add tbprofiler version 6.2.1

README.md

@@ -278,7 +278,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [SRST2](https://hub.docker.com/r/staphb/srst2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/srst2)](https://hub.docker.com/r/staphb/srst2) | <ul><li>0.2.0</li><li>[0.2.0 + custom Vibrio cholerae database](srst2/0.2.0-vibrio-230224/README.md)</li></ul> | https://github.com/katholt/srst2 |
 | [Staramr](https://hub.docker.com/r/staphb/staramr/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/staramr)](https://hub.docker.com/r/staphb/staramr) | <ul><li>[0.5.1](./staramr/0.5.1/)</li><li>[0.7.1](./staramr/0.7.1/)</li><li>[0.8.0](./staramr/0.8.0/)</li><li>[0.10.0](./staramr/0.10.0/)</li></ul> | https://github.com/phac-nml/staramr |
 | [sylph](https://hub.docker.com/r/staphb/sylph) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/sylph)](https://hub.docker.com/r/staphb/sylph) | <ul><li>[0.4.1](./sylph/0.4.1)</li><li>[0.5.1](./sylph/0.5.1)</li><li>[0.6.0](./sylph/0.6.0)</li><li>[0.6.1](./sylph/0.6.1)</li></ul> | https://github.com/bluenote-1577/sylph |
-| [TBProfiler](https://hub.docker.com/r/staphb/tbprofiler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tbprofiler)](https://hub.docker.com/r/staphb/tbprofiler) | <ul><li>[4.3.0](./tbprofiler/4.3.0/)</li><li>[4.4.0](./tbprofiler/4.4.0/)</li><li>[4.4.2](./tbprofiler/4.4.2/)</li><li>[5.0.1](tbprofiler/5.0.1/)</li><li>[6.2.0](tbprofiler/6.2.0/)</li></ul> | https://github.com/jodyphelan/TBProfiler |
+| [TBProfiler](https://hub.docker.com/r/staphb/tbprofiler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tbprofiler)](https://hub.docker.com/r/staphb/tbprofiler) | <ul><li>[4.3.0](./tbprofiler/4.3.0/)</li><li>[4.4.0](./tbprofiler/4.4.0/)</li><li>[4.4.2](./tbprofiler/4.4.2/)</li><li>[5.0.1](tbprofiler/5.0.1/)</li><li>[6.2.0](tbprofiler/6.2.0/)</li><li>[6.2.1](tbprofiler/6.2.1/)</li></ul> | https://github.com/jodyphelan/TBProfiler |
 | [TipToft](https://hub.docker.com/r/staphb/tiptoft/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tiptoft)](https://hub.docker.com/r/staphb/tiptoft) | <ul><li>1.0.0</li><li>1.0.2</li></ul> | https://github.com/andrewjpage/tiptoft |
 | [Tostadas](https://hub.docker.com/r/staphb/tostadas/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/tostadas)](https://hub.docker.com/r/staphb/tostadas) | <ul><li>[0.2.0-beta](./tostadas/0.2.0-beta/)</li><li>[3.1.0](./tostadas/3.1.0/)</li></ul> | https://github.com/CDCgov/tostadas |
 | [Treemmer](https://hub.docker.com/r/staphb/treemmer/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/treemmer)](https://hub.docker.com/r/staphb/treemmer) | <ul><li>0.3</li></ul> | https://git.scicore.unibas.ch/TBRU/Treemmer (archived, moved to GitHub) </br> https://github.com/fmenardo/Treemmer |

