Closed bheimbu closed 1 year ago
Hello Bastian, if you're in office some time next week, I could come by and have a look at what's going on. I'm free on Monday, Wednesday and Thursday morning, or Tuesday early afternoon. At first, I also had trouble with the HPC, also with the conda installation. But there is the option of installing from source, I can show you how to do that - there are some additional peculiarities on the cluster (outdated files etc.), but I've found workarounds for the problems. Let me know if you'd like me to have a look. Cheers, Clara
Hi,
Monday morning sounds good. Does 10:30 am work for you?
Bastian
Sure! I'll ring at the door then.
Hi,
can we make Tuesday, I'm not in office on Monday as I've just realized.
Cheers Bastian
No problem. Is Tuesday at 2 pm okay?
Sry,
I‘ve forgotten to reply. Tuesday at 1 pm is fine.
See u then,
Bastian
Sent from my iPhone
On 18. Nov 2022, at 08:26, Clara Köhne @.***> wrote:
No problem. Is Tuesday at 1 pm okay?
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Hi guys,
I'm trying to install Patchwork on our GWDG HPC at the University of Göttingen. Have you accomplished to do so?
I have tried everything but failed. I tried to install from source but Julia always gives me something like this:
(@patchwork) pkg> status --outdated -m Status /home/uni08/bheimbu/.conda/envs/patchwork/share/julia/environments/patchwork/Manifest.toml
⌅ [28b8d3ca] GR v0.69.5 [<v0.70.1], (<v0.70.0): Plots
⌅ [d2c73de3] GR_jll v0.69.1+0 (<v0.70.0+1): GR
⌅ [e9f186c6] Libffi_jll v3.2.2+1 (<v3.4.4+0): Glib_jll, HarfBuzz_jll, Wayland_jll
⌅ [214eeab7] fzf_jll v0.29.0+0 (<v0.30.0+0): JLFzf
Meaning that some Packages are outdated, however manually updating them fails also because dependencies are changing, breaking everything.
I have created my conda environment with following command:
conda create -n patchwork -c bioconda -c conda-forge julia=1.8.2 diamond
and thenjulia --project=. -e "import Pkg; Pkg.instantiate()"
andjulia --project=. src/Patchwork.jl --help
.Any help is highly appreciated,
Bastian
ps: I'm sitting at Untere Karspüle 2, same building as you on the lower floor.