From 18154123f34e8091e3889c0e31eca825215aefaf Mon Sep 17 00:00:00 2001
From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Date: Mon, 12 Aug 2024 15:41:13 +0100
Subject: [PATCH 1/6] Update .gitpod.yml

Remove Singularity,
Update versions of TreeVal and CurationPretext
---
 .gitpod.yml | 40 ++--------------------------------------
 1 file changed, 2 insertions(+), 38 deletions(-)

diff --git a/.gitpod.yml b/.gitpod.yml
index d7259d7..4b03d5c 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -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: |
@@ -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
@@ -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

From f48b484dcdc3ef3c2eea448c011c28b318864e9c Mon Sep 17 00:00:00 2001
From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Date: Mon, 12 Aug 2024 15:57:50 +0100
Subject: [PATCH 2/6] Update .gitpod.yml

Updates to use nf-core
---
 .gitpod.yml | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/.gitpod.yml b/.gitpod.yml
index 4b03d5c..ca1b8cf 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -23,7 +23,15 @@ tasks:
 
       chmod +x nextflow
 
-      nextflow self-update
+      bash nextflow self-update
+
+  - name: Install NF-Core
+    init: |
+      pip install nf-core
+
+  - name: Download Containers
+    init: |
+      nf-core download sanger-tol/treeval --revision 1.1.1 --compress none -d --force --outdir sanger-treeval --container-cache-utilisation amend --container-system docker
 
   - name: Install JBrowse2
   # https://jbrowse.org/jb2/download/#jbrowse-cli-tools
@@ -38,13 +46,6 @@ tasks:
 
       npx serve . -l 3000
 
-  - name: Install TreeVal Pipeline
-  # https://github.com/sanger-tol/treeval
-    init: |
-      cd /workspace/treeval-curation/
-        
-      git clone -b 1.1.1 https://github.com/sanger-tol/treeval.git
-
   - name: Install Curtation Pretext
   # https://github.com/sanger-tol/curationpretext
     init: |

From 06c042c110e4be50efcb1364399988f622fecae3 Mon Sep 17 00:00:00 2001
From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Date: Mon, 12 Aug 2024 16:00:44 +0100
Subject: [PATCH 3/6] Update .gitpod.yml

---
 .gitpod.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.gitpod.yml b/.gitpod.yml
index ca1b8cf..8841c4b 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -29,8 +29,6 @@ tasks:
     init: |
       pip install nf-core
 
-  - name: Download Containers
-    init: |
       nf-core download sanger-tol/treeval --revision 1.1.1 --compress none -d --force --outdir sanger-treeval --container-cache-utilisation amend --container-system docker
 
   - name: Install JBrowse2

From 86c8c2c6ffd46353bbbf71eb8a2b33dcc8276a58 Mon Sep 17 00:00:00 2001
From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Date: Mon, 12 Aug 2024 19:24:03 +0100
Subject: [PATCH 4/6] Update .gitpod.yml

---
 .gitpod.yml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.gitpod.yml b/.gitpod.yml
index 8841c4b..d8a69ea 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -25,12 +25,6 @@ tasks:
 
       bash nextflow self-update
 
-  - name: Install NF-Core
-    init: |
-      pip install nf-core
-
-      nf-core download sanger-tol/treeval --revision 1.1.1 --compress none -d --force --outdir sanger-treeval --container-cache-utilisation amend --container-system docker
-
   - name: Install JBrowse2
   # https://jbrowse.org/jb2/download/#jbrowse-cli-tools
     command: |

From e0e244ed3449c65332587104bbf945c8ef3f3d45 Mon Sep 17 00:00:00 2001
From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Date: Mon, 12 Aug 2024 19:24:53 +0100
Subject: [PATCH 5/6] Create BGA-test.yaml

Add a BGA yaml
---
 BGA-test.yaml | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 BGA-test.yaml

diff --git a/BGA-test.yaml b/BGA-test.yaml
new file mode 100644
index 0000000..dd7aa22
--- /dev/null
+++ b/BGA-test.yaml
@@ -0,0 +1,36 @@
+assembly:
+  assem_level: scaffold
+  sample_id: Oscheius_DF5033
+  defined_class: nematode
+  assem_version: 1
+  project_id: DTOL
+reference_file: /workspace/treeval-curation/Oscheius_DF5033/genomic_data/Oscheius_DF5033.fa
+map_order: length
+assem_reads:
+  read_type: hifi
+  read_data: /workspace/treeval-curation/Oscheius_DF5033/pacbio/
+  supplementary_data: path
+hic_data:
+  hic_cram: /workspace/treeval-curation/Oscheius_DF5033/hic-arima2/
+  hic_aligner: minimap2
+alignment:
+  data_dir: /workspace/treeval-curation/gene_alignment_data/
+  geneset: "OscheiusTipulae.ASM1342590v1,CaenorhabditisElegans.WBcel235,Gae_host.Gae"
+  common_name: "not in use"
+self_comp:
+  motif_len: 0
+  mummer_chunk: 10
+intron:
+  size: "50k"
+telomere:
+  teloseq: TTAGGG
+synteny:
+  synteny_path: /workspace/treeval-curation/synteny
+  synteny_genomes: "SuperNematode"
+busco:
+  lineages_path: /workspace/treeval-curation/busco/v5
+  lineage: nematoda_odb10
+kmer_profile:
+  # kmer_length will act as input for kmer_read_cov fastk and as the name of folder in profile_dir
+  kmer_length: 31
+  dir: /workspace/treeval-curation/

From 35b670776370e28b419f1cdcd6e77a7f55a93ff7 Mon Sep 17 00:00:00 2001
From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Date: Mon, 12 Aug 2024 20:55:36 +0100
Subject: [PATCH 6/6] Update .gitpod.yml

---
 .gitpod.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitpod.yml b/.gitpod.yml
index d8a69ea..17231a3 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -38,7 +38,7 @@ tasks:
 
       npx serve . -l 3000
 
-  - name: Install Curtation Pretext
+  - name: Install Curation Pretext
   # https://github.com/sanger-tol/curationpretext
     init: |
       cd /workspace/treeval-curation/