From 7cee178e00814d5f0a4e8e91a0464a1e1f24a76a Mon Sep 17 00:00:00 2001 From: Erin Young Date: Tue, 29 Oct 2024 22:22:20 +0000 Subject: [PATCH 1/5] adding kleborate version 3.0.0 --- README.md | 2 +- kleborate/3.0.0/Dockerfile | 78 ++++++++++++++++++++++++++++++++++++++ kleborate/3.0.0/README.md | 53 ++++++++++++++++++++++++++ 3 files changed, 132 insertions(+), 1 deletion(-) create mode 100644 kleborate/3.0.0/Dockerfile create mode 100644 kleborate/3.0.0/README.md diff --git a/README.md b/README.md index 90ea43a87..53798cb1e 100644 --- a/README.md +++ b/README.md @@ -191,7 +191,7 @@ To learn more about the docker pull rate limits and the open source software pro | [iVar](https://hub.docker.com/r/staphb/ivar/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ivar)](https://hub.docker.com/r/staphb/ivar) | | https://github.com/andersen-lab/ivar | | [Jasmine](https://hub.docker.com/r/staphb/pbjasmine/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pbjasmine)](https://hub.docker.com/r/staphb/pbjasmine) | | https://github.com/PacificBiosciences/jasmine | | [Kaptive](https://hub.docker.com/r/staphb/kaptive/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kaptive)](https://hub.docker.com/r/staphb/kaptive) | | https://github.com/klebgenomics/Kaptive | -| [Kleborate](https://hub.docker.com/r/staphb/kleborate/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | | https://github.com/katholt/Kleborate/
https://github.com/katholt/Kaptive/ | +| [Kleborate](https://hub.docker.com/r/staphb/kleborate/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | | https://github.com/katholt/Kleborate/
https://github.com/katholt/Kaptive/ | | [kma](https://hub.docker.com/r/staphb/kma/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kma)](https://hub.docker.com/r/staphb/kma) | | https://bitbucket.org/genomicepidemiology/kma/ | | [Kraken](https://hub.docker.com/r/staphb/kraken/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kraken)](https://hub.docker.com/r/staphb/kraken) | | https://github.com/DerrickWood/kraken | | [Kraken2](https://hub.docker.com/r/staphb/kraken2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kraken2)](https://hub.docker.com/r/staphb/kraken2) | | https://github.com/DerrickWood/kraken2 | diff --git a/kleborate/3.0.0/Dockerfile b/kleborate/3.0.0/Dockerfile new file mode 100644 index 000000000..d6f4ebdc6 --- /dev/null +++ b/kleborate/3.0.0/Dockerfile @@ -0,0 +1,78 @@ +FROM ubuntu:noble as app + +# for easy upgrade later. ARG variables only persist during image build time +ARG KLEBORATE_VER="3.1.0" +ARG MINIMAP2_VER="2.28" +ARG MASH_VER="2.3" + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="Kleborate" +LABEL software.version="${KLEBORATE_VER}" +LABEL description="tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)" +LABEL website="https://github.com/katholt/Kleborate" +LABEL license="https://github.com/katholt/Kleborate/blob/master/LICENSE" +LABEL maintainer="Curtis Kapsak" +LABEL maintainer.email="kapsakcj@gmail.com" +LABEL maintainer2="Frank Ambrosio" +LABEL maintainer2.email="frank.ambrosio@theiagen.com" +LABEL maintainer3="Erin Young" +LABEL maintainer3.email="eriny@utah.gov" + +# install prerequisites. Cleanup apt garbage +RUN apt-get update && apt-get install -y --no-install-recommends \ + python3 \ + pipx \ + wget \ + ca-certificates \ + bzip2 \ + procps \ + curl \ + git && \ + rm -rf /var/lib/apt/lists/* && apt-get autoclean + +# mash; update UID and GID of mash files; make /data +# UID and GID changes because the original owner is UID: 1081147385 and GID: 1360859114 which does NOT play well with systems that limits GIDs and UIDs +RUN wget -q https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar && \ + tar -xvf mash-Linux64-v${MASH_VER}.tar --no-same-owner && \ + rm -rf mash-Linux64-v${MASH_VER}.tar && \ + chown root:root /mash-Linux64-v${MASH_VER}/* + +# install minimap2 binary; make /data +RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | \ + tar -jxvf - --no-same-owner + +# set PATH and TERM to avoid warnings +ENV PATH="/mash-Linux64-v${MASH_VER}:/minimap2-${MINIMAP2_VER}_x64-linux:/root/.local/bin:${PATH}" + +# install