Extraction of CRISPR counts written in rust.
This program takes two bam files and returns rows based on the target names in the headers (usually your guide names). By default it will return a row for the product of the target names. Alternatively specify --pair to return a row for each pair of target names, taking one from each bam (both files must have the same number and the sequence names must be in the desired order).
| type | long | Default | Details |
|---|---|---|---|
| Flag | --help | Display usage | |
| uint | --n-mismatch | 2 | The value of the SAM format field (specified by --tag-mismatch) must be less than this value. |
| String | --output-tsv | counts.tsv | The name of the file where the output counts will be written as tab separated values. |
| Flag | --pair | A row will be output for every pair of sequence names from BAM_R1 and BAM_R2 (whose headers must have an identical number of sequence names and be in the desired order). The default returns rows for the product. | |
| String | --tag-mismatch | NM | The name of the SAM format field containing the unsigned integer which will be filtered by comparison with --n-mismatch. Alignments where the value is less than --n-mismatch contribute to counts. |
| String | <SAMPLE_NAME> | This value will appear in the Sample_Name column of counts.long.tsv and as the column name in counts.wide.tsv (See https://github.com/roland-rad-lab/CRISPR\_analysis) | |
| BAM File | <BAM_R1> | BAM file for read one. | |
| BAM File | <BAM_R2> | BAM file for read two. |
The included Dockerfile can be used to create a container for this program.
# Build is an empty directory or contains things we wish to include in our image (sometimes called context)
mkdir -p build
curl -L https://raw.githubusercontent.com/roland-rad-lab/CRISPR_rust/main/Dockerfile.crispr-rust > build/Dockerfile.crispr-rust
# Using Docker
cd build && sudo docker build --force-rm --no-cache -t crispr-rust-0.0.4 -f Dockerfile.crispr-rust .
# Using podman (open source alternative to Docker)
# podman machine init --disk-size 50 --memory 4096
# podman machine start
podman --remote build --no-cache --rm --tag crispr-rust-0.0.4 -f build/Dockerfile.crispr-rust build
From here we can optionally choose to publish our image to an image repository so others can download it. In this case to our public repo at LRZ gitlab.
## Using Docker
# Our image name must exactly match our remote destination
docker tag crispr-rust-0.0.4 gitlab.lrz.de:5005/roland-rad-lab/images-public/crispr-rust:0.0.4
# Now we need to login using the access token with write permissions
docker login gitlab.lrz.de:5005 -u SECRET_GITLAB_ACCESS_TOKEN_NAME -p SECRET_GITLAB_ACCESS_TOKEN
docker push gitlab.lrz.de:5005/roland-rad-lab/images-public/crispr-rust:0.0.4
## Using podman (as an alternative to Docker)
# Our image name must exactly match our remote destination (pushing an image with an already existing tag probably won't work)
podman tag localhost/crispr-rust-0.0.4:latest gitlab.lrz.de:5005/roland-rad-lab/images-public/crispr-rust:0.0.4
# Now we need to login using the access token with write permissions
podman login gitlab.lrz.de:5005 -u SECRET_GITLAB_ACCESS_TOKEN_NAME -p SECRET_GITLAB_ACCESS_TOKEN
podman push gitlab.lrz.de:5005/roland-rad-lab/images-public/crispr-rust:0.0.4
Or we can export our image as a gzipped tarball and subsequently copy to and extract it on the system where we would like to use it.
# Optionally fetch image from a container repository (if you didn't build it locally)
## Using Docker
# docker login gitlab.lrz.de:5005 -u roland-rad-lab-images-public -p xUSAxe6kmRb1y13Ajzak
# docker pull gitlab.lrz.de:5005/roland-rad-lab/images-public/crispr-rust:0.0.4
# ch-builder2tar is part of https://github.com/hpc/charliecloud
ch-builder2tar -b docker gitlab.lrz.de:5005/roland-rad-lab/images-public/crispr-rust:0.0.4 target/
## Using podman
# podman login gitlab.lrz.de:5005 -u roland-rad-lab-images-public -p xUSAxe6kmRb1y13Ajzak
# podman pull gitlab.lrz.de:5005/roland-rad-lab/images-public/crispr-rust:0.0.4
# I opened an issue to add podman support to ch-builder2tar, including my implementation
# https://github.com/hpc/charliecloud/issues/1256