@sjcrh/proteinpaint-server 2.18.1 → 2.19.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/cards/bam.json +1 -1
- package/cards/dnanexusTips.txt +10 -10
- package/cards/exprank.json +1 -1
- package/cards/genomepaint.json +1 -1
- package/cards/index.json +25 -27
- package/cards/junction.json +4 -4
- package/cards/pgv.json +1 -1
- package/cards/singlecell.json +1 -1
- package/cards/study.json +1 -1
- package/cards/svview.txt +5 -5
- package/cards/tklist.json +1 -1
- package/package.json +1 -1
- package/server.js +1 -1
package/cards/bam.json
CHANGED
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@@ -253,7 +253,7 @@
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"buttons": [
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{
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"name": "Download BAM Slicing Script",
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"download": "https://
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+
"download": "https://proteinpaint.stjude.org/ppdemo/scripts/slice_bam4pp.py.gz"
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},
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{
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"name": "BAM track supporting information",
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package/cards/dnanexusTips.txt
CHANGED
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@@ -111,18 +111,18 @@
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Creating the URL from the DNAnexus website is easy but the URL expires in 24 hours. Login to the DNAnexus website and navigate to the appropriate project.
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<ul>
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<li>
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-
Find the file and
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<img style="width: 50vw; margin: 1vw 2vw;" src="https://
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Find the file and hover the mouse on the far right of the screen until three dots appear.
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<img style="width: 50vw; margin: 1vw 2vw;" src="https://proteinpaint.stjude.org/ppdemo/images/dnanexus_3dot_menu.png">
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</li>
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<li>
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Select 'Download' from the menu
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</li>
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<li>
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A popup 'Download Data' window will appear.
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A popup 'Download Data' window will appear. Hover over the file to see the 'Get URL' icon (🔗) on the right. Click on the (🔗) icon.
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</li>
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<li>
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The icon button will change to 'Copy URL'. Click to copy the link.
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<img style="width: 50vw; margin: 1vw 2vw;" src="https://
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<img style="width: 50vw; margin: 1vw 2vw;" src="https://proteinpaint.stjude.org/ppdemo/images/dnanexus_copy_URL.png">
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</li>
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</ul>
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Save the new URL. The next section describes how to create a ProteinPaint track using URL parameters.
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<p style="margin-left: 2vw;">
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Create a track from stringing together URL parameters described in this <a href='https://docs.google.com/document/d/1e0JVdcf1yQDZst3j77Xeoj_hDN72B6XZ1bo_cAd2rss/edit#heading=h.737pcqp1tlnt' target='URL param'>document</a>. <br><br>
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-
Start with "https://proteinpaint.stjude.org/?" and add the URL parameters separated by ampersands. In the example below, parameters for the genome, block, track name, and file URL to launch the genome browser. The final URL <a href="https://proteinpaint.stjude.org/?genome=hg19&block=1&bigwigurl=URL,https://
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<img style="width: 50vw; margin: 1vw 2vw;" src="https://
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Start with "https://proteinpaint.stjude.org/?" and add the URL parameters separated by ampersands. In the example below, parameters for the genome, block, track name, and file URL to launch the genome browser. The final URL <a href="https://proteinpaint.stjude.org/?genome=hg19&block=1&bigwigurl=URL,https://proteinpaint.stjude.org/ppdemo/hg19/bigwig/file.bw">https://proteinpaint.stjude.org/?genome=hg19&block=1&bigwigurl=URL,https://proteinpaint.stjude.org/ppdemo/hg19/bigwig/file.bw</a>, launches this bigwig track.
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<img style="width: 50vw; margin: 1vw 2vw;" src="https://proteinpaint.stjude.org/ppdemo/images/bigwig_url_ex.png">
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</p>
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<br>
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<br>
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<h2 id="fileviewer">ProteinPaint FileViewer</h2>
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<p style="margin-left: 2vw;">The ProteinPaint FileViewer launches VCF, BigWig, JSON BED, Splice Junction, and BAM tracks from the DNAnexus website. Download the ProteinPaint FileViewer from the blue button below.</p>
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<div style="margin:0vw 2vw; display: flex; justify-content: center; padding: 10px;">
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<button type="button" onclick="window.open('https://
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<button type="button" onclick="window.open('https://proteinpaint.stjude.org/ppdemo/fileviewers/ProteinPaint%20(VCF,%20bigWig,%20BEDj,%20junction,%20BAM).gz','_self', 'download')" style="background-color: #d0e3ff; padding: 8px; border-radius: 3px; border: none; display: inline-block;margin: 0px 10px; font-size: 1.1em;">Download ProteinPaint FileViewer</button>
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</div>
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<br>
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</li>
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<li>
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Select which files to visualize in ProteinPaint. Ensure to include index files.
