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Merge pull request #4 from morinlab/vsouza_fix_hub
Fix track hubs in hubs/ashm_hubs/
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -6,46 +6,46 @@ email [email protected] | |
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| genome hg19 | ||
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| track gamblr_ashm_regions | ||
| shortLabel gamblr_ashm regions | ||
| longLabel Regions where mutations were taken to hub gamblr_ashm | ||
| track regions | ||
| shortLabel regions | ||
| longLabel Regions of interest from where mutations were retrieved | ||
| visibility squish | ||
| priority 1 | ||
| type bigBed | ||
| bigDataUrl https://github.com/morinlab/LLMPP/raw/main/hubs/ashm_hubs/grch37/regions.bb | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/vsouza_fix_hub/hubs/ashm_hubs/grch37/regions.bb?raw=true | ||
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| track gamblr_ashm_genome_BL | ||
| shortLabel gamblr_ashm genome_BL | ||
| longLabel gamblr_ashm genome_BL | ||
| track genome_BL | ||
| shortLabel genome_BL | ||
| longLabel genome_BL | ||
| visibility squish | ||
| priority 2 | ||
| type bigBed | ||
| type bigBed 9 | ||
| itemRgb on | ||
| bigDataUrl https://github.com/morinlab/LLMPP/raw/main/hubs/ashm_hubs/grch37/genome_BL.bb | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/vsouza_fix_hub/hubs/ashm_hubs/grch37/genome_BL.bb?raw=true | ||
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| track gamblr_ashm_genome_DLBCL | ||
| shortLabel gamblr_ashm genome_DLBCL | ||
| longLabel gamblr_ashm genome_DLBCL | ||
| track genome_DLBCL | ||
| shortLabel genome_DLBCL | ||
| longLabel genome_DLBCL | ||
| visibility squish | ||
| priority 3 | ||
| type bigBed | ||
| type bigBed 9 | ||
| itemRgb on | ||
| bigDataUrl https://github.com/morinlab/LLMPP/raw/main/hubs/ashm_hubs/grch37/genome_DLBCL.bb | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/vsouza_fix_hub/hubs/ashm_hubs/grch37/genome_DLBCL.bb?raw=true | ||
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| track gamblr_ashm_genome_FL | ||
| shortLabel gamblr_ashm genome_FL | ||
| longLabel gamblr_ashm genome_FL | ||
| track genome_FL | ||
| shortLabel genome_FL | ||
| longLabel genome_FL | ||
| visibility squish | ||
| priority 4 | ||
| type bigBed | ||
| type bigBed 9 | ||
| itemRgb on | ||
| bigDataUrl https://github.com/morinlab/LLMPP/raw/main/hubs/ashm_hubs/grch37/genome_FL.bb | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/vsouza_fix_hub/hubs/ashm_hubs/grch37/genome_FL.bb?raw=true | ||
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| track gamblr_ashm_capture_DLBCL | ||
| shortLabel gamblr_ashm capture_DLBCL | ||
| longLabel gamblr_ashm capture_DLBCL | ||
| track capture_DLBCL | ||
| shortLabel capture_DLBCL | ||
| longLabel capture_DLBCL | ||
| visibility squish | ||
| priority 5 | ||
| type bigBed | ||
| type bigBed 9 | ||
| itemRgb on | ||
| bigDataUrl https://github.com/morinlab/LLMPP/raw/main/hubs/ashm_hubs/grch37/capture_DLBCL.bb | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/vsouza_fix_hub/hubs/ashm_hubs/grch37/capture_DLBCL.bb?raw=true | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -6,46 +6,46 @@ email [email protected] | |
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| genome hg38 | ||
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||
| track gamblr_ashm_regions | ||
| shortLabel gamblr_ashm regions | ||
| longLabel Regions where mutations were taken to hub gamblr_ashm | ||
| track regions | ||
| shortLabel regions | ||
| longLabel Regions of interest from where mutations were retrieved | ||
| visibility squish | ||
| priority 1 | ||
| type bigBed | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/main/hubs/ashm_hubs/hg38/regions.bb?raw=true | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/vsouza_fix_hub/hubs/ashm_hubs/hg38/regions.bb?raw=true | ||
