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.

Sign up for GitHub

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

Jump to bottom

docs: do not activate python env #461

Merged
merged 1 commit into from
May 31, 2024
Merged

docs: do not activate python env #461

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
19 changes: 8 additions & 11 deletions docs/run_on_restricted_system_env.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,11 +15,8 @@ Fetch the pipeline and install requirements
TAG_OR_BRANCH="vX.Y.X"

# Clone selected version
git clone --branch ${VERSION} https://github.com/genomic-medicine-sweden/Twist_Solid.git
git clone --branch ${TAG_OR_BRANCH} https://github.com/genomic-medicine-sweden/Twist_Solid.git
cd Twist_Solid
# Python 3.8 or newer
python3 -m venv venv && source venv/bin/activate
pip install -r requirements.txt
```

## Environment
Expand Down Expand Up @@ -50,12 +47,12 @@ hydra-genetics prepare-environment create-singularity-files -c config/config.yam

```bash
# NextSeq
hydra-genetics --debug references download -o design_and_ref_files -v config/references/design_files.hg19.yaml -v config/references/nextseq.hg19.pon.yaml -v config/references/references.hg19.yaml
hydra-genetics --debug references download -o design_and_ref_files -v config/references/design_files.hg19.yaml -v config/references/nextseq.hg19.pon.yaml -v config/references/references.hg19.yaml

#NovaSeq, not all files are prepare for novaseq
hydra-genetics references download -o design_and_ref_files -v config/references/design_files.hg19.yaml -v config/references/novaseq.hg19.pon.yaml -v config/references/references.hg19.yaml
#NovaSeq, not all files are prepare for novaseq
hydra-genetics references download -o design_and_ref_files -v config/references/design_files.hg19.yaml -v config/references/novaseq.hg19.pon.yaml -v config/references/references.hg19.yaml

# Compress data
# Compress data
tar -czvf design_and_ref_files.tar.gz design_and_ref_files
```

Expand All @@ -66,7 +63,7 @@ tar -czvf design_and_ref_files.tar.gz design_and_ref_files
The following file/folders have been created and need to be moved to your server:

1. file: design_and_ref_files.tar.gz
2. file Twist_Solid_{TAG_OR_BRANCH}.tar.gz
2. file: Twist_Solid_{TAG_OR_BRANCH}.tar.gz
3. folder: singularity_cache

---
Expand All @@ -81,7 +78,7 @@ The following file/folders have been created and need to be moved to your server
# Extract tar.
TAG_OR_BRANCH="vX.Y.X"
tar -xvf Twist_Solid_${TAG_OR_BRANCH}.tar.gz
cd Twist_Solid_{TAG_OR_BRANCH}
cd Twist_Solid_${TAG_OR_BRANCH}
mkdir venv && tar xvf env.tar.gz -C venv/
source venv/bin/activate

Expand Down Expand Up @@ -142,7 +139,7 @@ Copy a profile and modify it to match your system, ex```Twist_Solid_${TAG_OR_BRA
```yaml
# Found at Twist_Solid_{TAG_OR_BRANCH}/snakemake-wrappers, use absolute_path with 'git+file:/'
wrapper-prefix="PATH_TO_WRAPPERS"
# ex: wrapper-prefix="git+file://proj/sens2022566/nobackup/patriksm/Twist_Solid_add-{TAG_OR_BRANCH}/snakemake-wrappers/"
# ex: wrapper-prefix: "git+file://proj/sens2022566/nobackup/patriksm/Twist_Solid_add-{TAG_OR_BRANCH}/snakemake-wrappers/"

# Update account info, change ADD_YOUR_ACCOUNT to your bianca project id
drmaa: " -A ADD_YOUR_ACCOUNT -N 1-1 -t {resources.time} -n {resources.threads} --mem={resources.mem_mb} --mem-per-cpu={resources.mem_per_cpu} --mem-per-cpu={resources.mem_per_cpu} --partition={resources.partition} -J {rule} -e slurm_out/{rule}_%j.err -o slurm_out/{rule}_%j.out"
Expand Down
Loading