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<img style="width: 50vw; margin: 1vw 2vw;" src="https://
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<img style="width: 50vw; margin: 1vw 2vw;" src="https://proteinpaint.stjude.org/ppdemo/fileviewers/select_files.png">
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</li>
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<li>
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Click Launch Viewer in the bottom right of the window.
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<li>
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The following interface will appear in the browser:
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<img style="width: 20vw; margin: 1vw 4vw; display: block;" src="https://
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<img style="width: 20vw; margin: 1vw 4vw; display: block;" src="https://proteinpaint.stjude.org/ppdemo/fileviewers/interface.png">
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Select the reference genome. Then, enter a genomic position or search for a gene to launch the visualization. ProteinPaint will launch in a new tab, like the example below.<br>
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<img style="width: 50vw; margin: 1vw 1vw;" src="https://
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<img style="width: 50vw; margin: 1vw 1vw;" src="https://proteinpaint.stjude.org/ppdemo/fileviewers/final.png">
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</li>
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</ul>
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</p>
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package/cards/exprank.json
CHANGED
package/cards/genomepaint.json
CHANGED
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"links": [
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{
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"name": "Download Data & Processing Pipeline",
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"download": "https://
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"download": "https://proteinpaint.stjude.org/ppdemo/hg38/GP/GDC.variation.datafile.processing.zip"
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},
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{
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"name": "Data Processing Docs",
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package/cards/index.json
CHANGED
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"name": "GenomePaint",
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"section": "tracks",
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"description": "Explore coding and non-coding variants in cancer",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/gpaint-square.png",
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"sandboxJson": "genomepaint",
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"searchterms": ["GenomePaint"]
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},
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"name": "BigWig",
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"section": "tracks",
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"description": "Quantitative data at genomic positions",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/bigwig-square.png",
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"sandboxJson": "bigwig"
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},
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{
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"name": "JSON BED",
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"section": "tracks",
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"description": "Genomic feature annotation",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/bedj-square.png",
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"sandboxJson": "bedj",
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"searchterms": []
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},
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"name": "Allelic imbalance",
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"section": "tracks",
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"description": "From tumor and germline DNA",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/aicheck-square.png",
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"sandboxJson": "ai",
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"searchterms": ["aicheck", "tumor", "normal", "DNA"]
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},
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"name": "Profile gene value",
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"section": "tracks",
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"description": "Profiling results & gene-level values",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/pgv-square.png",
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"sandboxJson": "pgv",
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"searchterms": ["pgv", "chromHMM", "profiling results", "gene level", "gene expression"]
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},
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"name": "Expression rank",
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"section": "tracks",
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"description": "Against all samples from a cohort",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/exprank-square.png",
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"sandboxJson": "exprank",
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"searchterms": []
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},
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"name": "Hi-C",
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"section": "tracks",
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"description": "Chromatin interaction at a locus",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/hic-square.png",
