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SENC_terminal_commands.txt
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SENC_terminal_commands.txt
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# lines starting with 'tr' take out formatting issues when using non-unix text editors
# I use notepad to modify the files that do not have 'unix' in their name and then run these lines to get the correct unix format.
## for multiple jobs per node
cd sims.out.130214/
tr '\r' '\n' < SENC_Olympus_Batch_nodes.txt > SENC_Olympus_Batch_nodes_unix.txt
tr '\r' '\n' < SENC_Olympus_Execute_nodes.sh > SENC_Olympus_Execute_nodes_unix.sh
chmod u+x SENC_Olympus_Execute_nodes_unix.sh
./SENC_Olympus_Execute_nodes_unix.sh
## zipping output for specified simulations
cd sims.out.130214/
tr '\r' '\n' < SENC_Olympus_Batch_zipping.txt > SENC_Olympus_Batch_zipping_unix.txt
tr '\r' '\n' < SENC_Olympus_zipping.sh > SENC_Olympus_zipping_unix.sh
chmod u+x SENC_Olympus_zipping_unix.sh
./SENC_Olympus_zipping_unix.sh
## for sim analysis
cd senc.analysis/
tr '\r' '\n' < SENC_Olympus_Batch_analysis.txt > SENC_Olympus_Batch_analysis_unix.txt
tr '\r' '\n' < SENC_Olympus_Execute_analysis.sh > SENC_Olympus_Execute_analysis_unix.sh
chmod u+x SENC_Olympus_Execute_analysis_unix.sh
./SENC_Olympus_Execute_analysis_unix.sh
squeue -p shared -u steg815
## for zipping files for easy transport
cd SENC.2nd.run/
zip slurm.archive3.zip slurm*
mv slurm.archive3.zip ~/
zip senc.params3.zip SENC_params.out*
mv senc.params3.zip ~/
zip senc.time.rich3.zip SENC_time.rich*
mv senc.time.rich3.zip ~/
zip senc.stats3.zip SENC_Stats*
mv senc.stats3.zip ~/
zip clade.example.figs3.zip clade_example*
mv clade.example.figs3.zip ~/
zip lat.grad.figs3.zip lat_grad_thru*
mv lat.grad.figs3.zip ~/
zip corrs.v.age.figs3.zip corrs_vs_*
mv corrs.v.age.figs3.zip ~/
zip all.pops3.zip SENC_all.pops*
mv all.pops3.zip ~/
zip sim.out3.zip sim.*
mv sim.out3.zip ~/
zip senc.phylo3.zip SENC_phylo*
mv senc.phylo3.zip ~/