Difference between revisions of "Quast"
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Its '''setup.py''' script is highly customised and does not accept the usual '''--prefix=''' and --install-scripts''' options. | 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 | + | 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, this would be: |
#!/usr/bin/env python2.7 | #!/usr/bin/env python2.7 | ||
Revision as of 17:49, 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, this would be:
#!/usr/bin/env python2.7
