如何在docker容器中通过nextflow无缝运行python脚本，而不出现任何与路径或环境相关的问题？

Question

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）创建docker图像。Nextflow脚本有一个简单的python脚本启动。问题是，当我在docker容器中运行相同的python命令时（在交互模式下），它工作得很好。但当我使用nextflow和docker容器启动它时，它会抛出错误

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映像的名称--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，这将给出与glob.glob模块相关的错误，因为它没有列出docker容器中必须列出的文件

然而，当我在docker容器中简单地运行上面的python代码时，它就会毫无表情地运行

> 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，此代码才会抛出错误。 我已经确保使用的python是容器中的python

问题:

1. 有什么想法/想法可以让它工作吗

有趣的是，
哪个python的输出-->；容器中的python
但是，
$PWD的输出-->；从中启动nextflow的目录
pwd的输出-->；nextflow的工作目录

1. 当我们在nextflow进程中添加容器时，nextflow进程（run_PKTBaseRun）中的命令不是从容器workdir运行的？因此pwd的值不应该是容器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

1. 是否有办法确保nextflow进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批处理上运行它之前，需要确保它在本地服务器上正常运行

期待您的建议和想法。多谢各位

Answer 1

尝试转义\$PWD，它将为您提供安装在docker中的nextflow进程workdir。我很好奇你是否用其他方法解决了这个问题

尝试在nextflow进程脚本中运行此脚本

export pdir=\$PWD
echo \$pdir