[med-svn] [Git][med-team/aevol][master] Use the working script to debug

[Saira Hussain]

Saira Hussain pushed to branch master at Debian Med / aevol


Commits:
ee794a13 by Saira Hussain at 2019-07-24T07:44:12Z
Use the working script to debug

- - - - -


1 changed file:

- debian/tests/run-unit-tests


Changes:

=====================================
debian/tests/run-unit-tests
=====================================
@@ -19,12 +19,116 @@ gunzip -r *
 # Just for debugging
 set -x
 
-# Test 1
+# Run simulation
 cd wild_type
 aevol_create
-aevol_run -n 50 -p -1
+aevol_run -n 100 -p -1
 
-# Test 2
+# Test setup
+outdirsA="line01 line02 line03 line04 line05"
+outdirsB="line06 line07 line08 line09 line10"
+outdirsC="line11 line12 line13 line14 line15"
+for mydir in $outdirsA $outdirsB $outdirsC
+do
+  aevol_propagate -o ../$mydir
+done
 
+cd ..
+
+# For each experiment, create a file with the parameters to change
+echo "# New environment
+ENV_GAUSSIAN  0.5   0.2   0.05
+ENV_GAUSSIAN  0.5   0.4   0.05
+ENV_GAUSSIAN  0.5   0.8   0.05
+ENV_VARIATION none
+# New rearrangement rates
+DUPLICATION_RATE    1e-4
+DELETION_RATE       1e-4
+TRANSLOCATION_RATE  1e-4
+INVERSION_RATE      1e-4" > newparam-groupA.in
+
+echo "# New environment
+ENV_GAUSSIAN  0.5   0.2   0.05
+ENV_GAUSSIAN  0.5   0.4   0.05
+ENV_GAUSSIAN  0.5   0.8   0.05
+ENV_VARIATION none
+# New rearrangement rates
+DUPLICATION_RATE    1e-6
+DELETION_RATE       1e-6
+TRANSLOCATION_RATE  1e-6
+INVERSION_RATE      1e-6" > newparam-groupB.in
+
+echo "# New environment
+ENV_GAUSSIAN  0.5   0.2   0.05
+ENV_GAUSSIAN  0.5   0.4   0.05
+ENV_GAUSSIAN  0.5   0.8   0.05
+ENV_VARIATION none" > newparam-groupC.in
+
+
+# Apply these modifications
+#
+for mydir in $outdirsA
+do
+   cd $mydir
+   aevol_modify -f ../newparam-groupA.in
+   cd ..
+done
+
+for mydir in $outdirsB
+do
+  cd $mydir
+  aevol_modify -f ../newparam-groupB.in
+  cd ..
+done
+
+for mydir in $outdirsC
+do
+  cd $mydir
+  aevol_modify -f ../newparam-groupC.in
+  cd ..
+done
+
+# Run the simulations
+#
+for mydir in $outdirsA $outdirsB $outdirsC
+do
+  cd $mydir
+  aevol_run -e 200 -p -1
+  cd ..
+done
+
+# aevol_misc_create_eps 
+for mydir in $outdirsA $outdirsB $outdirsC
+do
+  cd $mydir
+  aevol_misc_create_eps &
+  cd ..
+done
+
+
+# aevol_misc_robustness 
+for mydir in $outdirsA $outdirsB $outdirsC
+do
+   cd $mydir
+   aevol_misc_robustness &
+   cd ..
+done
+
+
+# aevol_misc_lineage 
+for mydir in $outdirsA $outdirsB $outdirsC
+do
+   cd $mydir
+   aevol_misc_lineage
+   cd ..
+done
+
+
+# aevol_misc_ancstats 
+for mydir in $outdirsA $outdirsB $outdirsC
+do
+   cd $mydir
+   aevol_misc_ancestor_stats lineage-*.ae -M &
+   cd ..
+done
 
-# Test 3



View it on GitLab: https://salsa.debian.org/med-team/aevol/commit/ee794a137ac5c4c48255d5b3a18eec53c9a395f3

-- 
View it on GitLab: https://salsa.debian.org/med-team/aevol/commit/ee794a137ac5c4c48255d5b3a18eec53c9a395f3
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