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meta1127/ghost-mp-docker

By meta1127

•Updated over 9 years ago

GHOST-MP on Docker http://www.bi.cs.titech.ac.jp/ghostmp/

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meta1127/ghost-mp-docker repository overview

⁠GHOST-MP-Docker

GHOST-MP is a parallel sequence similarity search tool. It searches for similar sequences among nucleotide query sequences and amino acid sequence database like BLASTX. http://www.bi.cs.titech.ac.jp/ghostmp/⁠

⁠Note

  • This Docker image works on only 1 node (1 container)..

⁠Usage

  • Please refer to here⁠ for details of command.
  • Please prepare yourself db.fasta and query.fasta.

⁠Interactive mode

docker run -it meta1127/ghostmp
./ghostmp_makedb -i db.fasta -o db
mpirun -n NUM_PROCESS ./ghostmp_search -i query.fasta -d db -o result
...
exit

⁠Interactive mode (data mount)

In this command, your current directory $(pwd) will be mounted to [/data] path in container.

docker run -it -v $(pwd):/data/  meta1127/ghostmp
./ghostmp_makedb -i /data/db.fasta -o /data/db
mpirun -n NUM_PROCESS ./ghostmp_search -i /data/query.fasta -d /data/db -o /data/result
...
exit

⁠Build (Optional)

# git clone
git clone https://github.com/metaVariable/GHOST-MP-Docker.git
cd GHOST-MP-Docker

# build  image
docker build . -t meta1127/ghostmp

⁠DockerHub

https://hub.docker.com/r/meta1127/ghost-mp-docker/⁠

Tag summary

Content type

Image

Digest

Size

146.2 MB

Last updated

over 9 years ago

docker pull meta1127/ghost-mp-docker