adds blast 2.16.0

README.md

@@ -122,7 +122,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [bcftools](https://hub.docker.com/r/staphb/bcftools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bcftools)](https://hub.docker.com/r/staphb/bcftools) | <ul><li>[1.10.2](./bcftools/1.10.2/)</li><li>[1.11](./bcftools/1.11/)</li><li>[1.12](./bcftools/1.12/)</li><li>[1.13](./bcftools/1.13/)</li><li>[1.14](./bcftools/1.14/)</li><li>[1.15](./bcftools/1.15/)</li><li>[1.16](./bcftools/1.16/)</li><li>[1.17](./bcftools/1.17/)</li><li>[1.18](bcftools/1.18/)</li><li>[1.19](./bcftools/1.19/)</li><li>[1.20](./bcftools/1.20/)</li><li>[1.20.c](./bcftools/1.20.c/)</li></ul> | https://github.com/samtools/bcftools |
 | [bedtools](https://hub.docker.com/r/staphb/bedtools/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bedtools)](https://hub.docker.com/r/staphb/bedtools) | <ul><li>2.29.2</li><li>2.30.0</li><li>[2.31.0](bedtools/2.31.0/)</li><li>[2.31.1](bedtools/2.31.1/)</li></ul> | https://bedtools.readthedocs.io/en/latest/ <br/>https://github.com/arq5x/bedtools2 |
 | [berrywood-report-env](https://hub.docker.com/r/staphb/berrywood-report-env/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/berrywood-report-env)](https://hub.docker.com/r/staphb/berrywood-report-env) | <ul><li>1.0</li></ul> | none |
-| [blast+](https://hub.docker.com/r/staphb/blast/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/blast)](https://hub.docker.com/r/staphb/blast) | <ul><li>[2.13.0](blast/2.13.0/)</li><li>[2.14.0](blast/2.14.0/)</li><li>[2.14.1](blast/2.14.1/)</li><li>[2.15.0](blast/2.15.0/)</li></ul> | https://www.ncbi.nlm.nih.gov/books/NBK279690/ |
+| [blast+](https://hub.docker.com/r/staphb/blast/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/blast)](https://hub.docker.com/r/staphb/blast) | <ul><li>[2.13.0](blast/2.13.0/)</li><li>[2.14.0](blast/2.14.0/)</li><li>[2.14.1](blast/2.14.1/)</li><li>[2.15.0](blast/2.15.0/)</li><li>[2.16.0](./blast/2.16.0/)</li></ul> | https://www.ncbi.nlm.nih.gov/books/NBK279690/ |
 | [bowtie2](https://hub.docker.com/r/staphb/bowtie2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bowtie2)](https://hub.docker.com/r/staphb/bowtie2) | <ul><li>[2.4.4](./bowtie2/2.4.4/)</li><li>[2.4.5](./bowtie2/2.4.5/)</li><li>[2.5.1](./bowtie2/2.5.1/)</li><li>[2.5.3](./bowtie2/2.5.3/)</li><li>[2.5.4](./bowtie2/2.5.4/)</li></ul> | http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml <br/>https://github.com/BenLangmead/bowtie2 |
 | [Bracken](https://hub.docker.com/r/staphb/bracken/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/bracken)](https://hub.docker.com/r/staphb/bracken) | <ul><li>[2.9](./bracken/2.9)</li></ul> | https://ccb.jhu.edu/software/bracken/index.shtml?t=manual <br/>https://github.com/jenniferlu717/Bracken |
 | [BUSCO](https://hub.docker.com/r/staphb/busco/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/busco)](https://hub.docker.com/r/staphb/busco) | <ul><li>[5.4.7](./busco/5.4.7/)</li><li>[5.6.1](./busco/5.6.1/)</li><li>[5.6.1-prok-bacteria_odb10_2024-01-08](./busco/5.6.1-prok-bacteria_odb10_2024-01-08/)</li><li>[5.7.1](./busco/5.7.1/)</li><li>[5.7.1-prok-bacteria_odb10_2024-01-08](./busco/5.7.1-prok-bacteria_odb10_2024-01-08/)</li></ul> | https://busco.ezlab.org/busco_userguide.html <br/>https://gitlab.com/ezlab/busco |

