@jbrowse/img 1.7.11 → 2.0.0
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/README.md +5 -17
- package/package.json +7 -7
package/README.md
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@@ -29,8 +29,6 @@ guide](DEVELOPER.md) for details
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## Example usages
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This will show some example usages
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### Use with local files
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We can call this script on local files, and it doesn't require a web browser,
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@@ -56,7 +54,7 @@ If `--out` is not specified it writes to out.svg
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Supply a file with the png extension to `--out`, uses rsvg-convert so you will
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need to install rsvg-convert to your system e.g. with `sudo apt install librsvg2-bin`
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```
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```bash
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jb2export --fasta yourfile.fa --bam yourfile.bam --loc chr1:1,000,000-1,001,000 --out file.png
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```
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Supply a file with the pdf extension to `--out`, uses rsvg-convert so you will
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need to install rsvg-convert to your system e.g. with `sudo apt install librsvg2-bin`
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```
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```bash
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jb2export --fasta yourfile.fa --bam yourfile.bam --loc chr1:1,000,000-1,001,000 --out file.pdf
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```
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@@ -76,8 +74,7 @@ This example shows using remote files, e.g. with human hg19 and several tracks
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Note the use of --aliases, which smoothes over refname differences e.g. fasta
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contains 1 for chr1, and bigbed contains chr1, gff contains NC_000001.10
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```
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```bash
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jb2export --fasta https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz \
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--aliases https://jbrowse.org/genomes/hg19/hg19_aliases.txt \
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--bigbed https://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/clinvar/clinvarMain.bb \
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@@ -158,7 +155,7 @@ If you use jbrowse-web, you can select File->Export session which produces a
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session.json file, and then use the --session parameter. Make sure to specify
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the assembly also, it currently does not infer the assembly from the session
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```
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```bash
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jb2export --config data/skbr3/config.json \
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--session session.json \
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--assembly hg19
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```bash
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jb2export --config data/volvox/config.json \
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--assembly volvox
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--assembly volvox \
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--configtracks volvox_sv \
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--loc ctgA:1-50,000
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```
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## Troubleshooting
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### I see the message 'useLayoutEffect does nothing on the server'
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This is a harmless warning, we are working on fixing it though
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### I don't get any outputted svg and no message
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The error reporting from the app is not very good at the moment so often has
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peerDependencies that may produce some warnings. It should work even despite
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making warnings, but you can use yarn to install or use legacy peer
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dependencies if you want to avoid install time warningsvg
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### The program keeps running after saying it completed?
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We are looking into this still. The file should have been generated though, and
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the program will complete
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package/package.json
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{
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"name": "@jbrowse/img",
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"version": "
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"version": "2.0.0",
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"main": "index.js",
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"author": "JBrowse Team",
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"license": "Apache-2.0",
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},
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"dependencies": {
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"@babel/runtime": "^7.17.9",
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"@jbrowse/plugin-linear-genome-view": "^
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"@jbrowse/react-linear-genome-view": "^
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"@jbrowse/plugin-linear-genome-view": "^2.0.0",
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"@jbrowse/react-linear-genome-view": "^2.0.0",
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"abortcontroller-polyfill": "^1.7.3",
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"canvas": "^2.9.1",
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"jsdom": "^19.0.0",
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"mobx": "^
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"mobx": "^6.6.0",
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"node-fetch": "^2.6.7",
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"react": "^17.0.
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"react-dom": "^17.0.
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"react": "^17.0.0",
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"react-dom": "^17.0.0",
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"tmp": "^0.2.1",
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"yargs": "^17.3.0"
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},
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"publishConfig": {
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"access": "public"
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},
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"gitHead": "
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"gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
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}
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