update/eciYali/4.1.2/2022 07 03 21 44 20

.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
+version = 4.1.2
 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

ecHumanGEM/scripts/changeMedia_batch.m

@@ -116,7 +116,7 @@
     unusedMets = [];
     for i=1:length(mediaComps)
         %Get metabolite indx
-        metIndx = getIndexes(model,strcat(mediaComps{i},'[s]'),'metcomps');
+        metIndx = getIndexes(model,strcat(mediaComps{i},'[e]'),'metcomps');
         %Get rxns for metabolite
         metRxns = find(model.S(metIndx,:));
         %Get the uptake reaction for the metabolite

eciYali/model/eciYali_exchangeFluxes.txt

@@ -0,0 +1,14 @@
+EXCHANGE FLUXES:
+y001634	(acetate exchange):	2.3438
+y001672	(carbon dioxide exchange):	28.9916
+y001761	(ethanol exchange):	25.3257
+y002100	(water exchange):	32.4473
+y002111	(growth):	0.27611
+y001654_REV	(ammonium exchange (reversible)):	2.4692
+y001714_REV	(D-glucose exchange (reversible)):	15.8046
+y001832_REV	(H+ exchange (reversible)):	19.3115
+y001947_REV	(myo-inositol exchange (reversible)):	0.00099398
+y001992_REV	(oxygen exchange (reversible)):	1.7295
+y002005_REV	(phosphate exchange (reversible)):	0.13137
+y002060_REV	(sulphate exchange (reversible)):	0.053837
+prot_pool_exchange	(prot_pool_exchange):	0.13459

eciYali/model/eciYali_topUsedEnzymes.txt

@@ -1,11 +1,11 @@
 prots_Min_glucose,Usages_Min_glucose
-Q6C968,0.120623
-Q6C0G7,0.088982
-Q6CDD3,0.07734
-Q6C2D9,0.047742
-Q6CGM4,0.047179
-Q6C8C2,0.036163
-Q6C9P6,0.033763
-Q6C4K5,0.027544
-Q6C627,0.027194
-Q6CAF8,0.023699
+Q6C968,0.120625
+Q6C0G7,0.088984
+Q6CDD3,0.077342
+Q6C2D9,0.047743
+Q6CGM4,0.04718
+Q6C8C2,0.036164
+Q6C9P6,0.033764
+Q6C4K5,0.027545
+Q6C627,0.027195
+Q6CAF8,0.0237

tools.py

@@ -14,7 +14,7 @@
 DURL = 'download_url'
 IDIR = 'install_dir'
 SCRIPTSDIR = 'scripts'
-PIPELINE_BASE_BRANCH = 'master'
+PIPELINE_BASE_BRANCH = 'main'
 
 logging.basicConfig(level=logging.DEBUG)
 l = logging.getLogger(__name__)
@@ -67,8 +67,8 @@ def mat_model(self, gem):
     def pr_target(self):
         return self.config['BASE']['pull_request_target']
 
-    def git_clone(self, section, branch='master'):
-        cmd = sp.check_output(['git', 'clone', self.config[section][URL], '--depth', '1', '--branch', branch, self.install_dir(section)])
+    def git_clone(self, section, branch=PIPELINE_BASE_BRANCH):
+        cmd = sp.check_output(['hub', 'clone', self.config[section][URL], '--depth', '1', '--branch', branch, self.install_dir(section)])
         l.info(cmd.decode('utf-8'))
 
     def download(self, gem):
@@ -99,15 +99,16 @@ def git_add_and_pr(self, gem, matlab_output):
             cmd = sp.check_output(['git', 'commit', '-m', 'chore: update {} based on {}'.format(gem, self.version(gem))])
             l.info(cmd.decode('utf-8'))
             l.critical('Will push and create PR')
+            cmd = sp.check_output(['git', 'push'])
+            l.info(cmd.decode('utf-8'))
             # Create PR and also push
             pr_filename = "/tmp/githubpr"
             with open(pr_filename, "w") as f:
                 f.write("update {} based on {}\n\n".format(gem, self.version(gem)))
                 f.write("```matlab\n")
                 f.write(matlab_output)
                 f.write("\n```\n")
-            my_env = environ.copy()
-            cmd = sp.check_output(['hub', 'pull-request', '-F', pr_filename, '-b', self.pr_target(), '-p'], env=my_env)
+            cmd = sp.check_output(['gh', 'pr', 'create', '--body-file', pr_filename, '--base', self.pr_target(), '--fill'])
             l.info(cmd.decode('utf-8'))
         except sp.CalledProcessError:
             l.critical('While upgrading {} to {} no changes were detected'.format(gem, self.version(gem)))
@@ -137,7 +138,7 @@ def check_dependencies(self):
                     l.info('{} is still {}'.format(tool, tool_version))
         # Check COBRA, RAVEN, GECKO versions
         self.cleanup('GECKO')
-        self.git_clone('GECKO')
+        self.git_clone('GECKO', self.config['GECKO']['branch'])
         for tool in ['COBRA', 'RAVEN', 'GECKO']:
             tool_version = self.git_tag(tool)
             if tool_version != self.version(tool):