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Release 0.1.4
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‎Makefile

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@@ -24,8 +24,8 @@ SHELL=/bin/bash
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VENV?=.env
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PYTHON_SRC=$(shell find src/elb bin -type f -name "*.py" ! -path "*eggs*" ! -path "*${VENV}*" ! -name __init__.py ! -path "*.tox*" ! -path "*coverage*" ! -path "*cache*" ! -path "./build*")
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YAML_TEMPLATES=$(shell find src/elb/templates -type f)
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PYTHON_SRC=$(shell find src/elastic_blast bin -type f -name "*.py" ! -path "*eggs*" ! -path "*${VENV}*" ! -name __init__.py ! -path "*.tox*" ! -path "*coverage*" ! -path "*cache*" ! -path "./build*")
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YAML_TEMPLATES=$(shell find src/elastic_blast/templates -type f)
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all: elastic-blast
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@@ -77,11 +77,11 @@ validate-iam-policy: iam-policy.json
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-AWS_PAGER='' aws accessanalyzer validate-policy --no-paginate --policy-document file://$< --policy-type RESOURCE_POLICY
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.PHONY: validate-cf-templates
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validate-cf-templates: src/elb/templates/elastic-blast-cf.yaml
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validate-cf-templates: src/elastic_blast/templates/elastic-blast-cf.yaml
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AWS_PAGER='' aws --region us-east-1 cloudformation validate-template --template-body file://$<
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.PHONY: cfn-lint
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cfn-lint: src/elb/templates/elastic-blast-cf.yaml ${VENV}
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cfn-lint: src/elastic_blast/templates/elastic-blast-cf.yaml ${VENV}
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source ${VENV}/bin/activate && cfn-lint -t $<
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#############################################################################
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.PHONY: mypy
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mypy: ${VENV}
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source ${VENV}/bin/activate && mypy src/elb/
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source ${VENV}/bin/activate && mypy src/elastic_blast/
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.PHONY: yamllint
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yamllint: ${VENV}
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source ${VENV}/bin/activate && \
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yamllint -d share/etc/yamllint-config.yaml src/elb/templates/elastic-blast-cf.yaml
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yamllint -d share/etc/yamllint-config.yaml src/elastic_blast/templates/elastic-blast-cf.yaml
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source ${VENV}/bin/activate && \
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yamllint -d share/etc/yamllint-config.yaml src/elb/templates/storage-gcp.yaml
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yamllint -d share/etc/yamllint-config.yaml src/elastic_blast/templates/storage-gcp.yaml
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source ${VENV}/bin/activate && \
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yamllint -d share/etc/yamllint-config.yaml src/elb/templates/storage-gcp-ssd.yaml
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yamllint -d share/etc/yamllint-config.yaml src/elastic_blast/templates/storage-gcp-ssd.yaml
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source ${VENV}/bin/activate && \
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yamllint -d share/etc/yamllint-config.yaml src/elb/templates/pvc.yaml.template
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yamllint -d share/etc/yamllint-config.yaml src/elastic_blast/templates/pvc.yaml.template
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source ${VENV}/bin/activate && \
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yamllint -d share/etc/yamllint-config.yaml src/elb/templates/job-init-*
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yamllint -d share/etc/yamllint-config.yaml src/elastic_blast/templates/job-init-*
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source ${VENV}/bin/activate && \
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yamllint -d share/etc/yamllint-config.yaml src/elb/templates/blast-batch-job*
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yamllint -d share/etc/yamllint-config.yaml src/elastic_blast/templates/blast-batch-job*
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‎Makefile-create-blastdb-metadata

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# Makefile to test create-blastdb-metadata.py script
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# Author: Christiam Camacho (camacho@ncbi.nlm.nih.gov)
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# Created: Tue 15 Jun 2021 11:01:20 AM EDT
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SHELL=/bin/bash
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.PHONY: all clean check check_python
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#########################################################################
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# Python support
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all:
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bin/create-blastdb-metadata.py --help
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bin/create-blastdb-metadata.py --version
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check: check_python
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bin/create-blastdb-metadata.py --db tests/blastdb/testdb --dbtype prot --out testdb.json
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cat testdb.json | jq -Mr '.' >/dev/null
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rm testdb.json
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check_python:
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python3 -m py_compile bin/create-blastdb-metadata.py
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python3 -m unittest bin/create-blastdb-metadata.py
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clean:
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find . -name __pycache__ | xargs ${RM} -fr

