Skip to content

Commit 24ba757

Browse files
committed
More docs updates
1 parent 1121059 commit 24ba757

1 file changed

Lines changed: 9 additions & 3 deletions

File tree

docs/organisers/denbi-nodesetup.md

Lines changed: 9 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -150,7 +150,10 @@ Install bioinformatics software
150150
done
151151
```
152152

153-
> ⚠️ monitor to look for failures in log! (2025: denovo-assembly.yml -> TO FIX)
153+
> ⚠️ monitor to look for failures in log!
154+
> 2025:
155+
>
156+
> - denovo-assembly.yml -> tried adding binette but causes conflict with concoct, comment out concoct first, then inside environment after construction install with `conda install concoct`. However left as original for now
154157

155158
<!-- IN 2025 - Docker was already installed on the VM by default!
156159
- Install [docker](https://docs.docker.com/engine/install/ubuntu/)
@@ -234,14 +237,17 @@ Install bioinformatics software
234237
echo "export PATH=$PATH:~/bin/metaWRAP/bin" >> ~/.bashrc && source ~/.bashrc
235238
```
236239

237-
- Set up Volume (NOTE: this now may happen automatically on instance generation, however instructions here in case you reboot and have to remount)
240+
- Set up Volume
241+
242+
NOTE: **this now may happen automatically on instance generation**, however instructions here in case you reboot and have to remount)
238243

239244
- Cloud Portal > Virtual Machines > Instances > Volumes > Create and Attach Volume
240245
- Specify e.g. roughly total amount divided by number of nodes
241246
- Attach to the setup VM
242247
- Go back to VM and follow these [instructions](https://cloud.denbi.de/wiki/simple_vm/volumes/#mount-a-volume)
243248

244249
```bash
250+
## THIS WAS AUTOM
245251
lsblk -o NAME,SIZE,MOUNTPOINT,FSTYPE,TYPE | egrep -v "^loop"
246252
## Record NAME column i.d, e.g. `vdd`
247253
sudo mkfs.ext4 /dev/<NAME> ## Don't do if already existing
@@ -259,7 +265,7 @@ Install bioinformatics software
259265

260266
- Inside `/vol/volume` make a directory for each of the sessions, then download the required data.
261267

262-
e.g. to download from the [Zenodo archives](https://zenodo.org/communities/spaam-community/records?q=%22Introduction%20to%20Ancient%20Metagenomics%20Textbook%20%28Edition%202023%29%22&l=list&p=1&s=10&sort=bestmatch) from 2023
268+
e.g. to download from the [Zenodo archives](https://zenodo.org/communities/spaam-community/records?q=%22Introduction%20to%20Ancient%20Metagenomics%20Textbook%20%28Edition%202023%29%22&l=list&p=1&s=10&sort=bestmatch) from 2024
263269

264270
```bash
265271
cd /vol/volume/

0 commit comments

Comments
 (0)