Below are the dependencies to run Bacalyze natively in Linux Operating System. The commands to install specifically for Ubuntu are also given. Please refer to the documentations of the respective dependencies for other linux distributions.
Below are the dependencies to run Bacalyze natively in Linux Operating System. The commands to install specifically for Ubuntu are also given. Please refer to the documentations of the respective dependencies for other linux distributions.
| Sl No. | Dependencies | Command to install (Ubuntu) |
|---|---|---|
| 1 | Python version 3.11 and above | Must manually install from source for Ubuntu LTS version < 20.04. Available by default for Ubuntu LTS version 20.04 and above |
| 2 | BWA | apt install bwa |
| 3 | Fastp | apt install fastp |
| 4 | SAMtools | apt install samtools |
| 5 | VCFtools | apt install vcftools |
| 6 | Curl | apt install curl |
| 7 | OpenJDK 17 + | apt install openjdk-17-jdk-headless |
| 8 | Git | apt install git |
| 9 | NextFlow | Refer NextFlow documentation here. |
| 10 | Pandas | pip3 install pandas |
| 11 | Scikit-learn | pip3 install scikit-learn |
| 12 | Mlxtend | pip3 install mlxtend |
| 13 | Biopython | pip3 install biopython |
| 14 | Resfinder | pip3 install resfinder |
| 15 | MobileElementFinder | pip3 install MobileElementFinder |
| 16 | Ncbi-blast++ | apt install ncbi-blast++ |
| 17 | Seaborn | pip3 install seaborn |
| 18 | SPAdes | apt install spades |
| 19 | BCFtools | apt install bcftools |
| 20 | wxPython | apt install python-wxtools && pip3 install wxPython |