Dockerization

+nohup.out
+log_of_the_run.sh
+results/
+logs/
+data/
+esl*
+.vscode/
+__pycache__/
+.git/
+errors.txt
+known_issues.txt
+known_issues_reasons.txt
+kill_rnanet.sh
+Dockerfile
+LICENSE
+README.md
+automate.sh
+build_docker_image.sh
\ No newline at end of file

+FROM alpine:latest
+COPY . /RNANet
+WORKDIR /
+RUN apk update && apk add --no-cache \
+        curl \
+        freetype-dev \
+        gcc g++ \
+        linux-headers \
+        lapack-dev \
+        make \
+        musl-dev \
+        openblas-dev \
+        python3 python3-dev py3-pip py3-six py3-wheel \
+        py3-matplotlib py3-requests py3-scipy py3-setproctitle py3-sqlalchemy py3-tqdm \
+        sqlite \
+    \
+    && python3 -m pip install biopython==1.76 pandas psutil pymysql && \
+    \
+    wget -q -O /etc/apk/keys/sgerrand.rsa.pub https://alpine-pkgs.sgerrand.com/sgerrand.rsa.pub && \
+    wget https://github.com/sgerrand/alpine-pkg-glibc/releases/download/2.32-r0/glibc-2.32-r0.apk && \
+    apk add glibc-2.32-r0.apk && \
+    rm glibc-2.32-r0.apk && \
+    \
+    mkdir /3D && mkdir /sequences && \
+    \
+    mv /RNANet/x3dna-dssr /usr/local/bin/x3dna-dssr && chmod +x /usr/local/bin/x3dna-dssr && \
+    \
+    curl -SL http://eddylab.org/infernal/infernal-1.1.3.tar.gz | tar xz  && cd infernal-1.1.3 && \
+    ./configure && make -j 16 && make install && cd easel && make install && cd / && \
+    \
+    curl -SL https://github.com/epruesse/SINA/releases/download/v1.7.1/sina-1.7.1-linux.tar.gz | tar xz && mv sina-1.7.1-linux /sina && \
+    ln -s /sina/bin/sina /usr/local/bin/sina && \
+    \
+    rm -rf /infernal-1.1.3 && \
+    \
+    apk del openblas-dev gcc g++ gfortran binutils \
+        curl \
+        linux-headers \
+        make \
+        musl-dev \
+        py3-pip py3-wheel \
+        freetype-dev zlib-dev
+VOLUME ["/3D", "/sequences", "/runDir"]
+WORKDIR /runDir
+ENTRYPOINT ["/RNANet/RNAnet.py", "--3d-folder", "/3D", "--seq-folder", "/sequences" ]
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+#!/bin/bash
+
+# echo "WARNING: The purpose of this file is to document how the docker image was built.";
+# echo "You cannot execute it directly, because of licensing reasons. Please get your own";
+# echo "DSSR 2.0 executable at http://innovation.columbia.edu/technologies/CU20391";
+# echo "and place it in this folder.";
+# exit 0;
+
+THISDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+
+####################################################### Dependencies ##############################################################
+
+# The $THISDIR folder is supposed to contain the x3dna-dssr executable
+cp `which x3dna-dssr` $THISDIR
+
+######################################################## Build Docker image ######################################################
+# Execute the Dockerfile and build the image
+docker build -t persalteas/rnanet .
+
+############################################################## Cleaning ##########################################################
+rm x3dna-dssr
+
+# to run, use something like:
+# docker run -v /home/persalteas/Data/RNA/3D/:/3D -v /home/persalteas/Data/RNA/sequences/:/sequences -v /home/persalteas/labo/:/runDir persalteas/rnanet [ additional options here ]
+# Without additional options, this runs a standard pass with known issues support, log output, and no statistics. The default resolution threshold is 4.0 Angstroms.
\ No newline at end of file

@@ -329,9 +329,7 @@ def parallel_stats_pairs(f):
         with sqlite3.connect(runDir + "/results/RNANet.db") as conn:
         with sqlite3.connect(runDir + "/results/RNANet.db") as conn:
             # Get comma separated lists of basepairs per nucleotide
             # Get comma separated lists of basepairs per nucleotide
             interactions = pd.DataFrame(
             interactions = pd.DataFrame(
-                            sql_ask_database(conn, 
-                                            f"SELECT nt_code as nt1, index_chain, paired, pair_type_LW FROM (SELECT chain_id FROM chain WHERE chain_id='{cid}') NATURAL JOIN nucleotide;",
-                                            warn_every=0), 
+                            sql_ask_database(conn, f"SELECT nt_code as nt1, index_chain, paired, pair_type_LW FROM nucleotide WHERE chain_id='{cid}';"), 
                             columns = ["nt1", "index_chain", "paired", "pair_type_LW"]
                             columns = ["nt1", "index_chain", "paired", "pair_type_LW"]
                            )
                            )
         # expand the comma-separated lists in real lists
         # expand the comma-separated lists in real lists