update/ecHumanGEM/v1.12.0/2022 07 03 23 31 31

.github/workflows/automation.yml

@@ -1,6 +1,9 @@
 name: automation
 
 on:
+  push:
+    branches-ignore:
+        - "update/**"
   schedule:
     - cron: '3 2 1 * *'
 
@@ -10,12 +13,12 @@ jobs:
     timeout-minutes: 1200
 
     steps:
-    - name: Clone repository on current branch
-      run: |
-        rm -rf *
-        git clone https://github.com/$GITHUB_REPOSITORY --branch ${GITHUB_REF#refs/heads/} latest-ecModels
+      - name: Clone repository on current branch
+        run: |
+          rm -rf *
+          git clone https://github.com/$GITHUB_REPOSITORY --branch ${GITHUB_REF#refs/heads/} latest-ecModels
 
-    - name: Run the pipeline
-      run: |
-        cd latest-ecModels
-        python3 run.py ${GITHUB_REF#refs/heads/}
+      - name: Run the pipeline
+        run: |
+          cd latest-ecModels
+          python3 run.py ${GITHUB_REF#refs/heads/}

config.ini

@@ -1,6 +1,6 @@
 [BASE]
 url = https://github.com/SysBioChalmers/ecModels
-pull_request_target = master
+pull_request_target = main
 install_dir = /home/m/ecModels-dependencies/
 
 [MATLAB]
@@ -13,7 +13,7 @@ install_dir = cobratoolbox/
 
 [RAVEN]
 url = https://github.com/SysBioChalmers/RAVEN
-version = v2.4.1
+version = v2.6.2
 install_dir = RAVEN/
 
 [libSBML]
@@ -23,8 +23,8 @@ install_dir = libSBML/
 
 [Gurobi]
 url = https://www.gurobi.com/downloads/gurobi-software/
-version = v9.1.1
-install_dir = gurobi/
+version = v9.5.1
+install_dir = gurobi951/
 
 [GECKO]
 url = https://github.com/SysBioChalmers/GECKO
@@ -36,7 +36,7 @@ branch = master
 type = 'gem'
 url = https://github.com/SysBioChalmers/yeast-GEM
 download_url = 
-model_filename = /ModelFiles/mat/yeastGEM.mat
+model_filename = /model/yeast-GEM.mat
 mat_model = .model
 install_dir = yeast-GEM
 version = v8.3.1
@@ -46,17 +46,17 @@ database_tag = sce
 type = 'gem'
 url = https://github.com/SysBioChalmers/Yarrowia_lipolytica_W29-GEM
 download_url = 
-model_filename = /ModelFiles/mat/iYali.mat
+model_filename = /model/iYali.mat
 mat_model = .model
 install_dir = Yali-GEM
 version = v0
 database_tag = yli
 
 [eciSM966]
 type = 'gem'
-url = https://github.com/SysBioChalmers/Kluyveromyces_marxianus-GEM
-download_url = 
-model_filename = /modelFiles/mat/Kluyveromyces_marxianus-GEM.mat
+url = 
+download_url = https://raw.githubusercontent.com/SysBioChalmers/Kluyveromyces_marxianus-GEM/master/modelFiles/mat/Kluyveromyces_marxianus-GEM.mat
+model_filename = /Kluyveromyces_marxianus-GEM.mat
 mat_model = .model
 install_dir = iSM966
 version = v0
@@ -79,6 +79,6 @@ download_url =
 model_filename = /model/Human-GEM.mat
 mat_model = .ihuman
 install_dir = Human-GEM
-version = v0
+version = v1.12.0
 database_tag = hsa