Difference between revisions of "Quast"
(Created page with "= Introduction = Quast is a software package that assesses genome assemblies. It is developed by the group that develops SPAdes. = Usage = To load: module load quast An...") |
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module load quast | module load quast | ||
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| + | Quast is installed in the default python installation, so technically, thsi module laod directive is not required. However, it is useful because it loads other modules. | ||
An example run: | An example run: | ||
quast.py test_data/contigs_1.fasta test_data/contigs_2.fasta -R test_data/reference.fasta.gz -G test_data/genes.gff | quast.py test_data/contigs_1.fasta test_data/contigs_2.fasta -R test_data/reference.fasta.gz -G test_data/genes.gff | ||
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| + | = Installation Notes = | ||
| + | |||
| + | Quast does not envisage installation into a non-standard directory. | ||
| + | |||
| + | Its '''setup.py''' script is highly customised and does not accept the usual '''--prefix=''' and --install-scripts''' options. | ||
| + | The key to installing it in a non-standard location is inserting the right python executable at the head of the '''setup.py''' scritp of the quaast source distribution. I.e for marvin, thsi would be: | ||
| + | |||
| + | #!/usr/bin/env python2.7 | ||
Revision as of 14:45, 6 February 2017
Introduction
Quast is a software package that assesses genome assemblies. It is developed by the group that develops SPAdes.
Usage
To load:
module load quast
Quast is installed in the default python installation, so technically, thsi module laod directive is not required. However, it is useful because it loads other modules.
An example run:
quast.py test_data/contigs_1.fasta test_data/contigs_2.fasta -R test_data/reference.fasta.gz -G test_data/genes.gff
Installation Notes
Quast does not envisage installation into a non-standard directory.
Its setup.py script is highly customised and does not accept the usual --prefix= and --install-scripts options. The key to installing it in a non-standard location is inserting the right python executable at the head of the setup.py scritp of the quaast source distribution. I.e for marvin, thsi would be:
#!/usr/bin/env python2.7
