Philip Badzuh (Inactive) added a comment - 29/Sep/21 10:00 AM The current testing progress is listed below. Stopping now to report what seems to be a recurring issue. hg38 and hg19 genomes tested: http://127.0.0.1:8000/rest_api/?hubUrl=https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/20200227123210/hub.txt&fileName=/ “This feature is not reachable” error in IGB. File reachable via browser. e.g. https://ftp.ncbi.nih.gov/snp/population_frequency/TrackHub/20200227123210/hg38/ALFA_EUR.bb http://127.0.0.1:8000/rest_api/?hubUrl=http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/current_release/homo_sapiens/hub/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://krishna.gs.washington.edu/download/CADD/bigWig/CADD-browserTracks/hub.txt&fileName=/ “This feature is not reachable” error in IGB. File reachable via browser. http://127.0.0.1:8000/rest_api/?hubUrl=http://www.bcgsc.ca/downloads/edcc/data/CEMT/hub/bcgsc_datahub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://s3.us-east-2.amazonaws.com/brainepigenome/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://raw.githubusercontent.com/Kraus-Lab/publichubs/master/breast_cancer_lncrna_pmid_26236012/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://raw.githubusercontent.com/Iuliana-Ionita-Laza/Colocalization_tracks/master/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://cotneylab.cam.uchc.edu/~jcotney/CRANIOFACIAL_HUB/Craniofacial_Data_Hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://cotneylab.cam.uchc.edu/~jcotney/HEART_HUB/heart_hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://openslice.fenyolab.org/tracks/CPTAC/cptac/v1/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://lisanwanglab.org/DASHR/tracks/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://dashr2.lisanwanglab.org/tracks/DASHR2_hub.txt&fileName=/ “This feature is not reachable” error in IGB. File reachable via browser. http://127.0.0.1:8000/rest_api/?hubUrl=http://dbrip.org/dbRIPHub/hub.txt&fileName=/ Doesn’t show as data source for hg19 http://127.0.0.1:8000/rest_api/?hubUrl=https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/dbvarhub/hub.txt&fileName=/ “This feature is not reachable” error in IGB. File reachable via browser. For both hg38 and hg19 http://127.0.0.1:8000/rest_api/?hubUrl=http://smithlab.usc.edu/trackdata/methylation/hub.txt&fileName=/ “This feature is not reachable” error in IGB. File reachable via browser. For both hg38 and hg19 http://127.0.0.1:8000/rest_api/?hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://api.wenglab.org/screen_v13/hubs/dna20/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://api.wenglab.org/screen_v13/hubs/rna22/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://ftp.ensembl.org/pub/papers/regulation/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://epd.epfl.ch/ucsc/epdHub/epdHub.txt&fileName=/ Trust following certificate? Warning/confirmation “This feature is not reachable” error in IGB. File reachable via browser. For both hg38 and hg19 http://127.0.0.1:8000/rest_api/?hubUrl=https://raw.githubusercontent.com/AndyMSSMLab/UCSC_exp_meth_VNTR/main/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://www.facebase.org/trackhub/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://fantom.gsc.riken.jp/5/datahub/hub.txt&fileName=/ java.lang.RuntimeException: Error reading BBFile header for: http://fantom.gsc.riken.jp/5/datahub/hg19/enhancers/Human_FANTOM-NET_enhancers.bb at org.broad.igv.bbfile.BBFileReader.<init>(BBFileReader.java:147) http://127.0.0.1:8000/rest_api/?hubUrl=http://fantom.gsc.riken.jp/5/suppl/Ohmiya_et_al_2014/data/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://genecards.weizmann.ac.il/geneloc/gh_hub/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://ngs.sanger.ac.uk/production/grit/track_hub/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtexAnalysis/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://www.imperial.ac.uk/medicine/beta-cell-genome-regulation-laboratory/data/HILNCs/HILNCs.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://orio.niehs.nih.gov/ucscview/nguyen/p53BAER/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://bx.psu.edu/~yuzhang/Roadmap_ideas/ideas_hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://s3.amazonaws.com/DLPFC_n36/humanDLPFC/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=https://www.lncipedia.org/trackhub/hub.txt&fileName=/ http://127.0.0.1:8000/rest_api/?hubUrl=http://epigenomesportal.ca/hub/hub.txt&fileName=/

Philip Badzuh (Inactive) added a comment - 29/Sep/21 10:00 AM - edited Observed IGB usability issues: Prolonged startup and genome loading times Loading data sources is blocking. Make asynchronous Cache data source metadata files Removing data sources causes IGB to hang Sometimes temporarily Sometimes entirely due to: Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: unable to create new native thread Rearranging data source order doesn’t behave as expected Sometimes it isn’t the selected data source that is moved when the arrow buttons are used Not free to move custom data sources below some defaults Loraine note: Rearrange data source order is a known bug. No need to re-test in the cloned issue.

Philip Badzuh (Inactive) added a comment - 01/Oct/21 10:47 AM I forgot to push the changes I added to improve testing and fix a minor issue with the annots.xml endpoint. Please see them here .

Ann Loraine added a comment - 04/Oct/21 9:21 AM Please submit PR. attn: Philip Badzuh

Philip Badzuh (Inactive) added a comment - 04/Oct/21 10:18 AM Please see PR here .

Ann Loraine added a comment - 06/Oct/21 2:57 AM PR merged and new code is deployed to translate.bioviz.org.