Release 1.2.0

.github/workflows/build-multi-pex.yml

@@ -7,15 +7,15 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: ["3.8"]
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Build PEX file
@@ -28,7 +28,7 @@ jobs:
       - name: Create tarball
         run: tar -czvf elastic-blast-no-suffix.tar.gz elastic-blast elastic-blast.md5
       - name: Produce downloadable artifact
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: elastic-blast-no-suffix
           path: elastic-blast-no-suffix.tar.gz
@@ -38,16 +38,16 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10"]
 
     steps:
 
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Build PEX file
@@ -60,7 +60,7 @@ jobs:
       - name: Create tarball
         run: tar -czvf elastic-blast${{ matrix.python-version }}.tar.gz elastic-blast${{ matrix.python-version }} elastic-blast${{ matrix.python-version }}.md5
       - name: Produce downloadable artifact
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: elastic-blast-${{ matrix.python-version }}
           path: elastic-blast${{ matrix.python-version }}.tar.gz
@@ -70,21 +70,21 @@ jobs:
     needs: [build-single, build-multiple]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Download artifacts
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
       - name: Display structure of downloaded files
         run: ls -lR
       - name: Create tarball
         run: |
           tar axvf elastic-blast-no-suffix/elastic-blast-no-suffix.tar.gz
-          tar axvf elastic-blast-3.7/elastic-blast3.7.tar.gz
           tar axvf elastic-blast-3.8/elastic-blast3.8.tar.gz
           tar axvf elastic-blast-3.9/elastic-blast3.9.tar.gz
+          tar axvf elastic-blast-3.10/elastic-blast3.10.tar.gz
           rm -fvr elastic-blast-*.tar.gz
-          tar -czvf ~/elastic-blast.tar.gz elastic-blast elastic-blast*md5 elastic-blast3.[789]
+          tar -czvf ~/elastic-blast.tar.gz elastic-blast elastic-blast*md5 elastic-blast3.*
       - name: 'Upload Artifact'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: elastic-blast
           path: ~/elastic-blast.tar.gz

.gitignore

@@ -44,3 +44,4 @@ submit-and-wait-for-results.sh
 aws-docker-login.txt
 elb-run-report.csv
 aws-credentials
+.elb-venv

CITATION.cff

@@ -1,8 +1,8 @@
 cff-version: "1.2.0"
 message: "If you use this software, please cite it using these metadata."
 title: ElasticBLAST
-version: "1.1.0"
-date-released: 2023-05-11
+version: "1.2.0"
+date-released: 2023-11-27
 license: "NCBI Public Domain"
 repository-code: "https://github.com/ncbi/elastic-blast/"
 url: "https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/"

bin/blast-tuner.py

@@ -98,8 +98,10 @@ def main():
         if args.total_query_length:
             query_data = SeqData(args.total_query_length,
                                  sp.get_query_mol_type(args.program))
+
+        # MT mode is only used to inform selection of ElasticBLAST batch-length, memory,
+        # and machine type as the best guess. BLAST+ selects MT mode.
         mt_mode = get_mt_mode(args.program, args.options, db_metadata, query_data)
-        options += f' {mt_mode}'
 
         num_cpus = get_num_cpus(cloud_provider = cloud_provider,
                                 program = args.program,

bin/elastic-blast

@@ -45,7 +45,7 @@ from elastic_blast.config import configure
 from elastic_blast.elb_config import ElasticBlastConfig
 from elastic_blast.constants import ElbCommand
 from elastic_blast.constants import ELB_DFLT_LOGLEVEL, ELB_DFLT_LOGFILE
-from elastic_blast.constants import CFG_CLOUD_PROVIDER, CFG_CP_GCP_PROJECT
+from elastic_blast.constants import CFG_BLAST_RESULTS, CFG_BLAST, ELB_GCS_PREFIX
 
 DESC = r"""This application facilitates running BLAST on large amounts of query sequence data
 on the cloud"""
@@ -75,7 +75,8 @@ def main():
         cfg = configure(args)
         logging.info(f"ElasticBLAST {args.subcommand} {VERSION}")
         logging.info(f'python version: {":".join(sys.version.split())}')
-        if CFG_CP_GCP_PROJECT in cfg[CFG_CLOUD_PROVIDER]:
+        if CFG_BLAST_RESULTS in cfg[CFG_BLAST] and \
+                cfg[CFG_BLAST][CFG_BLAST_RESULTS].startswith(ELB_GCS_PREFIX):
             check_prerequisites()
         else:
             check_auxiliary_versions()
@@ -113,8 +114,8 @@ def reject_string_with_unicode(content: str) -> None:
 
 
 def reject_cli_args_with_unicode(args: List[str]) -> None:
-        for arg in args:
-            reject_string_with_unicode(arg)
+    for arg in args:
+        reject_string_with_unicode(arg)
 
 
 def file_must_exist(path: str) -> str:

docker-blast/Dockerfile

@@ -18,42 +18,26 @@
 #   
 # Please cite NCBI in any work or product based on this material.
 
