docker image for 0.2.6

[NicoleGruenheit]

Hi,

I would like to use the newest version but the latest docker image is for version 0.2.2. Would it be possible to update the docker image?

Cheers, Nicole

[dawnmy]

Hi Nicole,

I will build a docker image next week for latest version 0.2.7

Best, Zhi-Luo

[dawnmy]

@NicoleGruenheit I have uploaded the CPU version (tag: 0.2.7-cpu). You should be able to pull it with:

docker pull dawnmy/ribodetector:0.2.7-cpu

Then you can run it with something like:

docker run -v <your local data dir>:<docker data dir> --rm dawnmy/ribodetector:0.2.7-cpu \
  ribodetector_cpu  -t 10 \
  -l 100 \
  -i <data dir/reads.1.fq.gz> <data dir/reads.2.fq.gz> \
  -e rrna \
  --chunk_size 512 \
  -o <data dir/reads.nonrrna.1.fq> <data dir/reads.nonrrna.2.fq>

We will upload the GPU version soon. But the GPU version image is very large. If you don't have GPU available on the computer, it would be better to install only the CPU version.

[dawnmy]

GPU version is also uploaded.

docker pull dawnmy/ribodetector:0.2.7

Memory and shared memory parameters need to be set with docker run, e.g.:

docker run --memory=<64>G --shm-size <32>G --gpus all \
  -v <your local data dir>:<docker data dir> --rm dawnmy/ribodetector:0.2.7-cpu \
  ribodetector_cpu  -t 10 \
  -l 100 \
  -i <data dir/reads.1.fq.gz> <data dir/reads.2.fq.gz> \
  -e rrna \
  --chunk_size 512 \
  -m 12
  -o <data dir/reads.nonrrna.1.fq> <data dir/reads.nonrrna.2.fq>