|
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||
| track gamblr_ashm_genome_BL | ||
| shortLabel gamblr_ashm genome_BL | ||
| longLabel gamblr_ashm genome_BL | ||
| track genome_BL | ||
| shortLabel genome_BL | ||
| longLabel genome_BL | ||
| visibility squish | ||
| priority 2 | ||
| type bigBed | ||
| type bigBed 9 | ||
| itemRgb on | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/main/hubs/ashm_hubs/hg38/genome_BL.bb?raw=true | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/vsouza_fix_hub/hubs/ashm_hubs/hg38/genome_BL.bb?raw=true | ||
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||
| track gamblr_ashm_genome_DLBCL | ||
| shortLabel gamblr_ashm genome_DLBCL | ||
| longLabel gamblr_ashm genome_DLBCL | ||
| track genome_DLBCL | ||
| shortLabel genome_DLBCL | ||
| longLabel genome_DLBCL | ||
| visibility squish | ||
| priority 3 | ||
| type bigBed | ||
| type bigBed 9 | ||
| itemRgb on | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/main/hubs/ashm_hubs/hg38/genome_DLBCL.bb?raw=true | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/vsouza_fix_hub/hubs/ashm_hubs/hg38/genome_DLBCL.bb?raw=true | ||
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||
| track gamblr_ashm_genome_FL | ||
| shortLabel gamblr_ashm genome_FL | ||
| longLabel gamblr_ashm genome_FL | ||
| track genome_FL | ||
| shortLabel genome_FL | ||
| longLabel genome_FL | ||
| visibility squish | ||
| priority 4 | ||
| type bigBed | ||
| type bigBed 9 | ||
| itemRgb on | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/main/hubs/ashm_hubs/hg38/genome_FL.bb?raw=true | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/vsouza_fix_hub/hubs/ashm_hubs/hg38/genome_FL.bb?raw=true | ||
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| track gamblr_ashm_capture_DLBCL | ||
| shortLabel gamblr_ashm capture_DLBCL | ||
| longLabel gamblr_ashm capture_DLBCL | ||
| track capture_DLBCL | ||
| shortLabel capture_DLBCL | ||
| longLabel capture_DLBCL | ||
| visibility squish | ||
| priority 5 | ||
| type bigBed | ||
| type bigBed 9 | ||
| itemRgb on | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/main/hubs/ashm_hubs/hg38/capture_DLBCL.bb?raw=true | ||
| bigDataUrl https://github.com/morinlab/LLMPP/blob/vsouza_fix_hub/hubs/ashm_hubs/hg38/capture_DLBCL.bb?raw=true | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -11,31 +11,31 @@ my_meta = get_gambl_metadata(seq_type_filter = c("genome", "capture")) %>% | |
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| # create hub for grch37 | ||
| build_browser_hub( | ||
| regions_bed = GAMBLR.data::grch37_ashm_regions, | ||
| these_samples_metadata = my_meta, | ||
| these_seq_types = c("genome", "capture"), | ||
| projection = "grch37", | ||
| local_web_host_dir = "~/repos/LLMPP", | ||
| hub_dir = "hubs/ashm_hubs", | ||
| as_bigbed = TRUE, | ||
| splitColumnName = "pathology", | ||
| hub_name = "gamblr_ashm", | ||
| shortLabel = "gamblr ashm", | ||
| longLabel = "GAMBLR public aSHM mutations from grch37 projection", | ||
| email = "[email protected]" | ||
| contact_email = "[email protected]" | ||
| ) | ||
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| # create hub for hg38 | ||
| build_browser_hub( | ||
| regions_bed = GAMBLR.data::hg38_ashm_regions, | ||
| these_samples_metadata = my_meta, | ||
| these_seq_types = c("genome", "capture"), | ||
| projection = "hg38", | ||
| local_web_host_dir = "~/repos/LLMPP", | ||
| hub_dir = "hubs/ashm_hubs", | ||
| as_bigbed = TRUE, | ||
| splitColumnName = "pathology", | ||
| hub_name = "gamblr_ashm", | ||
| shortLabel = "gamblr ashm", | ||
| longLabel = "GAMBLR public aSHM mutations from hg38 projection", | ||
| email = "[email protected]" | ||
| contact_email = "[email protected]" | ||
| ) | ||
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