I'm getting disconnected from the server due to either OOM or too many spawned processes
microsoft/vscode-remote-release#10804 suggests that it may be telemetry?
Disabled all telemetry
Also seeing javascript 'node' processes as the culprit
Disabling telemetry didn't seem to matter. I've started using salloc to get an allocation and connecting straight to that node.
Emily got error:
could not establish connection to 'node': the remote host oes not meet the pre-requisites for running the VS Code server.
Solution: install older version of vscode :-| due to OS being too old
Starting with VS Code release 1.99 (March 2025), the prebuilt servers distributed by VS Code are only compatible with Linux distributions that are based on glibc 2.28 or later. These include for example, Debian 10, RHEL 8, or Ubuntu 20.04.
To get files to open instead of edit when double clicked: Options > Preferences > Panels > Double-Click > Operation to perform on double-click: Open
Find the item number, which is at the end of the download link
Put that into this: wget -O my_file.qs "https://ndownloader.figshare.com/files/item_number_here"
For flex data (SI-TS-**) use I7 normal and I5 reverse compliment
source ~/virtualEnvs/dnanexus/bin/activate dx login # login to server, choose which project to attach to dx build # build app from the json and associated file(s) deactivate
Examples in random_scripts/DNA_nexus
To use, either upload to project or copy from another project.
Click on app in folder on dna nexus site, select settings. When looking for files, make sure you select "Current folder and subfolders" or whatever so you can see your files.
source dnanexus/bin/activate
dx login
dx ls OS_stratification_2025_05_19/BAM/*RNA-Seq.bam
| perl -pe 's/ .+//' \
misc/RNAseq_bam_files.txt
dx describe --json --multi OS_stratification_2025_05_19/BAM/*RNA-Seq.bam.bai \
misc/RNAseq_file_metadata.json
dx download works well too, but had issues where md5sums were missing from the file metadata and the file was empty.
Ended up using dx make_download_url ${file_id} and then wget -c in a loop in 26_stratification_data project
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