Mercurial > repos > fubar > jbrowse2dev
diff jbrowse2/jbrowse2.xml @ 7:234cf4490901 draft
Uploaded
author | fubar |
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date | Fri, 05 Jan 2024 04:31:35 +0000 (12 months ago) |
parents | 88b9b105c09b |
children | 6a41f87b5d7f |
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--- a/jbrowse2/jbrowse2.xml Fri Jan 05 01:58:02 2024 +0000 +++ b/jbrowse2/jbrowse2.xml Fri Jan 05 04:31:35 2024 +0000 @@ -21,16 +21,11 @@ python '$__tool_directory__/jbrowse2.py' --jbrowse \${JBROWSE_SOURCE_DIR} ---standalone '$standalone' --outdir '$output.files_path' '$trackxml' && -#if str($standalone) != "data": - cp '$output.files_path/index.html' '$output' -#else: - cp '$dummyIndex' '$output' -#end if +cp '$output.files_path/index.html' '$output' ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. #if str($uglyTestingHack) == "enabled": @@ -212,14 +207,6 @@ </when> </conditional> - <param name="standalone" label="Include all reference and track data in the JBrowse2 object" type="select" - help="Default is efficient but will not work offline. Including reference sequences, tracks and indexes will allow standalone viewing, at the cost of copying and moving all data" > - <option value="complete">Complete: Choose ONLY if need to view offline, or if history cannot be published. WARNING: produces bloated downloads storing redundant copies of all data! - </option> - <option value="minimal" selected="true">Sufficient: Uses URLs for Galaxy data. Requires internet access and a published history to download, share and view remotely. - </option> - </param> - <repeat name="track_groups" title="Track Group"> <param label="Track Category" name="category" @@ -230,12 +217,12 @@ <repeat name="data_tracks" title="Annotation Track"> <conditional name="data_format" label="Track Options"> <param type="select" label="Track Type" name="data_format_select"> - <option value="blast">Blast XML</option> - <option value="gene_calls">GFF/GFF3/BED Features</option> - <option value="hic">HiC data (convert .cool with hicexplorer)</option> - <option value="pileup">BAM Pileups</option> - <option value="vcf">VCF SNPs</option> - <option value="wiggle">BigWig XY</option> + <option value="blast">Blast XML track - converted to GFF with actual gaps between hits</option> + <option value="gene_calls" selected="true">GFF/GFF3/BED feature tracks</option> + <option value="hic">HiC binary data. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option> + <option value="pileup">BAM Pileup track</option> + <option value="vcf">VCF SNP annotation track</option> + <option value="wiggle">BigWig XY track</option> </param> <when value="hic"> <expand macro="input_conditional" label="HiC Track Data" format="hic" help="Cool files must be converted first with hicexplorer" /> @@ -316,13 +303,12 @@ <param type="hidden" name="uglyTestingHack" value="" /> </inputs> <outputs> - <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.element_identifier - $standalone"/> + <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.element_identifier"/> </outputs> <tests> <test> <param name="reference_genome|genome_type_select" value="history"/> <param name="reference_genome|genome" value="merlin.fa"/> - <param name="standalone" value="minimal" /> <param name="uglyTestingHack" value="enabled" /> <output name="output"> <assert_contents> @@ -337,7 +323,6 @@ <test> <param name="reference_genome|genome_type_select" value="history"/> <param name="reference_genome|genome" value="merlin.fa"/> - <param name="standalone" value="minimal" /> <repeat name="track_groups"> <param name="category" value="Default" /> <repeat name="data_tracks"> @@ -364,7 +349,6 @@ <param name="genome_type_select" value="history"/> <param name="genome" value="merlin.fa"/> </conditional> - <param name="standalone" value="minimal" /> <repeat name="track_groups"> <param name="category" value="Auto Coloured" /> <repeat name="data_tracks"> @@ -388,7 +372,6 @@ <test> <param name="reference_genome|genome_type_select" value="history"/> <param name="reference_genome|genome" value="merlin.fa"/> - <param name="standalone" value="minimal" /> <param name="uglyTestingHack" value="enabled" /> <output name="output"> <assert_contents> @@ -410,6 +393,19 @@ and detailed track styling is not yet implemented. Send code. JBrowse1 development has now ceased in favour of JBrowse2. +Use and local viewing +===================== + +A JBrowse2 history item can be opened by viewing it (the "eye" icon). +They can also be downloaded as archives ("floppy disk" icon) to share and for local viewing. +One extra step is required before they can be viewed. A local python web server must be started using a script included in each archive. +Unpack the archive (tar -xvzf [filename].tgz) and the first level directory will contain a file named "servejb2.py" + +Assuming you have python3 installed, running + +*python3 servjb2.py* + +will serve the unarchived JBrowse2 configuration, so it can be browsed by pointing a web browser to localhost:8080 Overview -------- @@ -436,9 +432,7 @@ The first option you encounter is the **Fasta Sequence(s)**. This option now accepts multiple fasta files, allowing you to build JBrowse instances that contain data for multiple genomes or chrosomomes -(generally known as "landmark features" in gff3 terminology.) Up to 30 -will be shown from the dropdown selector within JBrowse, this is a known -issue. +(generally known as "landmark features" in gff3 terminology.) **Track Groups** represent a set of tracks in a single category. These can be used to let your users understand relationships between large @@ -449,25 +443,14 @@ Annotation Tracks ----------------- -Within Track Groups, you have one or more **Annotation Tracks**. Each -Annotation Track is a groups of datasets which have similar styling. -This allows you to rapidly build up JBrowse instances without having to -configure tracks individually. A massive improvement over previous -versions. For example, if you have five different GFF3 files from -various gene callers that you wish to display, you can take advantage of -this feature to style all of them similarly. - There are a few different types of tracks supported, each with their own set of options: GFF3/BED ~~~~~~~~ -These are your standard feature tracks. They usually highlight genes, -mRNAs and other features of interest along a genomic region. The -underlying tool and this help documentation focus primarily on GFF3 -data, and have not been tested extensively with other formats. Automatic -min/max detection will fail under BED datasets. +These are standard feature tracks. They usually highlight genes, +mRNAs and other features of interest along a genomic region. BAM Pileups ~~~~~~~~~~~ @@ -475,11 +458,6 @@ We support BAM files and can automatically generate SNP tracks based on that bam data. -.. image:: bam.png - -This is *strongly discouraged* for high coverage density datasets. -Unfortunately there are no other configuration options exposed for bam -files. BlastXML ~~~~~~~~ @@ -512,12 +490,7 @@ .. image:: bigwig.png -**XYPlot** -BigWig tracks can be displayed as a "density" plot which is a continuous -line which varies in colour, or as an "XYplot." XYplots are preferable -for users to visually identify specific features in a bigwig track, -however density tracks are more visually compact. VCFs/SNPs ~~~~~~~~~