‎Makefile-pypi

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# Makefile for distributing ElasticBLAST to PyPI
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# Author: Christiam Camacho (camacho@ncbi.nlm.nih.gov)
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# Created: Mon Jun 14 09:48:58 2021
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SHELL=/bin/bash
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.PHONY: deploy clean test-deployment test-production-deployment test-deployment-with-search
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MODULE?=elastic_blast
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PYPI?=testpypi
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VERSION?=0.0.56
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include Makefile-public
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deploy: dist/${MODULE}-${VERSION}.tar.gz
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${VENV}/bin/twine upload --verbose --repository ${PYPI} dist/${MODULE}-${VERSION}.tar.gz
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dist/${MODULE}-${VERSION}.tar.gz: ${VENV}
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${VENV}/bin/pip3 install -q twine
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source ${VENV}/bin/activate && python3 setup.py sdist
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clean:
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${RM} -fr ${VENV} src/*egg-info dist cfg.ini* submit-and-wait-for-results.sh*
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TMP_VENV:=$(shell mktemp -d)
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test-deployment:
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-python3 -m venv ${TMP_VENV} && \
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source ${TMP_VENV}/bin/activate && \
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pip install --extra-index-url https://test.pypi.org/simple/ ${MODULE}==${VERSION} && \
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elastic-blast.py --version
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########################################################################
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# Support for test-deployment-with-search: running a full search on AWS
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export ELB_RESULTS:=s3://elasticblast-${USER}/pypi-test-$(shell date +%F-%T)
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test-deployment-with-search: test-deployment submit-and-wait-for-results.sh cfg.ini
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@echo Will write results to ${ELB_RESULTS}
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source ${TMP_VENV}/bin/activate && ./submit-and-wait-for-results.sh cfg.ini
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submit-and-wait-for-results.sh:
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[ -f submit-and-wait-for-results.sh ] || curl -sO https://raw.githubusercontent.com/ncbi/elastic-blast-demos/master/submit-and-wait-for-results.sh
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[ -x submit-and-wait-for-results.sh ] || chmod +x submit-and-wait-for-results.sh
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sed -i~ -e 's,elastic-blast ,elastic-blast.py ,;s/status /status --verbose /' submit-and-wait-for-results.sh
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cfg.ini:
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curl -s https://raw.githubusercontent.com/ncbi/elastic-blast/master/share/etc/elb-aws-blastn-nt-8-nodes.ini -o $@
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sed -i~ -e 's/8x//;s/16/1/;s/1000G/334G/;s/nt/pdbnt/;s/60G/1G/;s,hepatitis.fsa.gz,MANE.GRCh38.v0.8.select_refseq_rna.fna,' $@
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########################################################################
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test-production-deployment:
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-python3 -m venv ${TMP_VENV} && \
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source ${TMP_VENV}/bin/activate && \
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pip install ${MODULE}==${VERSION} && \
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elastic-blast.py --version

‎README.md

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# ElasticBLAST
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ElasticBLAST
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============
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ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective.
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they cannot absolutely commit to act on all issue reports, except critical
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security vulnerabilities.
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## End-user documentation
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End-user documentation
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----------------------
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Please visit https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/
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## How to get ElasticBLAST
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How to get ElasticBLAST
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-----------------------
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Please see instructions here:
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https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/quickstart-aws.html#get-elasticblast
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## How to build ElasticBLAST
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How to build ElasticBLAST
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-------------------------
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`make elastic-blast`
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make elastic-blast
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### Requirements for building ElasticBLAST
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Requirements for building ElasticBLAST
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--------------------------------------
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In addition to the requirements listed in the page below, [AWS Command Line Interface](https://aws.amazon.com/cli/) is required.
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