This repo contains the source files for a docker image stored in 4dndcic/docker-4dn-bedtomultivec.
- Cloning the repo
- Tool specifications
- Building docker image
- Benchmarking tools
- Sample data
- Tool wrappers
git clone https://github.com/4dn-dcic/docker-4dn-bedtomultivec
cd docker-4dn-bedtomultivec
Major software tools used inside the docker container are downloaded by the script downloads.sh. This script also creates a symlink to a version-independent folder for each software tool. In order to build an updated docker image with a new version of the tools, ideally only downloads.sh should be modified, but not Dockerfile, unless the new tool requires a specific APT tool that need to be downloaded.
The downloads.sh file also contains comment lines that specifies the name and version of individual software tools.
You need docker daemon to rebuild the docker image. If you want to push it to a different docker repo, replace 4dndcic/4dn-bedtomultivec with your desired docker repo name. You need permission to push to 4dndcic/4dn-bedtomultivec.
docker build -t 4dndcic/4dn-bedtomultivec .
docker push 4dndcic/4dn-bedtomultivec
You can skip this if you want to use an already built image on docker hub (image name 4dndcic/4dn-bedtomultivec). The command 'docker run' (below) automatically pulls the image from docker hub.
To obtain run time and max mem stats, use usr/bin/time that is installed in the docker container. For example, run the following to benchmark du.
docker run 4dndcic/4dn-bedtomultivec /usr/bin/time du 2> log
cat log
The output looks as follows:
0.02user 0.82system 0:00.87elapsed 96%CPU (0avgtext+0avgdata 2024maxresident)k
0inputs+0outputs (0major+103minor)pagefaults 0swaps
The benchmarking result goes to STDERR, which can be collected by a file by redirecting with 2>.
Maxmem is 2024KB in this case ('maxresident'). Run time is 0.87 second. ('elapsed')
Sample data files that can be used for testing the tools are included in the sample_data folder. These data are not included in the docker image.
Tool wrappers are under the scripts directory and follow naming conventions run-xx.sh. These wrappers are copied to the docker image at built time and may be used as a single step in a workflow.
# default
docker run 4dndcic/4dn-bedtomultivec
# specific run command
docker run 4dndcic/4dn-bedtomultivec <run-xx.sh> <arg1> <arg2> ...
# may need -v option to mount data file/folder if they are used as arguments.
docker run -v /data1/:/d1/:rw -v /data2/:/d2/:rw 4dndcic/4dn-bedtobmultivec <run-xx.sh> /d1/file1 /d2/file2 ...
This converts a bed file into multivecformat to be visualized in Higlass
- Input: a bed file
- Output: a multivec file
Runs the following in the container
run-bedtomultivec <bedfile> <chromsizes file> <resolution> <rows_infos_file> <num_rows> <outdir>
# bedfile: input bedfile
# chromsizes file: a file containing the chromosome sizes and order
# resolution: the base resolution of the data. Used to determine how much space to allocate in the multivec file
# rows_infos_file: a file containing the names of the rows in the multivec file
# num_rows: the number of rows at each position in the multivec format
# outdir: output directory