diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 135c14c4ac4c473050f38b8cc32a1963322afcee..e7b412ea2bb30601f889f6711723a9261d133fd2 100644
--- a/astrocyte_pkg.yml
+++ b/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:
diff --git a/building/docker/motif-search/meme-5.5.4/Dockerfile b/building/docker/motif-search/meme-5.5.4/Dockerfile
new file mode 100755
index 0000000000000000000000000000000000000000..ae9197f5b0f80266069dcdbfd5f1388aad21ee10
--- /dev/null
+++ b/building/docker/motif-search/meme-5.5.4/Dockerfile
@@ -0,0 +1,73 @@
+#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"]
diff --git a/building/docker/motif-search/meme-5.5.4/entrypoint.sh b/building/docker/motif-search/meme-5.5.4/entrypoint.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ad47b594d82e570cce89e7ddb82d54e478e41e3b
--- /dev/null
+++ b/building/docker/motif-search/meme-5.5.4/entrypoint.sh
@@ -0,0 +1,23 @@
+#!/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/:$PATH
+
+# Enable strict mode:
+set -euo pipefail
+
+# exec the final command:
+exec "$@"
diff --git a/building/docker/motif-search/meme-5.5.4/meme-5.5.4.tar.gz b/building/docker/motif-search/meme-5.5.4/meme-5.5.4.tar.gz
new file mode 100755
index 0000000000000000000000000000000000000000..ffe3f5b59e25aa752207ddafa6084ebe0ab6be62
Binary files /dev/null and b/building/docker/motif-search/meme-5.5.4/meme-5.5.4.tar.gz differ
diff --git a/workflow/configs/biohpc.config b/workflow/configs/biohpc.config
index dd490f2d20d53d4135bccce471727a7b6f8e654e..aee07e3cb944189506a2a827a6f580ec6486fc47 100644
--- a/workflow/configs/biohpc.config
+++ b/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 {
diff --git a/workflow/scripts/motif_search.py b/workflow/scripts/motif_search.py
index ffa0939edad4dab3d8865ea0ea4acc47c7f04533..4544a732198b7dc3bdf08a45c6337838aed4ad03 100755
--- a/workflow/scripts/motif_search.py
+++ b/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)