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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,14 +1,148 @@ | ||
| image: nfcore/gitpod:latest | ||
| image: gitpod/workspace-full-vnc | ||
| # Update 7th September to reflect code base changes | ||
| ports: | ||
| - name: JBrowseWeb | ||
| description: The JBrowse Webserver port | ||
| port: 3000 | ||
| onOpen: open-browser | ||
| visibility: public | ||
|
|
||
| - name: HiGlass | ||
| description: The HiGlass port | ||
| port: 8989 | ||
| onOpen: open-browser | ||
| 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: | | ||
| cd /workspace/treeval-curation/ | ||
| wget -qO- https://get.nextflow.io | bash | ||
| chmod +x nextflow | ||
| nextflow self-update | ||
| - name: Install JBrowse2 | ||
| # https://jbrowse.org/jb2/download/#jbrowse-cli-tools | ||
| command: | | ||
| cd /workspace/treeval-curation/ | ||
| npm install -g @jbrowse/cli | ||
| jbrowse create jbrowse2 | ||
| cd jbrowse2/ | ||
| npx serve . -l 3000 | ||
| - name: Install TreeVal Pipeline | ||
| # https://github.com/sanger-tol/treeval | ||
| init: | | ||
| cd /workspace/treeval-curation/ | ||
| git clone -b pre-tag 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 | ||
| - name: Install HiGlass | ||
| # https://docs.higlass.io/tutorial.html | ||
| init: | | ||
| cd /workspace/treeval-curation/ | ||
| pip install higlass-manage | ||
| higlass-manage start | ||
| - name: Alias Nextflow | ||
| init: | | ||
| cd /workspace/treeval-curation/ | ||
| echo "alias nextflow_cmd='/workspace/treeval-curation/nextflow'" >> ~/.bashrc | ||
| source ~/.bashrc | ||
| - name: Download busco for nematode | ||
| init: | | ||
| cd /workspace/treeval-curation/ | ||
| curl https://dp24.cog.sanger.ac.uk/Busco.tar.gz | tar xzf - | ||
| - name: Download Nematode Test data and make synteny | ||
| init: | | ||
| cd /workspace/treeval-curation/ | ||
| curl https://dp24.cog.sanger.ac.uk/Nematode.tar.gz | tar xzf - | ||
| mkdir -p /workspace/treeval-curation/synteny/nematode/ | ||
| cp /workspace/treeval-curation/Oscheius_DF5033/genomic_data/Oscheius_DF5033.fa /workspace/treeval-curation/synteny/nematode/SuperNematode.fa | ||
| - name: Download Lepidoptera data | ||
| init: | | ||
| cd /workspace/treeval-curation/ | ||
| curl https://dp24.cog.sanger.ac.uk/ilTorViri5.tar.gz | tar xzf - | ||
| - name: Download Genomic Alignment data | ||
| init: | | ||
| cd /workspace/treeval-curation/ | ||
| curl https://dp24.cog.sanger.ac.uk/AlignmentData.tar.gz | tar xzf - | ||
| - name: Open Tutorial Page | ||
| 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 | ||
| # - cssho.vscode-svgviewer # SVG viewer | ||
| - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code | ||
| - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed | ||
| - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files | ||
| - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar | ||
| - mechatroner.rainbow-csv # Highlight columns in csv files in different colors | ||
| # - nextflow.nextflow # Nextflow syntax highlighting | ||
| - nextflow.nextflow # Nextflow syntax highlighting | ||
| - oderwat.indent-rainbow # Highlight indentation level | ||
| - streetsidesoftware.code-spell-checker # Spelling checker for source code |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| assembly: | ||
| level: scaffold | ||
| sample_id: grTriPseu1 | ||
| latin_name: to_provide_taxonomic_rank | ||
| classT: fungi | ||
| asmVersion: 1 | ||
| dbVersion: "1" | ||
| gevalType: DTOL | ||
| reference_file: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/assembly/draft/grTriPseu1.fa | ||
| assem_reads: | ||
| pacbio: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/genomic_data/pacbio/ | ||
| hic: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/genomic_data/hic-arima/ | ||
| supplementary: path | ||
| alignment: | ||
| data_dir: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/gene_alignment_data/ | ||
| common_name: "" # For future implementation (adding bee, wasp, ant etc) | ||
| geneset: "LaetiporusSulphureus.gfLaeSulp1" | ||
| #Path should end up looking like "{data_dir}{classT}/{common_name}/csv_data/{geneset}-data.csv" | ||
| self_comp: | ||
| motif_len: 0 | ||
| mummer_chunk: 10 | ||
| synteny: | ||
| synteny_genome_path: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/synteny/ | ||
| outdir: "NEEDS TESTING" | ||
| intron: | ||
| size: "50k" | ||
| telomere: | ||
| teloseq: TTAGGG | ||
| busco: | ||
| lineages_path: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/busco/subset/ | ||
| lineage: fungi_odb10 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| assembly: | ||
| level: scaffold | ||
| sample_id: grTriPseu1 | ||
| latin_name: to_provide_taxonomic_rank | ||
| classT: fungi | ||
| asmVersion: 1 | ||
| dbVersion: "1" | ||
| gevalType: DTOL | ||
| reference_file: /home/runner/work/treeval/treeval/TreeValTinyData/assembly/draft/grTriPseu1.fa | ||
| assem_reads: | ||
| pacbio: /home/runner/work/treeval/treeval/TreeValTinyData/genomic_data/pacbio/ | ||
| hic: /home/runner/work/treeval/treeval/TreeValTinyData/genomic_data/hic-arima/ | ||
| supplementary: path | ||
| alignment: | ||
| data_dir: /home/runner/work/treeval/treeval/TreeValTinyData/gene_alignment_data/ | ||
| common_name: "" # For future implementation (adding bee, wasp, ant etc) | ||
| geneset: "LaetiporusSulphureus.gfLaeSulp1" | ||
| #Path should end up looking like "{data_dir}{classT}/{common_name}/csv_data/{geneset}-data.csv" | ||
| self_comp: | ||
| motif_len: 0 | ||
| mummer_chunk: 10 | ||
| synteny: | ||
| synteny_genome_path: /home/runner/work/treeval/treeval/TreeValTinyData/synteny/ | ||
| outdir: "NEEDS TESTING" | ||
| intron: | ||
| size: "50k" | ||
| telomere: | ||
| teloseq: TTAGGG | ||
| busco: | ||
| lineages_path: /home/runner/work/treeval/treeval/TreeValTinyData/busco/subset/ | ||
| lineage: fungi_odb10 |
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