Small bugfix + prepare for Docker update

- Fixes #1 (thanks @suare012!)
- Updates dockerfiles
- Adds environment.yml for easier conda installation

Dockerfile

@@ -2,32 +2,31 @@ FROM conda/miniconda3
 
 RUN apt-get update && apt-get install -y git wget
 
-RUN conda create --name bigscape
-#RUN source activate bigscape
-RUN [ "/bin/bash", "-c","source activate bigscape"]
-RUN conda install -y \
- 	numpy \  
-	scipy \ 
-	scikit-learn 
-
-RUN conda install -c bioconda hmmer biopython fasttree
-RUN conda install -c anaconda networkx
-
+SHELL ["/bin/bash", "-c"]
 WORKDIR /usr/src
-## Cloning BiG-SCAPE
-RUN git clone https://git.wur.nl/medema-group/BiG-SCAPE.git
 
-## geting Pfam
-RUN wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/Pfam-A.hmm.gz
-#ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz.
-RUN gunzip Pfam-A.hmm.gz && hmmpress Pfam-A.hmm && mv Pfam-A.* /usr/src/BiG-SCAPE/.
+# Cloning BiG-SCAPE
+RUN git clone https://git.wur.nl/medema-group/BiG-SCAPE.git
 
-RUN chmod +x /usr/src/BiG-SCAPE/*py  
-RUN chmod 777 /home  
+# Create conda environment
+RUN conda env create -f /usr/src/BiG-SCAPE/environment.yml
+RUN echo "source activate bigscape" > ~/.bashrc
+ENV PATH /usr/local/envs/bigscape/bin:$PATH
 ENV PATH /usr/src/BiG-SCAPE:$PATH
+
+RUN cd BiG-SCAPE \
+ && wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/Pfam-A.hmm.gz \
+ && gunzip Pfam-A.hmm.gz \
+ && source activate bigscape \
+ && hmmpress Pfam-A.hmm \
+ && chmod +x /usr/src/BiG-SCAPE/*py \
+ && chmod a+w /usr/src/BiG-SCAPE/domains_color_file.tsv \
+ && chmod 777 /home
+
 USER 1000:1000
 RUN mkdir /home/input /home/output
 WORKDIR /home
+ENV LANG C.UTF-8
+ENV LC_ALL C.UTF-8
 ENTRYPOINT ["bigscape.py"]
 CMD ["--help"]
-

bigscape.py

@@ -1922,7 +1922,7 @@ def clusterJsonBatch(bgcs, pathBase, className, matrix, pos_alignments, cutoffs=
         with open(os.path.join(module_html_path, "bs_data.js"), "w") as bs_data_js:
             bs_data_js.write("var bs_data={};\n".format(json.dumps(bs_data, indent=4, separators=(',', ':'), sort_keys=True)))
             bs_data_js.write("dataLoaded('bs_data');\n")
-        shutil.copy(os.path.join(os.path.realpath(os.path.dirname(__file__)), "html_template", "index_html"), os.path.join(module_html_path, "index.html"))
+        shutil.copy(os.path.join(os.path.dirname(os.path.realpath(__file__)), "html_template", "index_html"), os.path.join(module_html_path, "index.html"))
 
         ## Write bgc_networks.js
         with open(os.path.join(module_html_path, "bs_networks.js"), "w") as bs_networks_js:
@@ -2101,7 +2101,7 @@ def CMD_parser():
                         domain_whitelist.txt file", default=False,
                         action="store_true")
 
-    parser.add_argument("--version", action="version", version="%(prog)s 20190604")
+    parser.add_argument("--version", action="version", version="%(prog)s 20191011")
 
     return parser.parse_args()
 
@@ -2846,7 +2846,7 @@ if __name__=="__main__":
     create_directory(network_files_folder, "Network Files", False)
 
     # copy html templates
-    dir_util.copy_tree(os.path.join(os.path.realpath(os.path.dirname(__file__)), "html_template", "output"), output_folder)
+    dir_util.copy_tree(os.path.join(os.path.dirname(os.path.realpath(__file__)), "html_template", "output"), output_folder)
 
     # make a new run folder in the html output & copy the overview_html
     network_html_folder = os.path.join(output_folder, "html_content", "networks", run_name)
@@ -2855,7 +2855,7 @@ if __name__=="__main__":
     for cutoff in cutoff_list:
         network_html_folder_cutoff = "{}_c{:.2f}".format(network_html_folder, cutoff)
         create_directory(network_html_folder_cutoff, "Network HTML Files", False)
-        shutil.copy(os.path.join(os.path.realpath(os.path.dirname(__file__)), "html_template", "overview_html"), os.path.join(network_html_folder_cutoff, "overview.html"))
+        shutil.copy(os.path.join(os.path.dirname(os.path.realpath(__file__)), "html_template", "overview_html"), os.path.join(network_html_folder_cutoff, "overview.html"))
         rundata_networks_per_run[network_html_folder_cutoff] = []
         html_subs_per_run[network_html_folder_cutoff] = []
         

environment.yml

+name: bigscape
+channels:
+  - bioconda
+dependencies:
+  - python=3.6
+  - hmmer
+  - biopython
+  - fasttree
+  - numpy
+  - scipy
+  - networkx
+  - scikit-learn=0.19.1

run_bigscape

@@ -5,8 +5,8 @@ if [[ $# -eq 0 ||  $1 == "-h" ||  $1 == "--help" ]]; then
 	--detach=false \
 	--rm \
 	--user=$(id -u):$(id -g) \
-	docker-registry.wur.nl/medema-group/big-scape \
-    	$@
+	docker-registry.wur.nl/medema-group/big-scape:20191010 \
+	$@
 else
 	set -o errexit
 	set -o nounset
@@ -44,14 +44,14 @@ else
 
 	#if [ ${INPUT_FILE} ${OUTPUT_FILE} ]; then
 	if [ ! -z ${INPUT_FILE} ] && [ ! -z ${OUTPUT_FILE} ]; then
-		echo bigscape is running now
+		echo Running BiG-SCAPE
 		docker run \
 	    	--volume ${INPUT_DIR}:${CONTAINER_SRC_DIR}:ro \
 	    	--volume ${OUTPUT_DIR}:${CONTAINER_DST_DIR}:rw \
 	    	--detach=false \
 	    	--rm \
 	    	--user=$(id -u):$(id -g) \
-	    	docker-registry.wur.nl/medema-group/big-scape\
+	    	docker-registry.wur.nl/medema-group/big-scape:20191010 \
 	    	-i ${CONTAINER_SRC_DIR}/${INPUT_FILE} \
 	    	-o ${CONTAINER_DST_DIR}/${OUTPUT_FILE}\
     		$@