Merge pull request #26 from EBI-Metagenomics/develop

Removed Aspera, added boto3 + FIRE and some refactoring

.github/workflows/test.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v2
@@ -22,8 +22,6 @@ jobs:
       - name: Install Dependencies
         run: |
           pip install .[test]
-          # Aspera installation #
-          . install-aspera.sh
       - name: 🧪 - Testing
         run: |
           pytest -v

Containerfile

@@ -1,21 +1,22 @@
-FROM python:3.9-slim
+FROM mambaorg/micromamba:1.5.8
 
 LABEL maintainer="Microbiome Informatics"
-LABEL version="0.9.0"
-LABEL description="EBI Fetch Tool Docker Image."
+LABEL version="1.0.0"
+LABEL description="EBI Fetch Tool."
 
-# We need curl to download aspera and ps for nextflow monitoring
-ENV DEBIAN_FRONTEND=noninteractive
+COPY --chown=$MAMBA_USER:$MAMBA_USER conda_environment.yml /tmp/env.yaml
 
-RUN apt update && apt install -y curl procps && rm -rf /var/lib/apt/lists/*
+RUN micromamba install -y -n base -f /tmp/env.yaml && \
+    micromamba clean --all --yes
 
-COPY . .
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
-RUN pip install --no-cache-dir .
+ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
 
-# Aspera is an IBM library for data sharing
-RUN ./install-aspera.sh
+COPY --chown=$MAMBA_USER:$MAMBA_USER . /opt/fetch-tool-src
 
-RUN export PATH=$PATH:/aspera-cli/cli/bin
+WORKDIR /opt/fetch-tool-src
 
-CMD [ fetch-read-tool ]
+RUN pip install . --no-cache-dir
+
+ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]

README.md

@@ -35,19 +35,12 @@ pre-commit will run a set of pre-configured tools before allowing you to commit
 
 This repo uses [pytest](https://docs.pytest.org).
 
-It requires the aspera cli installed in the default location (`install-aspera.sh` with no parameters).
-
-To run the test suite:
-```bash
-pytest
-```
-
 ## Install fetch tool
 
 ### Using Conda
 
 ```bash
-$ conda create -q -n fetch_tool python=3.8
+$ conda create -q -n fetch_tool python=3.10
 $ conda activate fetch_tool
 ```
 
@@ -60,33 +53,20 @@ $ pip install fetch-tool
 Install from the git repo
 
 ```bash
-$ pip install git+ssh://git@github.com/EBI-Metagenomics/fetch_tool.git
+$ pip install https://github.com/EBI-Metagenomics/fetch_tool/archive/master.zip
 ```
 
-#### Configuration file
+#### Configuration options
+
+The tool has a number of options, with sensible defaults for the most common use cases.
 
 Setup the configuration file, the template [fetchdata-config-template.json](config/fetchdata-config-template.json) for the configuration file.
 
 The required fields are:
-- For Aspera
-  - aspera_bin (the path to ascp, usually in the aspera installation under /cli/bin)
-  - aspera_cert (the path to the ascp provided cert, usually in the aspera installation under /cli/etc/asperaweb_id_dsa.openssh)
-- To pull private ENA data
+-
   - ena_api_user
   - ena_api_password
 
-### Install Aspera
-
-## Install
-
-Run the `install-aspera.sh` command here, it has only one optional parameter (the installation folder).
-
-```bash
-./install path/to/installation-i-want
-```
-
-Otherwise it will install it in $PWD/aspera-cli
-
 ## Fetch read files (amplicon and WGS data)
 
 ### Usage
@@ -122,7 +102,7 @@ optional arguments:
 Download amplicon study:
 
 ```bash
-$ fetch-read-tool -p SRP062869 -c fetchdata-config-local.json -v -d /home/<user>/temp/
+$ fetch-read-tool -p SRP062869 -v -d /home/<user>/temp/
 ```
 
 ## Fetch assembly files
@@ -163,5 +143,5 @@ optional arguments:
 Download assembly study:
 
 ```bash
-$ fetch-assembly-tool -p ERP111288 -c fetchdata-config-local.json -v -d /home/<user>/temp/
+$ fetch-assembly-tool -p ERP111288 -v -d /home/<user>/temp/
 ```

conda_environment.yml

@@ -0,0 +1,16 @@
+name: fetchtool
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.10
+  - pip=24.0
+  - conda-forge::procps-ng=4.0.4
+  - conda-forge::wget=1.21.4
+  - conda-forge::rsync=3.3.0
+  - conda-forge::pandas=2.2.2
+  - pip:
+    - requests==2.32.3
+    - flufl.lock==8.1.0
+    - boto3==1.34.134

config/testing.json

@@ -1,7 +1,5 @@
 {
   "url_max_attempts": 5,
   "ena_api_username": "",
-  "ena_api_password": "",
-  "aspera_bin": "",
-  "aspera_cert": ""
+  "ena_api_password": ""
 }

fetchtool/__init__.py

@@ -1 +1 @@
-__version__ = "0.9.0"
+__version__ = "1.0.0"