Added new Docker file for motif search (named meme-5.5.4) installed from...

Added new Docker file for motif search (named meme-5.5.4) installed from source, with all the necessary changes to use the new container for motif search. Updated the command line arguments for meme-chip to use v5.x syntax.

astrocyte_pkg.yml

@@ -66,7 +66,7 @@ workflow_containers:
   - docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/r:3.3.2
   - docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/python:3.6.1
   - docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/chipseq:1.0.0
-  - docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/motif-search:meme-4.11.1
+  - docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/motif-search:meme-5.5.4
 
 # A list of parameters used by the workflow, defining how to present them,
 # options etc in the web interface. For each parameter:

building/docker/motif-search/meme-5.5.4/Dockerfile

+#FROM ubuntu:20.04
+FROM continuumio/miniconda3:24.3.0-0
+
+WORKDIR /motif-search/
+
+ENV DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC
+
+# Environment variables for the campus proxy.
+ENV http_proxy="http://proxy.swmed.edu:3128" \
+    https_proxy="http://proxy.swmed.edu:3128"
+
+COPY ./meme-5.5.4.tar.gz  .
+# RUN wget https://meme-suite.org/meme/meme-software/5.5.4/meme-5.5.4.tar.gz
+RUN tar -zxf ./meme-5.5.4.tar.gz 
+RUN rm meme-5.5.4.tar.gz 
+
+COPY entrypoint.sh . 
+
+RUN apt update \
+    && apt-get install -y --no-install-recommends \
+    wget \
+	build-essential \
+    ca-certificates \
+    curl \
+    imagemagick \
+    libexpat1-dev \
+    libxml2-dev \
+	libxslt1-dev \
+	libgs-dev \
+    libgd-dev \
+	#libexslt1-dev \
+    python3 \
+    zlib1g-dev \
+	perl \
+	libxml-simple-perl \
+	libxml-libxml-perl \
+	libxml-parser-perl \
+	libhtml-template-compiled-perl \
+    libxml-opml-simplegen-perl \
+    libxml-libxml-debugging-perl \
+    && apt-get clean 
+  
+# Install meme-chip
+RUN cd meme-5.5.4 && \
+    ./configure --prefix=/motif-search/meme --with-url="http://meme-suite.org" --enable-build-libxml2 --enable-build-libxslt && \
+    make && \
+    # make test && \
+    make install && \
+	export PATH=/motif-search/meme/bin/:/motif-search/meme/libexec/meme-5.5.4:$PATH && \
+    meme -version && \
+    meme-chip --version && \
+    spamo --version && \
+    centrimo --version && \
+    # apt-get remove -y build-essential libxml2 libxml2-dev libxslt1-dev && \
+    apt-get clean
+
+# Enable the use of bash-specific conda commands in the layer.
+RUN eval "$(conda shell.bash hook)" && \
+    chmod +x entrypoint.sh && \
+    #conda create -y -c bioconda -c conda-forge -c defaults -n motifSearch python=2.7.12 pip=9.0.1 && \
+    conda create -y -c bioconda -c conda-forge -c defaults -n motifSearch python=3.6.1 && \
+	conda activate motifSearch && \
+    python --version && \
+    # Install pandas and numpy.
+    pip install numpy==1.12.1 && \
+    pip install pandas==0.20.1 && \
+    # Install BEDTools 2.26 .0
+    conda install -y --solver=libmamba -c bioconda bedtools=2.26.0 && \
+    bedtools --version && \
+    conda clean -y --all && \
+    conda deactivate 
+
+ENTRYPOINT ["/motif-search/entrypoint.sh"]

building/docker/motif-search/meme-5.5.4/entrypoint.sh

+#!/bin/bash --login
+# The --login ensures the bash configuration is loaded, enabling Conda.
+
+# Temporarily disable strict mode and activate conda:
+# set : Used to set or unset shell attributes (when options are specified, as shown here).
+# -e : Exit on non-zero return status.
+# -u : Treat unset variables and parameters other than special parameters "@" and "*" as an error when performaing parameter expansion.
+# -o : specify an option name. In our case here, we use the "pipefail" option.
+# pipefail : If set, the return value of a pipeline is the value of the last (rightmost) command to exit with a non-zeros status, or zero if all commands in the pipeline exit successfully.
+# Using + rather than - causes these options to be turned off.
+set +euo pipefail
+
+source /opt/conda/etc/profile.d/conda.sh
+
+conda activate motifSearch
+
+export PATH=/motif-search/meme/bin/:$PATH
+
+# Enable strict mode:
+set -euo pipefail
+
+# exec the final command:
+exec "$@"

workflow/configs/biohpc.config

@@ -79,7 +79,7 @@ process {
   }
   withName: motifSearch {
     executor = 'local'
-    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/motif-search:meme-4.11.1'
+    container = 'docker://git.biohpc.swmed.edu:5050/s219741/chipseq-analysis-containerized/motif-search:meme-5.5.4'
     //cpus = 32
   }
   withName: multiqcReport {

workflow/scripts/motif_search.py

@@ -139,8 +139,10 @@ def motif_search(filename, genome, experiment, peak):
         logger.error("bedtools error: %s", err)
 
     # Call memechip
+    #out, err = utils.run_pipe([
+    #    'meme-chip -oc %s -meme-minw 5 -meme-maxw 15 -meme-nmotifs 10 %s -norand' % (out_motif, out_fa)])
     out, err = utils.run_pipe([
-        'meme-chip -oc %s -meme-minw 5 -meme-maxw 15 -meme-nmotifs 10 %s -norand' % (out_motif, out_fa)])
+        'meme-chip -oc %s -minw 5 -maxw 15 -meme-nmotifs 10 %s -meme-norand ' % (out_motif, out_fa)])
     if err:
         logger.error("meme-chip error: %s", err)