shengwei/transdecoder Docker 镜像 - 轩辕镜像 | Docker 镜像高效稳定拉取服务

• initialize a container named transdecoder in background

INPUT_PATH=$(readlink -f ${TRINITY_RESULT_FOLDER})
docker run -t -d --rm \
           -v /etc/group:/etc/group:ro -v /etc/passwd:/etc/passwd:ro \
           -u $(id -u $USER):$(id -g $USER) \
           -v $INPUT_PATH:/mnt \
           -v /home/db/uniprot:/db/uniprot \
           -v /home/db/Pfam:/db/Pfam \
           --name transdecoder \
           shengwei/transdecoder:latest

• run transdecoder

docker exec transdecoder /bin/bash -c 'cd /mnt && TransDecoder.LongOrfs -t Trinity.fasta -m 50 -G universal' 
docker exec transdecoder /bin/bash -c 'cd /mnt && blastp -query Trinity.fasta.transdecoder_dir/longest_orfs.pep -db /db/uniprot/uniprot_sprot.fasta -max_target_seqs 1 -outfmt 6 -evalue 1e-5 -num_threads 20 > blastp.outfmt6' 
docker exec transdecoder /bin/bash -c 'cd /mnt && hmmscan --cpu 20 --domtblout pfam.domtblout /db/Pfam/Pfam-A.hmm Trinity.fasta.transdecoder_dir/longest_orfs.pep'
docker exec transdecoder /bin/bash -c 'cd /mnt && TransDecoder.Predict -t Trinity.fasta --retain_pfam_hits pfam.domtblout --retain_blastp_hits blastp.outfmt6'

• kill container

docker container kill transdecoder