https://github.com/arnaudbelcour/singularity_ubcg

Singularity recipe for UBCG Bacterial Core Genes
https://github.com/arnaudbelcour/singularity_ubcg

Last synced: 18 days ago
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Singularity recipe for UBCG Bacterial Core Genes

• Host: GitHub
• URL: https://github.com/arnaudbelcour/singularity_ubcg
• Owner: ArnaudBelcour
• Created: 2023-09-25T15:16:08.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2023-09-25T15:53:12.000Z (over 1 year ago)
• Last Synced: 2024-11-10T01:48:03.150Z (3 months ago)
• Size: 2.93 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Singularity for UBCG

Singularity recipe for [UBCG (Up-to-date Bacterial Core Genes)](http://leb.snu.ac.kr/ubcg2).

# Installation

Clone this repository, put the files from UBCG (UBCG.jar, programPath, UBCG.hmm) in the cloned folder together with the `ubcg.def`  and use the following command to create the singularity container:

```sudo singularity build ubcg.sif ubcg.def```

# Use

Call UBCG from the singularity using the command line:

```singularity exec ubcg2.sif java -jar /programs/UBCG.jar extract -i input_genome_fasta_file -bcg_dir output_ubcg_folder -label organism_name```

```singularity exec ubcg2.sif java -jar /programs/UBCG.jar align -ucg_dir output_ubcg_folder -run_id mytest1 -leaf uid,label```