我正在尝试使用 nextflow 和 docker 运行 python 脚本。我正在使用 dockerfile（如下所示）来创建 docker 映像。Nextflow 脚本有一个简单的 python 脚本启动。问题是当我从 docker 容器中（在交互模式下）运行相同的 python 命令时，它工作正常。但是当我使用带有 docker 容器的 nextflow 启动它时，它会引发错误。
Dockerfile：
#!/usr/local/bin/docker
# -*- version: 20.10.2 -*-
############################################
## MULTI-STAGE CONTAINER CONFIGURATION ##
FROM python:3.6.2
RUN apt-get update && apt-get install -y \
apt-transport-https \
software-properties-common \
unzip \
curl
RUN wget -O- https://apt.corretto.aws/corretto.key | apt-key add - && \
add-apt-repository 'deb https://apt.corretto.aws stable main' && \
apt-get update && \
apt-get install -y java-1.8.0-amazon-corretto-jdk
############################################
## PHEKNOWLATOR (PKT_KG) PROJECT SETTINGS ##
# create needed project directories
WORKDIR /PKT
RUN mkdir -p /PKT
RUN mkdir -p /PKT/resources
RUN mkdir -p /PKT/resources/construction_approach
RUN mkdir -p /PKT/resources/edge_data
RUN mkdir -p /PKT/resources/knowledge_graphs
RUN mkdir -p /PKT/resources/node_data
RUN mkdir -p /PKT/resources/ontologies
RUN mkdir -p /PKT/resources/processed_data
RUN mkdir -p /PKT/resources/relations_data
# copy scripts/files needed to run pkt_kg
COPY pkt_kg /PKT/pkt_kg
COPY Main.py /PKT
COPY setup.py /PKT
COPY README.rst /PKT
COPY resources /PKT/resources
# download and copy needed data
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/edge_source_list.txt && mv edge_source_list.txt resources/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/ontology_source_list.txt && mv ontology_source_list.txt resources/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/resource_info.txt && mv resource_info.txt resources/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/subclass_construction_map.pkl && mv subclass_construction_map.pkl resources/construction_approach/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/PheKnowLator_MergedOntologies.owl && mv PheKnowLator_MergedOntologies.owl resources/knowledge_graphs/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/node_metadata_dict.pkl && mv node_metadata_dict.pkl resources/node_data/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/DISEASE_MONDO_MAP.txt && mv DISEASE_MONDO_MAP.txt resources/processed_data/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/ENSEMBL_GENE_ENTREZ_GENE_MAP.txt && mv ENSEMBL_GENE_ENTREZ_GENE_MAP.txt resources/processed_data/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/ENTREZ_GENE_PRO_ONTOLOGY_MAP.txt && mv ENTREZ_GENE_PRO_ONTOLOGY_MAP.txt resources/processed_data/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/GENE_SYMBOL_ENSEMBL_TRANSCRIPT_MAP.txt && mv GENE_SYMBOL_ENSEMBL_TRANSCRIPT_MAP.txt resources/processed_data/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/HPA_GTEx_TISSUE_CELL_MAP.txt && mv HPA_GTEx_TISSUE_CELL_MAP.txt resources/processed_data/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/MESH_CHEBI_MAP.txt && mv MESH_CHEBI_MAP.txt resources/processed_data/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/PHENOTYPE_HPO_MAP.txt && mv PHENOTYPE_HPO_MAP.txt resources/processed_data/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/STRING_PRO_ONTOLOGY_MAP.txt && mv STRING_PRO_ONTOLOGY_MAP.txt resources/processed_data/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/UNIPROT_ACCESSION_PRO_ONTOLOGY_MAP.txt && mv UNIPROT_ACCESSION_PRO_ONTOLOGY_MAP.txt resources/processed_data/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/INVERSE_RELATIONS.txt && mv INVERSE_RELATIONS.txt resources/relations_data/
RUN curl -O https://storage.googleapis.com/pheknowlator/current_build/data/processed_data/RELATIONS_LABELS.txt && mv RELATIONS_LABELS.txt resources/relations_data/
# install needed python libraries
RUN pip install --upgrade pip setuptools
WORKDIR /PKT
RUN pip install .
############################################
## GLOBAL ENVRIONMENT SETTINGS ##
# copy files needed to run docker container
COPY entrypoint.sh /PKT
# update permissions for all files
RUN chmod -R 755 /PKT
# set OWlTools memory (set to a high value, system will only use available memory)
ENV OWLTOOLS_MEMORY=500g
RUN echo $OWLTOOLS_MEMORY
# set python envrionment encoding
RUN export PYTHONIOENCODING=utf-8
docker 镜像的名称——pkt:2.0.0
Nextflow 脚本：
process run_PKTBaseRun{
echo True
container 'pkt:2.0.0'
publishDir "${params.outDir}", mode: 'copy'
output:
file '*' into output_ch
script:
"""
which python
$PWD
pwd
python /PKT/Main.py --onts /PKT/resources/ontology_source_list.txt \
--edg /PKT/resources/edge_source_list.txt \
--res /PKT/resources/resource_info.txt \
--out /PKT/resources/knowledge_graphs --app subclass --kg full --nde yes --rel yes --owl no
"""
}
现在当我执行：
nextflow run main.nf
然后这会给出与 glob.glob 模块相关的错误，因为它没有列出文件，因为它必须在 docker 容器中。
但是，当我在 docker 容器中简单地运行上面的 python 代码时，它会运行得无懈可击。
> docker run -it pkt:2.0.0 /bin/bash
/PKT> python Main.py --onts resources/ontology_source_list.txt \
--edg resources/edge_source_list.txt \
--res resources/resource_info.txt \
--out resources/knowledge_graphs --app subclass --kg full --nde yes --rel yes --owl no
只有当我将 nextflow 与 docker 结合使用时，此代码才会引发错误。我确保使用的 python 是容器内的。
问题：
- 有什么想法/想法让它发挥作用吗？
有趣的是，
which python --> python inside the container
BUT
的输出，$PWD 的输出 --> nextflow 启动
的目录 pwd 的输出 --> nextflow 的工作目录
- 当我们在nextflow进程中添加容器时，nextflow进程内部的命令（run_PKTBaseRun）不就是从容器workdir运行的吗？所以pwd的值不应该是container workdir的值而不是nextflow workdir的值吗？
所有必需的文件都已添加到 docker 映像中。
- 有没有办法确保 nextflow 过程中脚本部分中的命令从 docker root/workdir 运行？
这个 nextflow 和 docker 的想法是最终使用 awscli 在 aws 批处理上运行它。但是在 aws batch 上运行它之前，要确保它在本地服务器上运行良好。
期待您的建议和想法。谢谢你。