kleborate (kaptive must be installed first) +#RUN pip install kleborate +RUN pipx install kleborate==${KLEBORATE_VER} && \ + mkdir /data && \ + kleborate --help + + +# set working directory +WORKDIR /data + +CMD kleborate --help + +FROM app as test + +# from https://kleborate.readthedocs.io/en/latest/Installation.html +RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/813/595/GCF_002813595.1_ASM281359v1/GCF_002813595.1_ASM281359v1_genomic.fna.gz && \ + kleborate -a GCF_002813595.1_ASM281359v1_genomic.fna.gz -o kleborate_test -p kpsc + +# run Kleborate on assembly supplied with Kleborate code +RUN wget -q https://github.com/klebgenomics/Kleborate/archive/refs/tags/v${KLEBORATE_VER}.tar.gz && \ + tar -xvf v${KLEBORATE_VER}.tar.gz && \ + kleborate --resistance --kaptive --all \ + --assemblies /Kleborate/test/test_genomes/172.fasta.gz \ + --outfile /data/strain172-kleborate-test-out.tsv + +# run with pytest +RUN pip install pytest && \ + python3 -m pytest klobarate-v${KLEBORATE_VER} + +# print help and version info +RUN kleborate --help && kleborate --version \ No newline at end of file diff --git a/kleborate/3.0.0/README.md b/kleborate/3.0.0/README.md new file mode 100644 index 000000000..2377e2406 --- /dev/null +++ b/kleborate/3.0.0/README.md @@ -0,0 +1,53 @@ +# Kleborate container + +Main tool : [Kleborate](https://github.com/katholt/Kleborate) 2.4.1 + +Additional tools: + +- [kaptive](https://github.com/katholt/Kaptive) 2.0.8 +- ncbi-blast+ 2.9.0 +- [mash](https://github.com/marbl/Mash) 2.3 +- python 3.8.2 +- biopython 1.81 + +Full documentation: [https://github.com/katholt/Kleborate/wiki](https://github.com/katholt/Kleborate/wiki) + +Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for: + +- MLST sequence type +- species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.) +- ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA) +- virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2) +- antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases +- K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive + +## Why is there `staphb/kleborate:2.3.2` and `staphb/kleborate:2.3.2-2023-05`? What is the difference? + +A small change was made to the Kleborate v2.3.2 dockerfile to account for an odd UID (1081147385) and GID (1360859114) that owns the `mash` executable and license file. This can cause problems in "rootless" environments or environments where `docker` is run inside of a docker container such as in GitPod. These environments have more limits placed on UIDs and GIDs than your typical linux computers. Error shown below: + +``` +$ docker pull staphb/kleborate:2.3.2 +2.3.2: Pulling from staphb/kleborate +47c764472391: Pull complete +f1582e59f07e: Pull complete +a2c96ce05542: Pull complete +213b944f2044: Pull complete +e136842d98e3: Extracting [==================================================>] 1.847MB/1.847MB +d99354f29fdd: Download complete +499193a95fe3: Download complete +4f4fb700ef54: Download complete +failed to register layer: ApplyLayer exit status 1 stdout: stderr: failed to Lchown "/mash-Linux64-v2.3/LICENSE.txt" for UID 1081147385, GID 1360859114 (try increasing the number of subordinate IDs in /etc/subuid and /etc/subgid): lchown /mash-Linux64-v2.3/LICENSE.txt: invalid argument +``` + +The dockerfile now has a step to `chown` these files so that the `root` user owns them, which prevents these odd errors. + +The updated docker image is available under the docker image name: `staphb/kleborate:2.3.2-2023-05` + +## Example Usage + +```bash +# run Kleborate on assembly supplied with Kleborate code +kleborate --resistance --kaptive --all \ + --assemblies /Kleborate/test/test_genomes/172.fasta.gz \ + --outfile /data/strain172-kleborate-test-out.tsv +``` From 60b7a14bd534f9d2a484b91feea5aa4940c927bb Mon Sep 17 00:00:00 2001 From: Erin Young Date: Wed, 30 Oct 2024 19:45:56 +0000 Subject: [PATCH 2/5] adding kleborate version 3.1.2 --- README.md | 2 +- kleborate/3.0.0/README.md | 53 ------------------ kleborate/{3.0.0 => 3.1.2}/Dockerfile | 30 ++++------ kleborate/3.1.2/README.md | 79 +++++++++++++++++++++++++++ 4 files changed, 90 insertions(+), 74 deletions(-) delete mode 100644 kleborate/3.0.0/README.md rename kleborate/{3.0.0 => 3.1.2}/Dockerfile (76%) create mode 100644 kleborate/3.1.2/README.md diff --git a/README.md b/README.md index 53798cb1e..38f6aedcf 100644 --- a/README.md +++ b/README.md @@ -191,7 +191,7 @@ To learn more about the docker pull rate limits and the open source software pro | [iVar](https://hub.docker.com/r/staphb/ivar/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ivar)](https://hub.docker.com/r/staphb/ivar) | | https://github.com/andersen-lab/ivar | | [Jasmine](https://hub.docker.com/r/staphb/pbjasmine/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pbjasmine)](https://hub.docker.com/r/staphb/pbjasmine) | | https://github.com/PacificBiosciences/jasmine | | [Kaptive](https://hub.docker.com/r/staphb/kaptive/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kaptive)](https://hub.docker.com/r/staphb/kaptive) | | https://github.com/klebgenomics/Kaptive | -| [Kleborate](https://hub.docker.com/r/staphb/kleborate/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | | https://github.com/katholt/Kleborate/
https://github.com/katholt/Kaptive/ | +| [Kleborate](https://hub.docker.com/r/staphb/kleborate/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | | https://github.com/katholt/Kleborate/
https://github.com/katholt/Kaptive/ | | [kma](https://hub.docker.com/r/staphb/kma/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kma)](https://hub.docker.com/r/staphb/kma) | | https://bitbucket.org/genomicepidemiology/kma/ | | [Kraken](https://hub.docker.com/r/staphb/kraken/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kraken)](https://hub.docker.com/r/staphb/kraken) | | https://github.com/DerrickWood/kraken | | [Kraken2](https://hub.docker.com/r/staphb/kraken2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kraken2)](https://hub.docker.com/r/staphb/kraken2) | | https://github.com/DerrickWood/kraken2 | diff --git a/kleborate/3.0.0/README.md b/kleborate/3.0.0/README.md deleted file mode 100644 index 2377e2406..000000000 --- a/kleborate/3.0.0/README.md +++ /dev/null @@ -1,53 +0,0 @@ -# Kleborate container - -Main tool : [Kleborate](https://github.com/katholt/Kleborate) 2.4.1 - -Additional tools: - -- [kaptive](https://github.com/katholt/Kaptive) 2.0.8 -- ncbi-blast+ 2.9.0 -- [mash](https://github.com/marbl/Mash) 2.3 -- python 3.8.2 -- biopython 1.81 - -Full documentation: [https://github.com/katholt/Kleborate/wiki](https://github.com/katholt/Kleborate/wiki) - -Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for: - -- MLST sequence type -- species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.) -- ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA) -- virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2) -- antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases -- K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive - -## Why is there `staphb/kleborate:2.3.2` and `staphb/kleborate:2.3.2-2023-05`? What is the difference? - -A small change was made to the Kleborate v2.3.2 dockerfile to account for an odd UID (1081147385) and GID (1360859114) that owns the `mash` executable and license file. This can cause problems in "rootless" environments or environments where `docker` is run inside of a docker container such as in GitPod. These environments have more limits placed on UIDs and GIDs than your typical linux computers. Error shown below: - -``` -$ docker pull staphb/kleborate:2.3.2 -2.3.2: Pulling from staphb/kleborate -47c764472391: Pull complete -f1582e59f07e: Pull complete -a2c96ce05542: Pull complete -213b944f2044: Pull complete -e136842d98e3: Extracting [==================================================>] 1.847MB/1.847MB -d99354f29fdd: Download complete -499193a95fe3: Download complete -4f4fb700ef54: Download complete -failed to register layer: ApplyLayer exit status 1 stdout: stderr: failed to Lchown "/mash-Linux64-v2.3/LICENSE.txt" for UID 1081147385, GID 1360859114 (try increasing the number of subordinate IDs in /etc/subuid and /etc/subgid): lchown /mash-Linux64-v2.3/LICENSE.txt: invalid