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"sandboxJson": "hic",
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"searchterms": ["hic", "hicstraw", "chromatin interaction", "conformation"]
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},
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"name": "Lollipop",
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"section": "tracks",
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"description": "Coding mutations and gene fusions",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/lollipop-square.png",
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"sandboxJson": "lollipop",
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"searchterms": []
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},
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"name": "Splice Junction",
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"section": "tracks",
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"description": "Single sample and cohort",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/junction-cohort-square.png",
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"sandboxJson": "junction",
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"searchterms": []
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},
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"name": "Track list & facet table",
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"section": "tracks",
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"description": " ",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/tklist-square.png",
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"sandboxJson": "tklist",
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"searchterms": []
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},
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"name": "Arc Track",
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"section": "tracks",
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"description": "Pairwise chromatin interactions",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/arc-square.png",
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"sandboxJson":"arc",
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"searchterms": []
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},
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"section": "tracks",
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"ribbon": {"text": "beta"},
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"description": "Allele-specific expression analysis",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/ase-square.png",
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"sandboxJson": "ase",
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"searchterms": ["Allele-specific gene expression"]
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},
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"name": "Gene Fusion",
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"section": "tracks",
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"description": " ",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/genefusion-square.png",
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"sandboxJson": "genefusion",
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"searchterms": [""]
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},
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"type": "card",
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"name": "BAM",
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"section": "tracks",
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"ribbon": {"text": "beta"},
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"description": "Sequence reads alignment",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/bam-square.png",
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"sandboxJson": "bam",
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"searchterms": ["BLAT"]
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},
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"section": "tracks",
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"ribbon": {"text": "beta"},
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"description": "Deep sequencing",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/bampile-square.png",
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"sandboxJson": "bampile",
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"searchterms": []
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},
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"type": "card",
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"name": "GDC BAM slicing",
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"section": "tracks",
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"ribbon": {"text": "beta"},
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"disableTopTabs": true,
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"description": "Visualize sequencing reads in NCI GDC",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/bam-square.png",
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"sandboxJson": "gdcbam",
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"searchterms": []
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},
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"name": "Additional Track Features",
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"section": "tracks",
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"description": "ProteinPaint arguments applicable to any track",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/code-square.png",
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"sandboxJson": "tkFeatures",
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},
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"name": "FusionEditor",
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"section": "apps",
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"description": "Review CICERO output",