tbprofiler/6.2.1/Dockerfile

@@ -0,0 +1,67 @@
+FROM mambaorg/micromamba:1.5.8 as app
+
+USER root
+WORKDIR /
+
+ARG TBPROFILER_VER="6.2.1"
+
+# this version is the shortened commit hash on the `master` branch here https://github.com/jodyphelan/tbdb/
+# commits are found on https://github.com/jodyphelan/tbdb/commits/master
+# this was the latest commit as of 2024-05-10
+ARG TBDB_COMMIT="97b5876a1a9d2f06e8bb6076ed88baf481ef5fe5"
+
+# LABEL instructions tag the image with metadata that might be important to the user
+LABEL base.image="micromamba:1.5.8"
+LABEL dockerfile.version="1"
+LABEL software="tbprofiler"
+LABEL software.version="${TBPROFILER_VER}"
+LABEL description="The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using bcftools. These variants are then compared to a drug-resistance database."
+LABEL website="https://github.com/jodyphelan/TBProfiler/"
+LABEL license="https://github.com/jodyphelan/TBProfiler/blob/master/LICENSE"
+LABEL maintainer="John Arnn"
+LABEL maintainer.email="[email protected]"
+LABEL maintainer2="Curtis Kapsak"
+LABEL maintainer2.email="[email protected]"
+
+# Install dependencies via apt-get; cleanup apt garbage
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# install tb-profiler via bioconda; install into 'base' conda env
+RUN micromamba install --yes --name base --channel conda-forge --channel bioconda  \
+    tb-profiler=${TBPROFILER_VER} && \
+    micromamba clean --all --yes
+
+# hardcode 'base' env bin into PATH, so conda env does not have to be "activated" at run time
+ENV PATH="/opt/conda/bin:${PATH}"
+
+# Version of database can be confirmed at /opt/conda/share/tbprofiler/tbdb.version.json
+# can also run 'tb-profiler list_db' to find the same version info
+# In 5.0.1 updating_tbdb does not work with tb-profiler update_tbdb --commit ${TBDB_VER}
+#  ^^ this was resolved in 6.2.1
+#RUN tb-profiler update_tbdb -h && whatever
+
+# https://github.com/jodyphelan/tbdb
+
+RUN tb-profiler update_tbdb --commit ${TBDB_COMMIT}
+
+WORKDIR /data
+
+# Added command to bring help menu up upon running container.
+CMD tb-profiler
+
+# test stage
+FROM app as test
+
+# checking if tool is in PATH
+RUN tb-profiler && tb-profiler version
+
+WORKDIR /tests
+
+# download some TB FASTQs and run through tb-profiler
+RUN wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR166/009/ERR1664619/ERR1664619_1.fastq.gz && \
+    wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR166/009/ERR1664619/ERR1664619_2.fastq.gz && \
+    tb-profiler profile -1 ERR1664619_1.fastq.gz -2 ERR1664619_2.fastq.gz -t 2 -p ERR1664619 --txt

tbprofiler/6.2.1/README.md

@@ -0,0 +1,58 @@
+# TBProfiler Container
+
+Main tool: [TBProfiler](https://github.com/jodyphelan/TBProfiler)
+
+The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using bcftools. These variants are then compared to a drug-resistance database. It also predicts the number of reads supporting drug resistance variants as an insight into hetero-resistance.
+
+## Database
+
+This tool relies on a database to run. The version (AKA git commit hash) of the database that is included in the docker image is `97b5876`. This is from the GitHub repository https://github.com/jodyphelan/tbdb. This can be confirmed in the json file: `/opt/conda/share/tbprofiler/tbdb.version.json`:
+
+```bash
+$ grep 'commit' /opt/conda/share/tbprofiler/tbdb.version.json
+{"name": "tbdb", "commit": "5f3c51e", "Merge": "b1a2549 abddb8e", "Author": "Jody Phelan <[email protected]>", "Date": "Thu Jan 19 10:47:32 2023 +0000"}
+```
+
+Additionally you can run the command `tb-profiler list_db` to list the same information
+
+```bash
+$ tb-profiler list_db
+tbdb    97b5876 Jody Phelan <[email protected]>   Wed May 8 13:53:15 2024 +0100   /opt/conda/share/tbprofiler/tbdb
+```
+
+## Additional included tools/dependencies
+
+- bedtools 2.31.1
+- gatk4 4.5.0.0
+- kmc 3.2.4
+- pathogen-profiler 4.2.0
+- perl 5.32.1
+- python 3.10.14
+- trimmomatic 0.39
+- bwa 0.7.18
+- minimap2 2.28
+- samtools 1.20
+- bcftools 1.20
+- freebayes 1.3.6
+- tqdm 4.66.4
+- parallel 20240522
+- samclip 0.4.0
+- snpeff 5.2
+
+## Example Usage
+
+Run whole pipeline on Illumina paired-end reads:
+
+```bash
+tb-profiler profile -1 ERR1664619_1.fastq.gz -2 ERR1664619_2.fastq.gz -t 4 -p ERR1664619 --txt
+```
+
+Make alternative database:
+
+```bash
+tb-profiler create_db --prefix <new_library_name>
+tb-profiler load_library --prefix <new_library_name>
+```
+
+## Updates
+Release 5.0.1 implemented sqlite3 database locking with https://py-filelock.readthedocs.io/en/latest/index.html. This should fix issues using it over network filing systems (NFS). For more information, official documentation can be found [here.](https://jodyphelan.gitbook.io/tb-profiler/)