Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Documentation problem on cellranger.rst: rsync downloads don't work. #5

Open
alanhoyle opened this issue Aug 14, 2024 · 0 comments
Open

Comments

@alanhoyle
Copy link

alanhoyle commented Aug 14, 2024

docs/cellranger.rst reads in part:

The example below use the pbmc3k cellranger output files from the 10x website.
First, download the files with the command::
rsync -Lavzp genome-test.gi.ucsc.edu::cells/datasets/pbmc3kCellranger/ ./pbmc3kCellranger/ --progress

When I try running the rsync on our linux cluster, it just hangs indefinitely and times out:

$ rsync -Lavzp genome-test.gi.ucsc.edu::cells/datasets/pbmc3kCellranger/ ./pbmc3kCellranger/ --progress
rsync: [Receiver] failed to connect to genome-test.gi.ucsc.edu (128.114.198.32): Connection timed out (110)
rsync: [Receiver] failed to connect to genome-test.gi.ucsc.edu (2607:f5f0:136:1::26): Network is unreachable (101)
rsync error: error in socket IO (code 10) at clientserver.c(138) [Receiver=3.2.3]

When I try running it on my mac workstation, I get a different error:

> rsync -Lavzp genome-test.gi.ucsc.edu::cells/datasets/pbmc3kCellranger/ ./pbmc3kCellranger/ --progress
@ERROR: Unknown module 'cells'
rsync error: error starting client-server protocol (code 5) at /AppleInternal/Library/BuildRoots/4ff29661-3588-11ef-9513-e2437461156c/Library/Caches/com.apple.xbs/Sources/rsync/rsync/main.c(1402) [receiver=2.6.9]

I suspect this same issue would also affect the instructions in docs/scanpy.rst and docs/seurat.rst

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant