diff --git a/README.md b/README.md index 212440df5..38661e9aa 100644 --- a/README.md +++ b/README.md @@ -221,7 +221,7 @@ To learn more about the docker pull rate limits and the open source software pro | [panqc](https://hub.docker.com/r/staphb/panqc)
[![docker pulls](https://badgen.net/docker/pulls/staphb/panqc)](https://hub.docker.com/r/staphb/panqc) | | https://github.com/maxgmarin/panqc/releases/tag/0.4.0 | | [parallel-perl](https://hub.docker.com/r/staphb/parallel-perl)
[![docker pulls](https://badgen.net/docker/pulls/staphb/parallel-perl)](https://hub.docker.com/r/staphb/parallel-perl) | | https://www.gnu.org/software/parallel | | [parsnp](https://hub.docker.com/r/staphb/parsnp)
[![docker pulls](https://badgen.net/docker/pulls/staphb/parsnp)](https://hub.docker.com/r/staphb/parsnp) | | https://github.com/marbl/parsnp | -| [pasty](https://hub.docker.com/r/staphb/pasty)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pasty)](https://hub.docker.com/r/staphb/pasty) | | https://github.com/rpetit3/pasty | +| [pasty](https://hub.docker.com/r/staphb/pasty)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pasty)](https://hub.docker.com/r/staphb/pasty) | | https://github.com/rpetit3/pasty | | [pbmm2](https://hub.docker.com/r/staphb/pbmm2)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pbmm2)](https://hub.docker.com/r/staphb/pbmm2) | | https://github.com/PacificBiosciences/pbmm2 | | [Pavian](https://hub.docker.com/r/staphb/pavian)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pavian)](https://hub.docker.com/r/staphb/pavian) | | https://github.com/fbreitwieser/pavian | | [pbptyper](https://hub.docker.com/r/staphb/pbptyper)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pbptyper)](https://hub.docker.com/r/staphb/pbptyper) | | https://github.com/rpetit3/pbptyper | diff --git a/pasty/2.1.0/Dockerfile b/pasty/2.1.0/Dockerfile new file mode 100644 index 000000000..148e06baa --- /dev/null +++ b/pasty/2.1.0/Dockerfile @@ -0,0 +1,50 @@ +ARG PASTY_VER="2.1.0" + +FROM mambaorg/micromamba:1.5.8 AS app + +ARG PASTY_VER + +LABEL base.image="mambaorg/micromamba:1.5.8" +LABEL dockerfile.version="1" +LABEL software="pasty" +LABEL software.version="${PASTY_VERSION}" +LABEL description="In silico serogrouping of Pseudomonas aeruginosa isolates from genome assemblies" +LABEL website="https://github.com/rpetit3/pasty" +LABEL license="https://github.com/rpetit3/pasty/blob/main/LICENSE" +LABEL maintainer="Curtis Kapsak" +LABEL maintainer.email="curtis.kapsak@theiagen.com" +LABEL maintainer2="Kutluhan Incekara" +LABEL maintainer2.email="kutluhan.incekara@ct.gov" + +USER root + +RUN apt-get update && apt-get install -y --no-install-recommends \ + procps && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN micromamba install --name base -c conda-forge -c bioconda pasty=${PASTY_VER} &&\ + micromamba clean -afy + +ENV PATH="/opt/conda/bin/:$PATH" \ + LC_ALL=C + +CMD ["pasty", "--help"] + +WORKDIR /data + +## Test ## +FROM app AS test + +ARG PASTY_VER + +RUN apt-get update && apt-get install -y wget + +# adapted from https://github.com/rpetit3/pasty/blob/main/test/README.md +RUN wget -q https://github.com/rpetit3/pasty/archive/refs/tags/v${PASTY_VER}.tar.gz &&\ + tar -xvf v${PASTY_VER}.tar.gz &&\ + cd pasty-${PASTY_VER}/test/ &&\ + for i in $(ls data | grep "fna.gz"); do pasty --input ./data/$i --prefix $(basename $i .fna.gz) --outdir results/ --force; done &&\ + head -n 1 results/O1-GCF_001420225.tsv > staphb-test.tsv &&\ + ls results/ | grep -v "details" | grep -v "blastn" | xargs -I {} grep -v "schema_version" results/{} | sort -k1 >> staphb-test.tsv &&\ + cat staphb-test.tsv + diff --git a/pasty/2.1.0/README.md b/pasty/2.1.0/README.md new file mode 100644 index 000000000..7e7eb7e16 --- /dev/null +++ b/pasty/2.1.0/README.md @@ -0,0 +1,42 @@ +# pasty container + +Main tool : [pasty](https://github.com/rpetit3/pasty) + +Additional tools: + +- camlhmp 1.0.0 +- blast 2.16.0+ + +Full documentation: [https://github.com/rpetit3/pasty](https://github.com/rpetit3/pasty) + +A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates from genome assemblies + +## Example Usage + +```bash +pasty --input ./data/O1-GCF_001420225.fna.gz --prefix O1-GCF_001420225 --outdir results/ + +Running camlhmp with following parameters: + --input ./data/O1-GCF_001420225.fna.gz + --yaml /opt/conda/bin/../share/pasty/pa-osa.yaml + --targets /opt/conda/bin/../share/pasty/pa-osa.fasta + --outdir results/ + --prefix O1-GCF_001420225 + --min-pident 95 + --min-coverage 95 + +Starting camlhmp for P. aeruginosa serogrouping... +Running blastn... +Processing hits... +Final Results... + P. aeruginosa serogrouping +┏━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━┳━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━┓ +┃ sample ┃ type ┃ targets ┃ coverages ┃ hits ┃ schema ┃ schema_version ┃ camlhmp_version ┃ params ┃ comment ┃ +┡━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━╇━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━┩ +│ O1-GCF_001420225 │ O1 │ O1 │ 100.00 │ 1 │ pasty │ 2.1.0 │ 1.0.0 │ min-coverage=95;min-pident=95 │ │ +└──────────────────┴──────┴─────────┴───────────┴──────┴────────┴────────────────┴─────────────────┴───────────────────────────────┴─────────┘ +Writing outputs... +Final predicted type written to results/O1-GCF_001420225.tsv +Results against each type written to results/O1-GCF_001420225.details.tsv +blastn results written to results/O1-GCF_001420225.blastn.tsv +```