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"image": "https://proteinpaint.stjude.org/ppdemo/images/fusion-editor-square.png",
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"sandboxJson": "fusioneditor",
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"searchterms": []
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},
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"name": "2DMAF",
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"section": "apps",
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"description": "Somatic mutations from diagnosis & relapse",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/2dmaf-square.png",
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"sandboxJson": "2dmaf",
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"searchterms": ["2dmaf", "clonal evolution", "point mutations"]
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},
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"name": "Load mutations from text files",
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"section": "apps",
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"description": "Mutation heatmap",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/heatmap-square.png",
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"sandboxJson": "study",
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"searchterms": ["heat map"]
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},
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"name": "MA+Volcano plots",
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"section": "apps",
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"description": "Differential gene expression",
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"image": "https://
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"image": "https://proteinpaint.stjude.org/ppdemo/images/mavb-square.png",
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"sandboxJson": "mavb",
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"searchterms": ["differential gene expression", "RNAseq coverage"]
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},
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@@ -247,7 +245,7 @@
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"section": "apps",
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"hidden": true,
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"description": "Mutant allele fraction timeline chart by date",
|
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-
"image": "https://
|
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+
"image": "https://proteinpaint.stjude.org/ppdemo/images/maf-timeline-square.png",
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"sandboxJson": "maf.timeline",
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"searchterms": ["mutant allele fraction", "snv", "snv4"]
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},
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@@ -286,7 +284,7 @@
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"name": "Scatter Plot",
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"section": "apps",
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"description": "2D scatter plot of samples & metadata",
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-
"image": "https://
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+
"image": "https://proteinpaint.stjude.org/ppdemo/images/scatterplot-square.png",
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"ribbon": { "text": "updated", "expireDate": "2023-03-01" },
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"sandboxJson": "scatterplot",
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"searchterms": ["tSNE", "lasso"]
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@@ -296,7 +294,7 @@
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"name": "Single Cell",
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"section": "apps",
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"description": "Single-cell omics viewer",
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-
"image": "https://
|
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+
"image": "https://proteinpaint.stjude.org/ppdemo/images/singlecell-square.png",
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"sandboxJson": "singlecell",
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"searchterms": ["tsne", "gene expression", "multi-gene heatmap", "violin plot", "box plot"]
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},
|
|
@@ -305,7 +303,7 @@
|
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"name": "Data Browser",
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"section": "apps",
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"description": "Browse data from a custom cohort",
|
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-
"image": "https://
|
|
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+
"image": "https://proteinpaint.stjude.org/ppdemo/images/databrowser-square.png",
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"ribbon": {"text":"beta"},
|
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"sandboxJson": "databrowser",
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"searchterms": ["clinical", "dictionary"]
|
package/cards/junction.json
CHANGED
|
@@ -2,7 +2,7 @@
|
|
|
2
2
|
"ppcalls": [
|
|
3
3
|
{
|
|
4
4
|
"label": "A sample splice junction",
|
|
5
|
-
"download":"https://
|
|
5
|
+
"download":"https://proteinpaint.stjude.org/ppdemo/hg19/junction/junctionDemoData.tar.gz",
|
|
6
6
|
"urlparam": "?block=on&genome=hg19&junctionfile=RNA%20splice%20junction,proteinpaint_demo/hg19/junction/file.gz",
|
|
7
7
|
"datapreview": [
|
|
8
8
|
{
|
|
@@ -30,7 +30,7 @@
|
|
|
30
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|
{
|
|
31
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|
"label":"Cohort from an External JSON",
|
|
32
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|
"message": "",
|
|
33
|
-
"download": "https://
|
|
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|
+
"download": "https://proteinpaint.stjude.org/ppdemo/hg19/junction/junctionJsonDemoData.tar.gz",
