Updated Docker folder

Docker/CiDDER/Dockerfile

@@ -0,0 +1,24 @@
+FROM continuumio/miniconda3
+LABEL maintainer="Rauf Salamzade - Kalan Lab, UW-Madison"
+
+WORKDIR /usr/src
+SHELL ["/bin/bash", "-c"]
+
+RUN apt-get update && apt-get install -y git wget gcc
+RUN conda install -n base conda-libmamba-solver
+RUN conda config --set solver libmamba
+RUN conda create -p /usr/src/skder_conda_env/ -c conda-forge -c bioconda skder
+
+# Set env variables and download minimal databases (MIBiG v3.1 + PGAP HMMs)
+ENV PATH /usr/src/skder_conda_env/bin:$PATH
+
+# chmod 777 /home changes the permissions of the /home directory
+RUN chmod 777 /home
+USER 1000:1000
+RUN mkdir -p /home/input /home/output
+WORKDIR /home
+ENV LANG C.UTF-8
+ENV LC_ALL C.UTF-8
+
+ENTRYPOINT ["cidder"]
+CMD ["--help"]

Docker/CiDDER/run_cidder

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+#!/bin/bash
+
+# AUTHOR: Rauf Salamzade
+# AFFILIATION: Kalan Lab, UW-Madison
+# run_cidder.sh
+
+# function to determine absolute paths taken from peterh's respone on StackOverflow:
+# https://stackoverflow.com/questions/3915040/how-to-obtain-the-absolute-path-of-a-file-via-shell-bash-zsh-sh
+get_abs_filename() {
+  # $1 : relative filename
+  filename=$1
+  parentdir=$(dirname "${filename}")
+
+  if [ -d "${filename}" ]; then
+      echo "$(cd "${filename}" && pwd)"
+  elif [ -d "${parentdir}" ]; then
+    echo "$(cd "${parentdir}" && pwd)/$(basename "${filename}")"
+  fi
+}
+
+## The following is also adapted from analogous file from BIG-SCAPE
+if [[ $# -eq 0 || $1 == "-h" || $1 == "--help" || $1 == "-v" || $1 == "--version" ]]; then
+        docker pull raufs/cidder:latest
+        docker run \
+        --detach=false \
+        --rm \
+        --user=$(id -u):$(id -g) \
+        raufs/cidder:latest \
+
+else
+
+        set -o errexit
+        set -o nounset
+
+        # Links within the container
+        readonly CONTAINER_INPUT_DIR=/home/input
+        readonly CONTAINER_OUTPUT_DIR=/home/output
+
+        # variables for updating/input paths to account for Docker mounting
+
+        DOCKER_VOLUME_ARGS=""
+        EASY_ARGS=""
+        OUTPUT_PARENT_DIR="NA"
+        while [[ ! $# -eq 0 ]]; do
+                if [[ "$1" == '-g' || "$1" == '--genomes' ]]; then
+                        shift
+                        ABS_VALUE=$(get_abs_filename $1)
+                        INPUT_DIR=$(basename $ABS_VALUE)
+                        INPUT_PARENT_DIR=$(dirname $ABS_VALUE)
+                        EASY_ARGS+="-g $CONTAINER_INPUT_DIR/$INPUT_DIR/ "
+                        DOCKER_VOLUME_ARGS+="--volume $INPUT_PARENT_DIR:$CONTAINER_INPUT_DIR:ro "
+                        shift
+                elif [[ "$1" == '-o' || "$1" == '--output-directory' ]]; then
+                        shift
+                        ABS_VALUE=$(get_abs_filename $1)
+                        OUTPUT_DIR=$(basename $ABS_VALUE)
+                        OUTPUT_PARENT_DIR=$(dirname $ABS_VALUE)
+                        EASY_ARGS+="-o $CONTAINER_OUTPUT_DIR/$OUTPUT_DIR/ "
+                        DOCKER_VOLUME_ARGS+="--volume $OUTPUT_PARENT_DIR:$CONTAINER_OUTPUT_DIR:rw "
+                        shift       
+                elif [[ "$1" == '-gd' || "$1" == '--genomad-database' ]]; then
+                        shift
+                        ABS_VALUE=$(get_abs_filename $1)
+                        OUTPUT_DIR=$(basename $ABS_VALUE)
+                        OUTPUT_PARENT_DIR=$(dirname $ABS_VALUE)
+                        EASY_ARGS+="-o $CONTAINER_OUTPUT_DIR/$OUTPUT_DIR/ "
+                        DOCKER_VOLUME_ARGS+="--volume $OUTPUT_PARENT_DIR:$CONTAINER_OUTPUT_DIR:rw "
+                        shift
+                else
+                        EASY_ARGS+="$1 "
+                        shift
+                fi
+            done
+
+        if [[ ! -d ${OUTPUT_PARENT_DIR} && $OUTPUT_PARENT_DIR != "NA" ]]; then
+                mkdir ${OUTPUT_PARENT_DIR}
+        fi
+
+        echo ${EASY_ARGS}
+        # run workflow
+        docker pull raufs/cidder:latest
+        docker run ${DOCKER_VOLUME_ARGS} --detach=false --rm --user=$(id -u):$(id -g) raufs/cidder:latest ${EASY_ARGS}
+fi