Details
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Type:
Task
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Status: In Progress (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Spring 3, Summer 2026
Description
The Quickload Saver App once installed can save out all the currently available data sets in annots.xml Quickload format. (see: https://bitbucket.org/lorainelab/quickload-saver/src/main/ for code)
Even cooler, the user can click-drag file names from Web pages into their IGB and make changes to the track appearance within the interface, such as: changing foreground and background colors, changing the stack height (max_depth), changing track label font size (name_size), whether to show separate tracks for minus and plus, or not (show2tracks), and also change the track label text itself (title).
However, we have noticed that even if a user has changed the track label text, the Quickload Saver fails to save the user-designated value.
For instead, here is XML from when I tried to save a track whose label I had changed to "5k Human Ovarian Tumor Isolated with Chromium Nuclei Isolation Kit" from "5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam," the name of the file saved in 10X Genomics S3 bucket:
<file background="FFFFFF" connected="true" direction_type="NONE" foreground="993300" label_field="" max_depth="294" name="https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-vdj/7.0.0/5k_human_ovarian_tumor_CNIK_5pv2/5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam" name_size="16.0" negative_strand_color="3366FF" positive_strand_color="800080" reference="false" show2tracks="false" title="5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam"/>
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Description |
The Quickload Saver App once installed can save out all the currently available data sets in annots.xml Quickload format.
Even cooler, the user can click-drag file names from Web pages into their IGB and make changes to the track appearance within the interface, such as: changing foreground and background colors, changing the stack height (max_depth), changing track label font size (name_size), whether to show separate tracks for minus and plus, or not (show2tracks), and also change the track label text itself (title). However, we have noticed that even if a user has changed the track label text, the Quickload Saver fails to save the user-designated value. For instead, here is XML from when I tried to save a track whose label I had changed to "5k Human Ovarian Tumor Isolated with Chromium Nuclei Isolation Kit" from "5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam," the name of the file saved in 10X Genomics S3 bucket: {code} <file background="FFFFFF" connected="true" direction_type="NONE" foreground="993300" label_field="" max_depth="294" name="https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-vdj/7.0.0/5k_human_ovarian_tumor_CNIK_5pv2/5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam" name_size="16.0" negative_strand_color="3366FF" positive_strand_color="800080" reference="false" show2tracks="false" title="5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam"/> {code} |
The Quickload Saver App once installed can save out all the currently available data sets in annots.xml Quickload format. (see: https://bitbucket.org/lorainelab/quickload-saver/src/master/ for code)
Even cooler, the user can click-drag file names from Web pages into their IGB and make changes to the track appearance within the interface, such as: changing foreground and background colors, changing the stack height (max_depth), changing track label font size (name_size), whether to show separate tracks for minus and plus, or not (show2tracks), and also change the track label text itself (title). However, we have noticed that even if a user has changed the track label text, the Quickload Saver fails to save the user-designated value. For instead, here is XML from when I tried to save a track whose label I had changed to "5k Human Ovarian Tumor Isolated with Chromium Nuclei Isolation Kit" from "5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam," the name of the file saved in 10X Genomics S3 bucket: {code} <file background="FFFFFF" connected="true" direction_type="NONE" foreground="993300" label_field="" max_depth="294" name="https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-vdj/7.0.0/5k_human_ovarian_tumor_CNIK_5pv2/5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam" name_size="16.0" negative_strand_color="3366FF" positive_strand_color="800080" reference="false" show2tracks="false" title="5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam"/> {code} |
| Description |
The Quickload Saver App once installed can save out all the currently available data sets in annots.xml Quickload format. (see: https://bitbucket.org/lorainelab/quickload-saver/src/master/ for code)
Even cooler, the user can click-drag file names from Web pages into their IGB and make changes to the track appearance within the interface, such as: changing foreground and background colors, changing the stack height (max_depth), changing track label font size (name_size), whether to show separate tracks for minus and plus, or not (show2tracks), and also change the track label text itself (title). However, we have noticed that even if a user has changed the track label text, the Quickload Saver fails to save the user-designated value. For instead, here is XML from when I tried to save a track whose label I had changed to "5k Human Ovarian Tumor Isolated with Chromium Nuclei Isolation Kit" from "5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam," the name of the file saved in 10X Genomics S3 bucket: {code} <file background="FFFFFF" connected="true" direction_type="NONE" foreground="993300" label_field="" max_depth="294" name="https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-vdj/7.0.0/5k_human_ovarian_tumor_CNIK_5pv2/5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam" name_size="16.0" negative_strand_color="3366FF" positive_strand_color="800080" reference="false" show2tracks="false" title="5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam"/> {code} |
The Quickload Saver App once installed can save out all the currently available data sets in annots.xml Quickload format. (see: https://bitbucket.org/lorainelab/quickload-saver/src/main/ for code)
Even cooler, the user can click-drag file names from Web pages into their IGB and make changes to the track appearance within the interface, such as: changing foreground and background colors, changing the stack height (max_depth), changing track label font size (name_size), whether to show separate tracks for minus and plus, or not (show2tracks), and also change the track label text itself (title). However, we have noticed that even if a user has changed the track label text, the Quickload Saver fails to save the user-designated value. For instead, here is XML from when I tried to save a track whose label I had changed to "5k Human Ovarian Tumor Isolated with Chromium Nuclei Isolation Kit" from "5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam," the name of the file saved in 10X Genomics S3 bucket: {code} <file background="FFFFFF" connected="true" direction_type="NONE" foreground="993300" label_field="" max_depth="294" name="https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-vdj/7.0.0/5k_human_ovarian_tumor_CNIK_5pv2/5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam" name_size="16.0" negative_strand_color="3366FF" positive_strand_color="800080" reference="false" show2tracks="false" title="5k_human_ovarian_tumor_CNIK_5pv2_possorted_genome_bam.bam"/> {code} |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 3 [ 235 ] | Spring 3, Summer 2026 [ 235, 236 ] |
| Rank | Ranked higher |
Fixed an error with add local repositories in IGB: see commit
Upgraded Java version in Quickload-saver app. see commit