|
|
34
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|
"urlparam": "?genome=hg19&block=1&mdsjunctionfile=Demo,proteinpaint_demo/hg19/junction/json.gz",
|
|
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35
|
"datapreview": [
|
|
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36
|
{
|
|
@@ -57,7 +57,7 @@
|
|
|
57
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|
},
|
|
58
58
|
{
|
|
59
59
|
"label":"Cohort from a JSON Matrix File",
|
|
60
|
-
"download": "https://
|
|
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|
+
"download": "https://proteinpaint.stjude.org/ppdemo/hg19/junction/junctionMatrixDemoData.tar.gz",
|
|
61
61
|
"urlparam": "?genome=hg19&block=1&junctionmatrix=test,proteinpaint_demo/hg19/junction/matrix.gz",
|
|
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|
"datapreview": [
|
|
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|
{
|
|
@@ -81,7 +81,7 @@
|
|
|
81
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|
"buttons": [
|
|
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|
{
|
|
83
83
|
"name": "Download Matrix Script",
|
|
84
|
-
"download": "https://
|
|
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|
+
"download": "https://proteinpaint.stjude.org/ppdemo/scripts/rnapeg2matrix.py.gz"
|
|
85
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|
}
|
|
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|
],
|
|
87
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|
"testSpec": {
|
package/cards/pgv.json
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
{
|
|
2
2
|
"ppcalls": [
|
|
3
3
|
{
|
|
4
|
-
"download": "https://
|
|
4
|
+
"download": "https://proteinpaint.stjude.org/ppdemo/hg19/pgv/pgvDemoData.tar.gz",
|
|
5
5
|
"datapreview": [
|
|
6
6
|
{
|
|
7
7
|
"file": "proteinpaint_demo/hg19/pgv/sample1.gz",
|
package/cards/singlecell.json
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
{
|
|
2
2
|
"ppcalls": [
|
|
3
3
|
{
|
|
4
|
-
"download": "https://
|
|
4
|
+
"download": "https://proteinpaint.stjude.org/ppdemo/hg19/singlecell/singlecellDemoData.tar.gz",
|
|
5
5
|
"urlparam": "?genome=hg19&singlecell=proteinpaint_demo/hg19/singlecell/singlecell.json",
|
|
6
6
|
"jsonpath": "proteinpaint_demo/hg19/singlecell/singlecell.json",
|
|
7
7
|
"runargs": {
|
package/cards/study.json
CHANGED
|
@@ -11,7 +11,7 @@
|
|
|
11
11
|
},
|
|
12
12
|
{
|
|
13
13
|
"message": "A few tips on how to interact with the study view: <ul><li>Clicking on the gene tab opens the gene table with detailed information about mutation and sample counts.</li><li>Launch the genome browser by clicking on the heatmap gene labels.</li><li>Hover over the heatmap cells to reveal the mutation and sample information</li></ul>",
|
|
14
|
-
"download": "https://
|
|
14
|
+
"download": "https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/heatmapDemoData.tar.gz",
|
|
15
15
|
"jsonpath": "proteinpaint_demo/hg19/heatmap/heatmapDemo.json",
|
|
16
16
|
"runargs":{
|
|
17
17
|
"noheader": true,
|
package/cards/svview.txt
CHANGED
|
@@ -6,9 +6,9 @@
|
|
|
6
6
|
</p>
|
|
7
7
|
<br>
|
|
8
8
|
<div style="margin:0vw 2vw; display: flex; justify-content: center; padding: 10px;">
|
|
9
|
-
<button type="button" onclick="window.open('https://
|
|
9
|
+
<button type="button" onclick="window.open('https://proteinpaint.stjude.org/ppdemo/usecases/svview/svViewPyScript.tar.gz','_self', 'download')" style="background-color: #d0e3ff; padding: 8px; border-radius: 3px; border: none; display: inline-block;margin: 0px 10px; font-size: 1.1em;">Download Script</button>
|
|
10
10
|
|
|
11
|
-
<button type="button" onclick="window.open('https://
|
|
11
|
+
<button type="button" onclick="window.open('https://proteinpaint.stjude.org/ppdemo/usecases/svview/svViewDemoFiles.tar.gz','_self', 'download')" style="background-color: #d0e3ff; padding: 8px; border-radius: 3px; border: none; display: inline-block;margin: 0px 10px; font-size: 1.1em;">Download Example Files</button>
|
|
12
12
|
</div>
|
|
13
13
|
<div margin: 2vw;">
|
|
14
14
|
<h2 style="font-size: 1.2em;">ProteinPaint</h2>
|
|
@@ -43,7 +43,7 @@
|
|
|
43
43
|
|
|
44
44
|
<h2 style="font-size: 1.2em;">Run Script</h2>
|
|
45
45
|
<p style="margin-left: 2vw;font-size: 1em;">
|
|
46
|
-
Download the <a href="https://
|
|
46
|
+
Download the <a href="https://proteinpaint.stjude.org/ppdemo/usecases/svview/svViewPyScript.tar.gz" target="_self" download>SV view script</a>. Run the script from the command line with the following arguments:
|
|
47
47
|
</p>
|
|
48
48
|
<ul style="margin-left: 2vw;">
|
|
49
49
|
<li>
|
|
@@ -90,12 +90,12 @@
|
|
|
90
90
|
<p style="margin-left: 2vw;font-size: 1em;">
|
|
91
91
|
The results table is found in the csv file, named from the <span style="font-family:monospace; font-size:1.25em; opacity: 0.6;"> --out</span> or <span style="font-family:monospace; font-size:1.25em; opacity: 0.6;"> -o</span> argument.
|
|
92
92
|
</p>
|
|
93
|
-
<img style="width: 63vw; margin: 0vw 2vw;" src="https://
|
|
93
|
+
<img style="width: 63vw; margin: 0vw 2vw;" src="https://proteinpaint.stjude.org/ppdemo/usecases/svview/svview_images/output.png">
|
|
94
94
|
|
|
95
95
|
<h2 style="font-size: 1.2em;">SV View Example</h2>
|
|
96
96
|
<p style="margin-left: 2vw;font-size: 1em;">
|
|
97
97
|
Open the results from the csv file. Click on the links to review the SV views for both the left and right breakpoints. Shown below is the URL for the left position from the example data.
|
|
98
98
|
</p>
|
|
99
|
-
<img style="width: 60vw; margin: 0vw 2vw;" src="https://
|
|
99
|
+
<img style="width: 60vw; margin: 0vw 2vw;" src="https://proteinpaint.stjude.org/ppdemo/usecases/svview/svview_images/leftURL.png">
|
|
100
100
|
</div>
|
|
101
101
|
</div>
|
package/cards/tklist.json
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
{
|
|
2
2
|
"ppcalls": [
|
|
3
3
|
{
|
|
4
|
-
"download":"https://
|
|
4
|
+
"download":"https://proteinpaint.stjude.org/ppdemo/hg19/tklist/tklistDemoData.tar.gz",
|
|
5
5
|
"urlparam": "?genome=hg19&block=1&tkjsonfile=proteinpaint_demo/hg19/tklist/tracks.json",
|
|
6
6
|
"jsonpath": "proteinpaint_demo/hg19/tklist/tracks.json",
|
|
7
7
|
"runargs": {
|