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Merge pull request #770 from Haikelnb/master
Update blast+ to version 2.14.1
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| FROM ubuntu:focal as app | ||
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| ARG BLAST_VER="2.14.1" | ||
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| # LABEL instructions tag the image with metadata that might be important to the user | ||
| LABEL base.image="ubuntu:focal" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="blast+" | ||
| LABEL software.version=$BLAST_VER | ||
| LABEL description="Finds matches in sequencing reads" | ||
| LABEL website="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download" | ||
| LABEL license="https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
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| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates \ | ||
| libgomp1 && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # Install and/or setup more things. Make /data for use as a working dir | ||
| RUN wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${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 && \ | ||
| mkdir /data | ||
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| # 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 | ||
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| # WORKDIR sets working directory | ||
| WORKDIR /data | ||
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| # default command is to pull up help options for virulencefinder | ||
| # yes, there are more tools than blastn, but it's likely the most common one used | ||
| CMD [ "blastn", "-help" ] | ||
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| # A second FROM insruction creates a new stage | ||
| # We use `test` for the test image | ||
| FROM app as test | ||
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| # getting all the exectubles in bin | ||
| RUN ls /ncbi-blast-*/bin/ | ||
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| # getting a genome | ||
| RUN mkdir db && \ | ||
| wget 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 | ||
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| # getting a list of genes | ||
| RUN wget https://raw.githubusercontent.com/rrwick/Unicycler/main/unicycler/gene_data/dnaA.fasta | ||
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| # 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 |
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| # blast+ container | ||
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| Main tools: | ||
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| - [blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download) | ||
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| 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. | ||
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| blast+ is actually a suite of tools. blast+ v.2.14.1 includes: | ||
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| ```bash | ||
| $ ls /ncbi-blast-2.14.1+/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 | ||
| ``` | ||
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| Currently not supported, but could be: | ||
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| ```bash | ||
| get_species_taxids.sh # requires E-direct | ||
| update_blastdb.pl # requires perl | ||
| ``` | ||
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| ## Example Usage | ||
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| ```bash | ||
| # making a blast database | ||
| makeblastdb -dbtype nucl -in fasta.fa | ||
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| # query | ||
| tblastn -query query.fasta -db fasta.fa -outfmt '6' -out blast_hits.txt | ||
| ``` | ||
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| 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/) |