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Update .gitpod.yml
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Remove Singularity,
Update versions of TreeVal and CurationPretext
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DLBPointon authored Aug 12, 2024
1 parent cdca94a commit 1815412
Showing 1 changed file with 2 additions and 38 deletions.
40 changes: 2 additions & 38 deletions .gitpod.yml
Original file line number Diff line number Diff line change
Expand Up @@ -14,31 +14,6 @@ ports:
visibility: public

tasks:
- name: Install Singularity 3.11.4
# https://docs.sylabs.io/guides/3.0/user-guide/installation.html
init: |
cd /workspace/treeval-curation/
sudo apt-get update && sudo apt-get install -y \
build-essential \
libssl-dev \
uuid-dev \
libgpgme11-dev \
squashfs-tools \
libseccomp-dev \
pkg-config
mkdir -p $GOPATH/src/github.com/sylabs && \
cd $GOPATH/src/github.com/sylabs && \
wget https://github.com/sylabs/singularity/releases/download/v3.11.4/singularity-ce-3.11.4.tar.gz && \
tar -xzf singularity-ce-3.11.4.tar.gz && \
cd ./singularity-ce-3.11.4 && \
./mconfig
./mconfig && \
make -C ./builddir && \
sudo make -C ./builddir install
- name: Install Nextflow
# https://www.nextflow.io/docs/latest/getstarted.html
init: |
Expand Down Expand Up @@ -68,14 +43,14 @@ tasks:
init: |
cd /workspace/treeval-curation/
git clone -b pre-tag https://github.com/sanger-tol/treeval.git
git clone -b 1.1.1 https://github.com/sanger-tol/treeval.git
- name: Install Curtation Pretext
# https://github.com/sanger-tol/curationpretext
init: |
cd /workspace/treeval-curation/
git clone -b dev https://github.com/sanger-tol/curationpretext.git
git clone -b 1.0.0 https://github.com/sanger-tol/curationpretext.git
- name: Install HiGlass
# https://docs.higlass.io/tutorial.html
Expand Down Expand Up @@ -126,17 +101,6 @@ tasks:
init: |
gp preview https://bga23.org/treeval-curation/Tutorial/
github:
prebuilds:
# enable for the master/default branch (defaults to true)
master: true
# add a "Review in Gitpod" button as a comment to pull requests (defaults to true)
addComment: true
# add a "Review in Gitpod" button to pull requests (defaults to false)
addBadge: true
# add a label once the prebuild is ready to pull requests (defaults to false)
addLabel: prebuilt-in-gitpod

vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
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