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fethalen / Patchwork

Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data
GNU General Public License v3.0
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Cannot install Patchwork on HPC #49

Closed bheimbu closed 1 year ago

bheimbu commented 1 year ago

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 status --outdated -m Status /home/uni08/bheimbu/.conda/envs/patchwork/share/julia/environments/patchwork/Manifest.toml ⌅ [28b8d3ca] GR v0.69.5 [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Meaning that some Packages are outdated, however manually updating them fails also because dependencies are changing, breaking everything.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 then julia --project=. -e "import Pkg; Pkg.instantiate()" and julia --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.

ClaraKoehne commented 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of installing from source, I can show you how to do that - there are some additional peculiarities on the cluster (outdated files etc.), but I've found workarounds for the problems.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

bheimbu commented 1 year ago

Hi,

Monday morning sounds good. Does 10:30 am work for you?

Bastian

ClaraKoehne commented 1 year ago

Sure! I'll ring at the door then.

bheimbu commented 1 year ago

Hi,

can we make Tuesday, I'm not in office on Monday as I've just realized.

Cheers Bastian

ClaraKoehne commented 1 year ago

No problem. Is Tuesday at 2 pm okay?

bheimbu commented 1 year ago

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?

— Reply to this email directly, view it on GitHubhttps://github.com/fethalen/Patchwork/issues/49#issuecomment-1319641085, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AF67TI6QK3LXODXO5MFO4HLWI4VTLANCNFSM6AAAAAASDNLGSM. You are receiving this because you authored the thread.Message ID: @.***>