argument -``` - -The dockerfile now has a step to `chown` these files so that the `root` user owns them, which prevents these odd errors. - -The updated docker image is available under the docker image name: `staphb/kleborate:2.3.2-2023-05` - -## Example Usage - -```bash -# run Kleborate on assembly supplied with Kleborate code -kleborate --resistance --kaptive --all \ - --assemblies /Kleborate/test/test_genomes/172.fasta.gz \ - --outfile /data/strain172-kleborate-test-out.tsv -``` diff --git a/kleborate/3.0.0/Dockerfile b/kleborate/3.1.2/Dockerfile similarity index 76% rename from kleborate/3.0.0/Dockerfile rename to kleborate/3.1.2/Dockerfile index d6f4ebdc6..932adf16b 100644 --- a/kleborate/3.0.0/Dockerfile +++ b/kleborate/3.1.2/Dockerfile @@ -1,7 +1,7 @@ -FROM ubuntu:noble as app +FROM ubuntu:jammy as app # for easy upgrade later. ARG variables only persist during image build time -ARG KLEBORATE_VER="3.1.0" +ARG KLEBORATE_VER="3.1.2" ARG MINIMAP2_VER="2.28" ARG MASH_VER="2.3" @@ -22,7 +22,7 @@ LABEL maintainer3.email="eriny@utah.gov" # install prerequisites. Cleanup apt garbage RUN apt-get update && apt-get install -y --no-install-recommends \ python3 \ - pipx \ + python3-pip \ wget \ ca-certificates \ bzip2 \ @@ -47,10 +47,8 @@ ENV PATH="/mash-Linux64-v${MASH_VER}:/minimap2-${MINIMAP2_VER}_x64-linux:/root/. # install kleborate (kaptive must be installed first) #RUN pip install kleborate -RUN pipx install kleborate==${KLEBORATE_VER} && \ - mkdir /data && \ - kleborate --help - +RUN pip install --no-cache-dir kleborate==${KLEBORATE_VER} && \ + mkdir /data # set working directory WORKDIR /data @@ -59,20 +57,12 @@ CMD kleborate --help FROM app as test +WORKDIR /test + # from https://kleborate.readthedocs.io/en/latest/Installation.html RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/813/595/GCF_002813595.1_ASM281359v1/GCF_002813595.1_ASM281359v1_genomic.fna.gz && \ - kleborate -a GCF_002813595.1_ASM281359v1_genomic.fna.gz -o kleborate_test -p kpsc - -# run Kleborate on assembly supplied with Kleborate code -RUN wget -q https://github.com/klebgenomics/Kleborate/archive/refs/tags/v${KLEBORATE_VER}.tar.gz && \ - tar -xvf v${KLEBORATE_VER}.tar.gz && \ - kleborate --resistance --kaptive --all \ - --assemblies /Kleborate/test/test_genomes/172.fasta.gz \ - --outfile /data/strain172-kleborate-test-out.tsv - -# run with pytest -RUN pip install pytest && \ - python3 -m pytest klobarate-v${KLEBORATE_VER} + kleborate -a GCF_002813595.1_ASM281359v1_genomic.fna.gz -o kleborate_test -p kpsc && \ + head kleborate_test/klebsiella_pneumo_complex_output.txt # print help and version info -RUN kleborate --help && kleborate --version \ No newline at end of file +RUN kleborate --help && kleborate --version && kleborate --list_modules \ No newline at end of file diff --git a/kleborate/3.1.2/README.md b/kleborate/3.1.2/README.md new file mode 100644 index 000000000..2765be3f6 --- /dev/null +++ b/kleborate/3.1.2/README.md @@ -0,0 +1,79 @@ +# Kleborate container + +Main tool : [Kleborate](https://github.com/katholt/Kleborate) + +Additional tools: + +- [mash](https://github.com/marbl/Mash) version 2.3 +- [minimap2]() version 2.28 + +Full documentation: [https://github.com/katholt/Kleborate/wiki](https://github.com/katholt/Kleborate/wiki) + +Description: +> Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for: +> +> - MLST sequence type +> - species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.) +> - ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA) +> - virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2) +> - antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases +> - K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive + +## Included models + +Kleborate has models for both Klebsiella and Escherichia species. The available presets and models are listed below. + +Available presets: kpsc, kosc, escherichia + +``` +Available modules for Kleborate +------------------------------- +enterobacterales__species: Mash-based species detection for enterobacterales species + +escherichia__mlst_achtman: chromosomal MLST for Escherichia coli using the Achtman