs json files in nivo table or plot format to Stencil. Supported type of plots are ScatterPlot, LinePlot, BarPlot, Heatmap and Table.

Installing Stencil Galaxy tools

Clone the repository in the local_tools folder

cd /mnt/mountpoint/srv/galaxy/local_tools
sudo git clone https://github.com/CEGRcode/stencil-galaxy_tools

Tell galaxy where to look for stencil-galaxy_tools tools by adding the following section to /mnt/mountpoint/srv/galaxy/config/local_tool_conf.xml file if it is not already included.

<section id="STENCIL" name="STENCIL" >
    <tool file="stencil-galaxy_tools/preproc_stencil/deseq2_to_bar_plot_nivo_json.xml" />
    <tool file="stencil-galaxy_tools/preproc_stencil/deseq2_to_heatmap_plot_nivo_json.xml" />
    <tool file="stencil-galaxy_tools/preproc_stencil/deseq2_to_ma_plot_nivo_json.xml" />
    <tool file="stencil-galaxy_tools/preproc_stencil/deseq2_to_pca_plot_nivo_json.xml" />
    <tool file="stencil-galaxy_tools/preproc_stencil/deseq2_to_table_with_gene_name_nivo_json.xml" />
    <tool file="stencil-galaxy_tools/preproc_stencil/tagpileup_tabular_to_nivo_json.xml" />
    <tool file="stencil-galaxy_tools/post_stencil/post_nivo_table_and_plot_json_stencil.xml" />
    <tool file="stencil-galaxy_tools/post_stencil/post_static_plot_stencil.xml" />
  </section>

Restart Galaxy
```
sudo systemctl restart galaxy
```
Solve dependencies for local Galaxy tools that have been just added through Galaxy web interface. Admin -> Manage Dependencies

For more information about Stencil, please check the following paper.

Sun Q, Nematbakhsh A., Kuntala P., Kellogg G, Pugh B. and Lai W., 2022, STENCIL: A web templating engine for visualizing and sharing life science datasets, PLOS Computational Biology 18(2) e1009859