unicycler-software
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unicycler-software [2019/02/15 18:07] – created aorth | unicycler-software [2023/06/12 13:17] (current) – aorth | ||
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===== Information ===== | ===== Information ===== | ||
- | * Version: 0.47.0 | + | * Version: 0.5.0 |
* Added: February, 2019 | * Added: February, 2019 | ||
+ | * Updated: June, 2023 | ||
* Link: https:// | * Link: https:// | ||
===== Usage ===== | ===== Usage ===== | ||
- | See versions | + | See versions which are available: |
< | < | ||
Load one version into your environment and run it: | Load one version into your environment and run it: | ||
- | < | + | < |
$ unicycler</ | $ unicycler</ | ||
=== Example Batch Job === | === Example Batch Job === | ||
- | < | + | < |
+ | #SBATCH -p batch | ||
+ | #SBATCH -n 4 | ||
+ | #SBATCH -J unicycler | ||
+ | |||
+ | module load unicycler/ | ||
+ | |||
+ | readonly DATADIR=~/ | ||
+ | readonly OUTDIR=/ | ||
+ | |||
+ | # create output directory on compute node | ||
+ | mkdir -p ${OUTDIR} | ||
+ | |||
+ | # run unicycler with the number of threads allocated by SLURM | ||
+ | unicycler -t ${SLURM_NTASKS} -1 ${DATADIR}/ | ||
+ | |||
+ | echo | ||
+ | echo " | ||
+ | echo | ||
+ | echo " | ||
+ | |||
+ | By default Unicycler will use four CPU threads. Please make sure to set this parameter properly according to the SLURM job request. | ||
===== Installation ====== | ===== Installation ====== | ||
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< | < | ||
- | $ wget https:// | + | $ wget https:// |
- | $ unzip v0.4.7.zip | + | $ tar xf v0.5.0.tar.gz |
- | $ cd Unicycler-0.4.7 | + | $ cd Unicycler-0.5.0 |
- | $ sudo yum install centos-release-scl | + | $ module load python/3.8 |
- | $ sudo yum install devtoolset-6-gcc.x86_64 devtoolset-6-gcc-c++.x86_64 python36 python36-setuptools | + | $ sudo mkdir -p / |
- | $ scl enable devtoolset-6 bash | + | $ sudo chown aorth / |
- | $ sudo mkdir -p / | + | $ python3.8 |
- | $ sudo chown aorth / | + | $ sudo chown -R root:root / |
- | $ python36 | + | |
- | $ sudo chown -R root:root / | + | |
- | + | ||
- | The devtoolset is used because Unicycler requires a GCC compiler newer than 4.9.1. | + |
unicycler-software.txt · Last modified: 2023/06/12 13:17 by aorth