feat: create docker for ciri2

config/config.yaml

@@ -104,7 +104,7 @@ cutadapt_q: 20
 high_confidence_core_callers: "circExplorer,circExplorer_bwa"
 high_confidence_core_callers_plus_n: 1
 
-ciri_perl_script: "/data/CCBR_Pipeliner/bin/CIRI_v2.0.6/CIRI2.pl"
+ciri_perl_script: "/opt2/CIRI_v2.0.6/CIRI2.pl" # in docker container
 nclscan_dir: "/data/CCBR_Pipeliner/bin/NCLscan-1.7.0"
 circrnafinder_dir: "/data/CCBR_Pipeliner/bin/circRNA_finder-1.2"
 find_circ_dir: "/data/CCBR_Pipeliner/bin/find_circ"
@@ -118,6 +118,7 @@ containers:
   base: "docker://nciccbr/ccbr_ubuntu_base_20.04:v6"
   bowtie1: "docker://nciccbr/charlie_bowtie1:v0.1.0"
   circexplorer: 'docker://nciccbr/ccbr_circexplorer:v1.0'
+  ciri: 'docker://nciccbr/charlie_ciri2:v1'
   clear: "docker://nciccbr/ccbr_clear:latest"
   cutadapt: 'docker://nciccbr/charlie_cutadapt_fqfilter:v1'
   dcc: "docker://nciccbr/charlie_dcc:v0.1.0"

docker/ciri2/Dockerfile

@@ -0,0 +1,24 @@
+FROM nciccbr/ccbr_ubuntu_base_20.04:v6
+
+# build time variables
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+# install CIRI
+WORKDIR /opt2
+RUN wget -O CIRI.zip https://sourceforge.net/projects/ciri/files/CIRI2/CIRI_v2.0.6.zip/download && \
+    unzip CIRI.zip
+ENV PATH="/opt2/CIRI2_v2.0.6/:$PATH"
+
+# Save Dockerfile in the docker
+COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+
+# cleanup
+WORKDIR /data2
+RUN apt-get clean && apt-get purge \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

docker/ciri2/meta.yml

@@ -0,0 +1,4 @@
+dockerhub_namespace: nciccbr
+image_name: charlie_ciri2
+version: v1
+container: "$(dockerhub_namespace)/$(image_name):$(version)"

workflow/rules/findcircrna.smk

@@ -284,7 +284,7 @@ rule ciri:
         script=join(SCRIPTS_DIR, "filter_ciriout.py"),
         randomstr=str(uuid.uuid4()),
     threads: getthreads("ciri")
-    container: config['containers']['base']
+    container: config['containers']['ciri']
     shell:
         """
 set -exo pipefail