From 35ff885809e48da74b3044b605f848315675717d Mon Sep 17 00:00:00 2001
From: Haikel Bogale <70728342+Haikelnb@users.noreply.github.com>
Date: Tue, 24 Oct 2023 14:01:56 -0400
Subject: [PATCH] Create Dockerfile

---
 blast/2.14.1/Dockerfile | 63 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 blast/2.14.1/Dockerfile

diff --git a/blast/2.14.1/Dockerfile b/blast/2.14.1/Dockerfile
new file mode 100644
index 000000000..edecf6952
--- /dev/null
+++ b/blast/2.14.1/Dockerfile
@@ -0,0 +1,63 @@
+FROM ubuntu:focal as app
+
+ARG BLAST_VER="2.14.1"
+
+# 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=$BLAST_VER
+LABEL description="Finds matches in sequencing reads"
+LABEL website="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download"
+LABEL license="https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE"
+LABEL maintainer="Erin Young"
+LABEL maintainer.email="eriny@utah.gov"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+  wget \
+  ca-certificates \
+  libgomp1 && \
+  apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# Install and/or setup more things. Make /data for use as a working dir
+RUN wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${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
+
+# 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
+
+# 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" ]
+
+
+
+# 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/
+
+# 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
+
+# getting a list of genes
+RUN wget 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