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 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
