structure-software
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structure-software [2017/02/21 08:28] – joguya | structure-software [2022/06/13 08:37] (current) – aorth | ||
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* Latest version: 2.3.4 | * Latest version: 2.3.4 | ||
* Added: June, 2014 | * Added: June, 2014 | ||
- | * Link: http://pritchardlab.stanford.edu/ | + | * Link: https://web.stanford.edu/ |
===== Usage ===== | ===== Usage ===== | ||
- | See which versions | + | See which versions are available: |
< | < | ||
- | Load structure | + | Load one version into your environment and run it: |
- | < | + | < |
+ | $ structure</ | ||
==== Sample Script ===== | ==== Sample Script ===== | ||
- | Here's a script to run structure using SLURM job scheduler whereby each structure iteration is submitted as a separate SLURM batch job: | + | Here's a script to run structure using the SLURM job scheduler whereby each structure iteration is submitted as a separate SLURM batch job: |
- | < | + | < |
- | #!/bin/env bash | + | |
## shell script to run structure in the background using SLURM job scheduler | ## shell script to run structure in the background using SLURM job scheduler | ||
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readonly EXTRAPARAMS=$3 | readonly EXTRAPARAMS=$3 | ||
readonly INFILE=$4 | readonly INFILE=$4 | ||
- | readonly CWD=$PWD | ||
fi | fi | ||
+ | |||
+ | readonly CWD=$PWD | ||
for rep in $(seq 1 $REPS) | for rep in $(seq 1 $REPS) | ||
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do | do | ||
echo "REP: $rep POP: $pop" | echo "REP: $rep POP: $pop" | ||
+ | outfile=" | ||
sbatch << | sbatch << | ||
#!/bin/env bash | #!/bin/env bash | ||
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#SBATCH -J structure | #SBATCH -J structure | ||
#SBATCH -p batch | #SBATCH -p batch | ||
- | #SBATCH -w taurus | + | #SBATCH -w mammoth |
module load structure/ | module load structure/ | ||
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# run structure with a different random seed for each run | # run structure with a different random seed for each run | ||
- | outfile=" | ||
- | |||
structure-gcc492 -m $MAINPARAMS -e $EXTRAPARAMS -K $POPULATION | structure-gcc492 -m $MAINPARAMS -e $EXTRAPARAMS -K $POPULATION | ||
# copy back results to data dir. | # copy back results to data dir. | ||
- | mv -v ${outfile} $CWD/ | + | mv -v ${SCRATCH_DIR} $CWD |
- | echo "Your results are in: $CWD directory | + | echo "Your results are in: $CWD directory" |
BATCH_SCRIPT | BATCH_SCRIPT | ||
done | done | ||
- | done | + | done</ |
- | </ | + | |
Usage: | Usage: | ||
- | < | + | < |
- | ./ | + | |
- | </ | + | ===== Installation ===== |
+ | Notes from the sysadmin during installation: | ||
+ | |||
+ | < | ||
+ | $ wget https:// | ||
+ | $ tar xf structure_kernel_source.tar.gz | ||
+ | $ cd structure_kernel_src | ||
+ | $ make | ||
+ | $ sudo cp structure / |
structure-software.txt · Last modified: 2022/06/13 08:37 by aorth