-FROM ncbi/blast:latest as blast
+FROM ncbi/blast:2.15.0 as blast
 ARG version
 LABEL Description="NCBI BLAST" Vendor="NCBI/NLM/NIH" Version=${version} Maintainer=camacho@ncbi.nlm.nih.gov
 
-FROM google/cloud-sdk:slim
-# FROM resets ARGs, thus repeated ARG instruction
-ARG version
-
 USER root
 WORKDIR /root/
 
 COPY requirements.txt .
-RUN python3 -m pip install --no-cache-dir --upgrade pip && \
-    python3 -m pip install --no-cache-dir -r requirements.txt && \
-    rm -frv requirements.txt
 
 RUN apt-get -y -m update && \
-    apt-get install -y libgomp1 libnet-perl libidn11 libxml-simple-perl libjson-perl perl-doc liblmdb-dev time parallel vmtouch cpanminus curl wget libio-socket-ssl-perl libhtml-parser-perl unzip && \
+    apt-get install -y python3 python3-pip time parallel vmtouch curl wget unzip && \
 	rm -rf /var/lib/apt/lists/*  
 
-RUN mkdir -p /blast/bin /blast/lib
-COPY --from=blast /blast/bin /blast/bin
-COPY --from=blast /blast/lib /blast/lib
-COPY --from=blast /root/edirect /root/edirect
+RUN python3 -m pip install --no-cache-dir --upgrade pip && \
+    python3 -m pip install --no-cache-dir -r requirements.txt && \
+    rm -frv requirements.txt
+
 COPY splitq_download_db_search /blast/bin/
 RUN sed -i -e "s/\$VERSION/$version/" /blast/bin/splitq_download_db_search
 COPY fasta-split /blast/bin/
 
-
-RUN mkdir -p /blast/blastdb /blast/blastdb_custom
-RUN sed -i '$ a BLASTDB=/blast/blastdb:/blast/blastdb_custom' /etc/environment
-ENV BLASTDB /blast/blastdb:/blast/blastdb_custom
-ENV PATH="/root/edirect:/blast/bin:${PATH}"
-
-
-WORKDIR /blast
-
 CMD ["/bin/bash"]
 

docker-blast/Dockerfile-build-from-local-sources

@@ -52,7 +52,6 @@ RUN apt-get -y -m update && \
 
 RUN mkdir -p /blast/bin /blast/lib
 COPY --from=blast /blast/bin /blast/bin
-COPY update_blastdb.pl /blast/bin
 COPY --from=blast /blast/lib /blast/lib
 COPY --from=blast /root/edirect /root/edirect
 COPY splitq_download_db_search /blast/bin/

docker-blast/Makefile

@@ -30,7 +30,7 @@ GCP_IMG?=gcr.io/ncbi-sandbox-blast/${IMG}
 AWS_SERVER?=public.ecr.aws/i6v3i0i9
 AWS_IMG?=${AWS_SERVER}/elasticblast-elb
 AWS_REGION?=us-east-1
-VERSION?=1.2.0
+VERSION?=1.3.1
 
 ifeq (, $(shell which vmtouch 2>/dev/null))
 NOVMTOUCH?=--no-vmtouch
@@ -95,8 +95,8 @@ aws-check:
 
 .PHONY: clean 
 clean:
-	-docker image rm ${IMG}:${VERSION} ${IMG}:latest
-	${RM} -fr .env
+	docker image rm ${IMG}:${VERSION} ${IMG}:latest || true
+	${RM} -r .env
 
 .PHONY: check 
 check:

docker-blast/requirements.txt

@@ -2,4 +2,4 @@ awscli
 filelock
 boto3
 ec2_metadata==2.4.0
-requests==2.25.1
+requests>=2.31.0