gapfiller

Docker for gapfiller version 1.1.1 (installed in a debian:squeeze version, 2011)

building an image

docker build -t gapfiller:1.1.1 .

running

docker
run
--rm
--interactive
--user $(id -u):$(id -g)
--volume ${PWD}:/data
--workdir /data
gapfiller:1.1.1
GapFiller.pl -l <Your_sample>_library_SSPACE.txt -s <Your_sample>_scaffolds.fasta -n 20 -d 50 -t 10 -T 10 -i 10 -b <Your_sample_name> 1>GapFiller.out 2>GapFiller.err