added dockerfile, updated config to point to new container (#79)

Dockerfile

@@ -0,0 +1,46 @@
+FROM quay.io/hdc-workflows/ubuntu:20.04
+
+# bust cache
+ADD http://date.jsontest.com /etc/builddate
+
+LABEL maintainer "Jared Galloway <[email protected]>" \
+      version "1.1.4" \
+      description "Common PhIP-Seq Workflows"
+
+# install needed tools
+RUN apt-get update --fix-missing -qq && \
+    DEBIAN_FRONTEND=noninteractive \
+    apt-get install -y -q \
+    git \
+    curl \
+    locales \
+    libncurses5-dev  \
+    libncursesw5-dev \
+    build-essential \
+    pkg-config \
+    zlib1g-dev \
+    python3 \
+    python3-pip \ 
+    python3-venv \
+    zip \
+    wget
+
+ENV VIRTUAL_ENV=/opt/venv
+RUN python3 -m venv $VIRTUAL_ENV
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+
+# install phippery
+RUN pip install git+https://github.com/matsengrp/[email protected]
+
+# install pre-build binary Bowtie1.3
+RUN curl -fksSL https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.1/bowtie-1.3.1-linux-x86_64.zip \
+    --output bowtie-1.3.1-linux-x86_64.zip \
+    && unzip bowtie-1.3.1-linux-x86_64.zip \
+    && (cd /usr/bin/ && ln -s /bowtie-1.3.1-linux-x86_64/* ./)
+
+
+# install SAMtools
+RUN curl -fksSL https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 | tar xj && \
+    cd samtools-1.3.1 && \
+    make all all-htslib && make install install-htslib
+

bin/replicate-counts.py

@@ -28,6 +28,7 @@ def replicate_oligo_counts(ds, peptide_oligo_feature="Oligo"):
     Currently, this function only sets the raw counts, in place.
     """
 
+    # TODO remove this code
     # find all value counts greater than 1,
     #pep_anno_table = get_annotation_table(ds, "peptide")
     #oligo_vc = pep_anno_table["Oligo"].value_counts()

nextflow.config

@@ -104,7 +104,7 @@ params{
 process {
 
     // Default for any processes which do not match the selectors below
-    container = 'quay.io/hdc-workflows/phippery:1.2.0'
+    container = 'quay.io/matsengrp/phip-flow:latest'
 
     withName: 'run_edgeR|run_BEER' {
         container = 'quay.io/biocontainers/bioconductor-beer:1.2.0--r42hdfd78af_0'