----> Dependances

RUN yum -y update; yum clean all
RUN yum -y install curl wget fetch perl bzip2 make; yum clean all

# GNU parallel
RUN (wget -O - pi.dk/3 || curl pi.dk/3/ || fetch -o - pi.dk/3) | bash
RUN echo 'will cite' | parallel --citation &> /dev/null || true

----> Preparation
! Make sure that files (num = 4) do not have empty records !

##### KEGG pathways downloading
RUN mkdir pathways

# downloading list of names of pathways
RUN curl -s http://rest.kegg.jp/list/module | cut -f1 | cut -c 4- > pathways/list_pathways.txt

# taking DEFINITION file with pathway from KEGG file
# saving in format: <name:pathway>
RUN parallel -k echo -n '{}:' ';' curl -s http://rest.kegg.jp/get/{} '|' grep ^DEFINITION '|' cut -c 13- :::: pathways/list_pathways.txt > pathways/all_pathways.txt
    # OR
    # cat pathways/list_pathways.txt | while read line; do echo "$line:" && curl -s http://rest.kegg.jp/get/$line | grep ^DEFINITION | cut -c 13-; done > pathways/all_pathways.txt
# taking NAME
RUN parallel -k echo -n '{}:' ';' curl -s http://rest.kegg.jp/get/{} '|' grep ^NAME '|' cut -c 13- :::: pathways/list_pathways.txt > pathways/all_pathways_names.txt
# taking CLASS
RUN parallel -k echo -n '{}:' ';' curl -s http://rest.kegg.jp/get/{} '|' grep ^CLASS '|' cut -c 13- :::: pathways/list_pathways.txt > pathways/all_pathways_class.txt


##### Create a Graph for each pathway
ADD KEGG_pathways/make_graphs.py .
RUN python make_graphs.py -i pathways/all_pathways.txt


