Merge pull request #33 from rpetit3/master

Added Dockerfile to set up dependencies for MetaSUB_CAP

.gitignore

@@ -0,0 +1,38 @@
+*~
+
+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+__pycache__
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject

Dockerfile

@@ -0,0 +1,40 @@
+FROM continuumio/miniconda3
+
+
+
+RUN apt-get update \
+    && apt-get install -y locales git python3-dev python3-pip libyaml-dev \
+    && rm -rf /var/lib/apt/lists/* \
+    && localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8 \
+    && useradd -ms /bin/bash metasub
+
+ENV LC_ALL C.UTF-8
+ENV LANG C.UTF-8
+
+ADD cap_env.yml /tmp/environment.yml
+WORKDIR /home/metasub
+RUN conda env create -f=/tmp/environment.yml
+
+RUN mkdir /opt/metasub/ \
+    && cd /opt/metasub/
+
+ENTRYPOINT [ "/bin/bash", "-c" ]
+RUN /bin/bash -c "source activate cap \
+    && pip install --ignore-installed PyYAML moduleultra==0.1.5"
+
+
+USER metasub
+RUN cd /home/metasub \
+    && /bin/bash -c "source activate cap \
+    && mkdir base_repo \
+    && mkdir repo \
+    && cd /home/metasub/base_repo \
+    && moduleultra init \
+    && echo y | moduleultra install https://github.com/MetaSUB/MetaSUB_QC_Pipeline.git \
+    && echo y | moduleultra install https://github.com/MetaSUB/MetaSUB_CAP \
+    && moduleultra add pipeline metasub_cap \
+    && moduleultra add pipeline metasub_qc_cap"
+
+
+WORKDIR /home/metasub/repo
+RUN /bin/bash -c "source activate cap"

README.rst

@@ -92,6 +92,16 @@ Most cluster systems will need a custom submit script. You can set a default scr
    
    moduleultra config cluster_submit /path/to/submit_script
 
+
+Running with Docker
+-------------------
+
+To start a shell in the docker machine use the following command:
+
+.. code-block:: bash
+
+   docker run --rm -it -v $PWD:/home/metasub/repo metasub_cap:latest /bin/bash -c "source activate cap"
+
 Adding Modules
 --------------
 

cap_env.yml

@@ -0,0 +1,18 @@
+name: cap
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+  - maxibor
+dependencies:
+  - samtools
+  - snakemake==5.3.0
+  - bracken
+  - krakenhll
+  - mash
+  - diamond==0.8.36
+  - bowtie2
+  - adapterremoval2
+  - pip:
+    - humann2
+