blast/2.16.0/Dockerfile

@@ -0,0 +1,62 @@
+FROM ubuntu:jammy as app
+
+ARG BLAST_VER="2.16.0"
+
+# LABEL instructions tag the image with metadata that might be important to the user
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="blast+"
+LABEL software.version=$BLAST_VER
+LABEL description="Finds matches in sequencing reads"
+LABEL website="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download"
+LABEL license="https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="[email protected]"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+  wget \
+  ca-certificates \
+  libgomp1 && \
+  apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# Install and/or setup more things. Make /data for use as a working dir
+RUN wget -q https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VER}/ncbi-blast-${BLAST_VER}+-x64-linux.tar.gz && \
+  tar -xzf ncbi-blast-${BLAST_VER}+-x64-linux.tar.gz && \
+  rm ncbi-blast-${BLAST_VER}+-x64-linux.tar.gz
+
+# ENV instructions set environment variables that persist from the build into the resulting image
+# Use for e.g. $PATH and locale settings for compatibility with Singularity
+ENV PATH="/ncbi-blast-${BLAST_VER}+/bin:$PATH" \
+  LC_ALL=C
+
+# WORKDIR sets working directory
+WORKDIR /data
+
+# yes, there are more tools than blastn, but it's likely the most common one used
+CMD [ "blastn", "-help" ]
+
+# A second FROM insruction creates a new stage
+# We use `test` for the test image
+FROM app as test
+
+# getting all the exectubles in bin
+RUN ls /ncbi-blast-*/bin/
+
+# making sure PATH is set up
+RUN blastn -help
+
+# getting a genome
+RUN mkdir db && \
+  wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz -P db && \
+  gunzip db/GCF_000005845.2_ASM584v2_genomic.fna.gz && \
+  makeblastdb -dbtype nucl -in db/GCF_000005845.2_ASM584v2_genomic.fna
+
+# getting a list of genes
+RUN wget -q https://raw.githubusercontent.com/rrwick/Unicycler/main/unicycler/gene_data/dnaA.fasta
+
+# getting some blast results
+RUN tblastn -query dnaA.fasta \
+  -db db/GCF_000005845.2_ASM584v2_genomic.fna \
+  -outfmt '6' \
+  -out blast_hits.txt && \
+  head blast_hits.txt

blast/2.16.0/README.md

@@ -0,0 +1,60 @@
+# blast+ container
+
+Main tools:
+
+- [blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
+
+This is meant to assist in local blast searches. No blast databases will be maintained in this container. Be sure to mount your relevant Volumes with `--volumes` or `-v` when using the command line.
+
+blast+ is actually a suite of tools. blast+ v.2.16.0 includes:
+
+```bash
+$ ls /ncbi-blast-2.15.0+/bin/
+blast_formatter
+blast_formatter_vdb
+blast_vdb_cmd
+blastdb_aliastool
+blastdbcheck
+blastdbcmd
+blastn
+blastn_vdb
+blastp
+blastx
+cleanup-blastdb-volumes.py
+convert2blastmask
+deltablast
+dustmasker
+get_species_taxids.sh
+legacy_blast.pl
+makeblastdb
+makembindex
+makeprofiledb
+psiblast
+rpsblast
+rpstblastn
+segmasker
+tblastn
+tblastn_vdb
+tblastx
+update_blastdb.pl
+windowmasker
+```
+
+Currently not supported, but could be:
+
+```bash
+get_species_taxids.sh # requires E-direct
+update_blastdb.pl     # requires perl
+```
+
+## Example Usage
+
+```bash
+# making a blast database
+makeblastdb -dbtype nucl -in fasta.fa
+
+# query
+tblastn -query query.fasta -db fasta.fa -outfmt '6' -out blast_hits.txt
+```
+
+More documentation can be found at [https://www.ncbi.nlm.nih.gov/books/NBK569856/](https://www.ncbi.nlm.nih.gov/books/NBK569856/) and [https://www.ncbi.nlm.nih.gov/books/NBK279690/](https://www.ncbi.nlm.nih.gov/books/NBK279690/)