Merge pull request #5 from mbhall88/master

Add fall back on SRA if ENA fails

.gitignore

@@ -1,2 +1,3 @@
 *.fastq.gz
 *.json
+.idea

Dockerfile

@@ -0,0 +1,18 @@
+# Lots of help from the following blog posts:
+# https://jcristharif.com/conda-docker-tips.html
+# https://opensourcelibs.com/lib/micromamba-docker
+# https://uwekorn.com/2021/03/01/deploying-conda-environments-in-docker-how-to-do-it-right.html
+FROM mambaorg/micromamba:0.23.3
+
+ENV PYTHONDONTWRITEBYTECODE=true
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/env.yml
+
+RUN micromamba install -y --freeze-installed -n base -f /tmp/env.yml \
+ && micromamba clean -afy \
+ && find /opt/conda/ -follow -type f -name '*.a' -delete \
+ && find /opt/conda/ -follow -type f -name '*.pyc' -delete \
+ && find /opt/conda/ -follow -type f -name '*.js.map' -delete
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER fastq-dl.py /bin/fastq-dl
+ENV PATH "$MAMBA_ROOT_PREFIX/bin:$PATH"

environment.yml

@@ -0,0 +1,10 @@
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - pigz
+ - executor
+ - python >=3.6
+ - sra-tools >=2.9
+ - wget
+ - requests