scheme + +escherichia__mlst_pasteur: chromosomal MLST for Escherichia coli using the Pasteur scheme + +general__contig_stats: basic stats on the assembly's contigs + +klebsiella__abst: MLST on the KpSC aerobactin locus (iuc genes) + +klebsiella__cbst: MLST on the KpSC colibactin locus (clb genes) + +klebsiella__rmpa2: typing for the rmpA2 gene + +klebsiella__rmst: MLST on the KpSC Rmp locus (rmp genes) + +klebsiella__smst: MLST on the KpSC salmochelin locus (iro genes) + +klebsiella__ybst: MLST on the KpSC yersiniabactin locus (ybt and irp genes) + +klebsiella_oxytoca_complex__mlst: chromosomal MLST for the Klebsiella oxytoca species complex + +klebsiella_pneumo_complex__amr: Genotyping acquired genes and mutations for the Klebsiella pneumoniae species complex + +klebsiella_pneumo_complex__kaptive: In silico serotyping of K and L locus for the Klebsiella pneumoniae species complex + +klebsiella_pneumo_complex__mlst: chromosomal MLST for the Klebsiella pneumoniae species complex + +klebsiella_pneumo_complex__resistance_class_count: Resistance gene classes count, excluding the Bla_chr class which is intrinsicresults of the +klebsiella_pneumo_complex__amr module + +klebsiella_pneumo_complex__resistance_gene_count: Resistance genes counts, excluding the Bla class which is intrinsicresults of the +klebsiella_pneumo_complex__amr module + +klebsiella_pneumo_complex__resistance_score: resistance score (0-3) for the Klebsiella pneumoniae species complex, based on the results of the +klebsiella_pneumo_complex__amr module + +klebsiella_pneumo_complex__virulence_score: virulence score (0-5) for the Klebsiella pneumoniae species complex, based on the results of the abst, cbst +and ybst modules + +klebsiella_pneumo_complex__wzi: WZI typing for K antigen prediction +``` + + +## Example Usage + +```bash +kleborate -a sample.fasta -o outdir -p preset +``` From 4d716e804f2967eb300901162a2b4d079c413f19 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Wed, 30 Oct 2024 19:52:57 +0000 Subject: [PATCH 3/5] removed extra comments --- kleborate/3.1.2/Dockerfile | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/kleborate/3.1.2/Dockerfile b/kleborate/3.1.2/Dockerfile index 932adf16b..f06697d4e 100644 --- a/kleborate/3.1.2/Dockerfile +++ b/kleborate/3.1.2/Dockerfile @@ -45,8 +45,7 @@ RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/m # set PATH and TERM to avoid warnings ENV PATH="/mash-Linux64-v${MASH_VER}:/minimap2-${MINIMAP2_VER}_x64-linux:/root/.local/bin:${PATH}" -# install kleborate (kaptive must be installed first) -#RUN pip install kleborate +# install kleborate RUN pip install --no-cache-dir kleborate==${KLEBORATE_VER} && \ mkdir /data From 03dab4be5bd7d296aff301d9a71be5f04a54d3e0 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Wed, 30 Oct 2024 19:54:20 +0000 Subject: [PATCH 4/5] removed git --- kleborate/3.1.2/Dockerfile | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/kleborate/3.1.2/Dockerfile b/kleborate/3.1.2/Dockerfile index f06697d4e..4c0910974 100644 --- a/kleborate/3.1.2/Dockerfile +++ b/kleborate/3.1.2/Dockerfile @@ -27,8 +27,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ ca-certificates \ bzip2 \ procps \ - curl \ - git && \ + curl && \ rm -rf /var/lib/apt/lists/* && apt-get autoclean # mash; update UID and GID of mash files; make /data From d9a046f6ca2c73367c9d4ac4101c99e430ac3ee8 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Wed, 30 Oct 2024 19:55:35 +0000 Subject: [PATCH 5/5] fixed extra path --- kleborate/3.1.2/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/kleborate/3.1.2/Dockerfile b/kleborate/3.1.2/Dockerfile index 4c0910974..bb97c0119 100644 --- a/kleborate/3.1.2/Dockerfile +++ b/kleborate/3.1.2/Dockerfile @@ -42,7 +42,7 @@ RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/m tar -jxvf - --no-same-owner # set PATH and TERM to avoid warnings -ENV PATH="/mash-Linux64-v${MASH_VER}:/minimap2-${MINIMAP2_VER}_x64-linux:/root/.local/bin:${PATH}" +ENV PATH="/mash-Linux64-v${MASH_VER}:/minimap2-${MINIMAP2_VER}_x64-linux:${PATH}" # install kleborate RUN pip install --no-cache-dir kleborate==${KLEBORATE_VER} && \