-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
chore: Merge pull request #3 from brickmanlab/docs/reorg
docs: more stuff
- Loading branch information
Showing
22 changed files
with
207 additions
and
240 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,52 @@ | ||
# First time on danserver | ||
|
||
For starting on the server make sure to read: | ||
|
||
- [DanServer manual](https://sgn102.pages.ku.dk/a-not-long-tour-of-dangpu/) | ||
- [Genomics Platform wiki](https://sundgenomics.github.io) | ||
- **platforms**: [JupyterHub](http://dangpu01fl:8989) and [RStudio](http://dangpu01fl:8787) | ||
|
||
## First time on server checklist | ||
|
||
1. Login to danhead: `ssh [email protected]` | ||
2. Run `nano ~/.bash_profile` | ||
|
||
```text | ||
if [ -f ~/.bashrc ]; then | ||
. ~/.bashrc | ||
fi | ||
``` | ||
|
||
3. Run `nano ~/.bashrc` | ||
|
||
```text | ||
# .bashrc | ||
# Source global definitions | ||
if [ -f /etc/bashrc ]; then | ||
. /etc/bashrc | ||
fi | ||
# User specific environment | ||
if ! [[ "$PATH" =~ "$HOME/.local/bin:$HOME/bin:" ]] | ||
then | ||
PATH="$HOME/.local/bin:$HOME/bin:$PATH" | ||
fi | ||
export PATH | ||
# Uncomment the following line if you don't like systemctl's auto-paging feature: | ||
# export SYSTEMD_PAGER= | ||
# User specific aliases and functions | ||
### Source DanGPU definitions | ||
if [ -f /maps/projects/dan1/apps/etc/bashrc ]; then | ||
. /maps/projects/dan1/apps/etc/bashrc | ||
fi | ||
### Source Brickman definitions | ||
if [ -f /maps/projects/dan1/data/Brickman/config/brickman.bashrc ]; then | ||
. /maps/projects/dan1/data/Brickman/config/brickman.bashrc | ||
fi | ||
``` | ||
|
||
4. Logout and login again, you should have see now `Brickman` folder |
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,31 @@ | ||
# Running pipelines | ||
|
||
By default, we run [nf-core](https://nf-co.re) pipelines. To run a pipeline, read | ||
the official [documentation with an example](https://nf-co.re/configs/ku_sund_danhead). | ||
|
||
## Monitoring runs with Nextflow Tower | ||
|
||
This is a guide on how to use [Nextflow Tower](https://help.tower.nf/23.1/) to | ||
monitor nf-core pipeline runs. | ||
|
||
We have created an API token for our GitHub account (brickmanlab) and restricted | ||
it to run only pipelines, nothing else. The `TOWER_WORKSPACE_ID` and `TOWER_ACCESS_TOKEN` | ||
are stored in `Brickman/config/brickman.bashrc`. | ||
|
||
To do more advance stuff, you have to create your own [personal access token](https://tower.nf/tokens). | ||
|
||
### Tower CLI installation | ||
|
||
The tower cli[^1] is required to be installed only once to connect the server as | ||
a computing resource. Afterward, it's not required any more[^2]. | ||
|
||
``` bash | ||
# Download the latest version of Tower CLI: | ||
wget https://github.com/seqeralabs/tower-cli/releases/download/v0.7.3/tw-0.7.3-linux-x86_64 | ||
|
||
# Make the file executable and move to directory accessible by $PATH variable: | ||
mkdir ~/.local/bin && mv tw-* tw && chmod +x ~/.local/bin/tw | ||
``` | ||
|
||
[^1]: [Tower CLI configuration](https://github.com/seqeralabs/tower-cli/#2-configuration) | ||
[^2]: [Tower Agent](https://help.tower.nf/22.3/agent/) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,73 @@ | ||
# Conda & modules | ||
|
||
## Conda | ||
|
||
If you work with `conda` you can use `mamba` instead, which is **faster** tool | ||
to install packages. | ||
|
||
We created shared `conda` environments to simplify your life. | ||
|
||
- To list all available envs: `conda env list` | ||
- To activate env: `source activate brickman` | ||
|
||
### Creating own shared environment | ||
|
||
Here is an example how we created shared environment called `brickman`. | ||
|
||
```bash | ||
module load miniconda/latest | ||
|
||
conda create --prefix /maps/projects/dan1/data/Brickman/conda/envs/brickman python=3.10 | ||
source activate brickman | ||
pip install cruft cookiecutter | ||
|
||
chmod -R 755 /maps/projects/dan1/data/Brickman/conda/envs/brickman | ||
``` | ||
|
||
To install shared `conda` environment for the lab, follow the steps below. | ||
|
||
1. Create a configuration file which contains the list of packages you want | ||
to use. Use prefix `brickman-<NGS>.yml` | ||
2. Populate the configuration file | ||
3. Create the conda environment | ||
|
||
```bash | ||
mamba env create -p /projects/dan1/data/Brickman/conda/envs/brickman-<NGS>.yml -f brickman-<NGS>.yml | ||
``` | ||
|
||
### Example conda environment | ||
|
||
Configuration for `brickman-chipseq` environment. | ||
|
||
```yaml | ||
name: brickman-chipseq | ||
channels: | ||
- conda-forge | ||
- bioconda | ||
- anaconda | ||
- defaults | ||
dependencies: | ||
- bioconda::bedtools==2.31.0 | ||
- bioconda::deeptools==2.31.0 | ||
- bioconda::homer==4.11 | ||
- bioconda::intervene==0.6.4 | ||
- bioconda::macs2==2.2.9.1 | ||
- bioconda::pygenometracks==3.8 | ||
- bioconda::seacr==1.3 | ||
- bioconda::samtools==1.17 | ||
prefix: /projects/dan1/data/Brickman/conda/envs/brickman-chipseq | ||
``` | ||
To install the environment, run | ||
```bash | ||
mamba env create -p /projects/dan1/data/Brickman/conda/envs/brickman-chipseq -f brickman-chipseq.yml | ||
``` | ||
|
||
## Modules | ||
|
||
```bash | ||
module avail | ||
|
||
module load miniconda/latest | ||
``` |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
File renamed without changes.
This file was deleted.
Oops, something went wrong.
This file was deleted.
Oops, something went wrong.
This file was deleted.
Oops, something went wrong.
Oops, something went wrong.