Merge pull request #304 from ENCODE-DCC/dev

v2.2.2

Author: leepc12

.circleci/config.yml

@@ -66,7 +66,7 @@ jobs:
           name: build image
           command: |
             source ${BASH_ENV}
-            export DOCKER_CACHE_TAG=v2.1.0
+            export DOCKER_CACHE_TAG="WRN-503_ccd006dd-a484-4337-9754-fdf3d5b6d7b9"
             echo "pulling ${DOCKER_CACHE_TAG}!"
             docker pull encodedcc/chip-seq-pipeline:${DOCKER_CACHE_TAG}
             docker login -u=${DOCKERHUB_USER} -p=${DOCKERHUB_PASS}

chip.wdl

@@ -7,10 +7,10 @@ struct RuntimeEnvironment {
 }
 
 workflow chip {
-    String pipeline_ver = 'v2.2.1'
+    String pipeline_ver = 'v2.2.2'
 
     meta {
-        version: 'v2.2.1'
+        version: 'v2.2.2'
 
         author: 'Jin wook Lee'
         email: '[email protected]'
@@ -19,8 +19,8 @@ workflow chip {
 
         specification_document: 'https://docs.google.com/document/d/1lG_Rd7fnYgRpSIqrIfuVlAz2dW1VaSQThzk836Db99c/edit?usp=sharing'
 
-        default_docker: 'encodedcc/chip-seq-pipeline:v2.2.1'
-        default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.2.1.sif'
+        default_docker: 'encodedcc/chip-seq-pipeline:v2.2.2'
+        default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.2.2.sif'
         croo_out_def: 'https://storage.googleapis.com/encode-pipeline-output-definition/chip.croo.v5.json'
 
         parameter_group: {
@@ -71,8 +71,8 @@ workflow chip {
     }
     input {
         # group: runtime_environment
-        String docker = 'encodedcc/chip-seq-pipeline:v2.2.1'
-        String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.2.1.sif'
+        String docker = 'encodedcc/chip-seq-pipeline:v2.2.2'
+        String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.2.2.sif'
         String conda = 'encd-chip'
         String conda_macs2 = 'encd-chip-macs2'
         String conda_spp = 'encd-chip-spp'

dev/docker_image/Dockerfile

@@ -30,7 +30,7 @@ ENV PATH="/software:${PATH}"
 RUN wget https://github.com/openssl/openssl/archive/OpenSSL_1_0_2t.tar.gz && tar zxvf OpenSSL_1_0_2t.tar.gz && cd openssl-OpenSSL_1_0_2t/ && ./config && make && make install && cd ../ && rm -rf openssl-OpenSSL_1_0_2t* && rm /usr/bin/openssl && ln -s /usr/local/ssl/bin/openssl /usr/bin/openssl
 
 # Install system/math python packages (python3)
-RUN pip3 install --no-cache-dir jsondiff==1.1.1 common python-dateutil cython pandas==0.25.1 jinja2==2.10.1 matplotlib==3.1.1
+RUN pip3 install --no-cache-dir jsondiff==1.1.1 common python-dateutil pandas==0.25.1 jinja2==2.10.1 matplotlib==3.1.1
 
 # Install genomic python package (python3)
 RUN pip3 install --no-cache-dir pyBigwig==0.3.13 cutadapt==2.5 pyfaidx==0.5.5.2 pybedtools==0.8.0 pysam==0.15.3 deeptools==3.3.1
@@ -40,9 +40,10 @@ RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.r-project.org'; opt
     Rscript -e "install.packages('snow')" && \
     Rscript -e "install.packages('snowfall')" && \
     Rscript -e "install.packages('bitops')" && \
-    Rscript -e "install.packages('caTools')" && \
     Rscript -e "install.packages('Rcpp')"
 
+RUN wget "https://cran.r-project.org/src/contrib/Archive/caTools/caTools_1.17.1.4.tar.gz" && R CMD INSTALL caTools_1.17.1.4.tar.gz && rm -f caTools_1.17.1.4.tar.gz
+
 # Install bioconductor and Rsamtools which is required by spp package
 RUN Rscript -e "source('http://bioconductor.org/biocLite.R'); biocLite('Rsamtools')"
 
@@ -94,13 +95,16 @@ RUN git clone --branch 2.0.4.2 --single-branch https://github.com/kundajelab/idr
 RUN pip2 install --no-cache-dir numpy scipy matplotlib==2.2.4 bx-python==0.8.2 biopython==1.76
 RUN pip3 install --no-cache-dir biopython==1.76
 
-# Install genomic python packages (python2)
-RUN pip2 install --no-cache-dir metaseq==0.5.6
-
 # Install MACS2 (python3)
-RUN pip3 install --no-cache-dir Cython
+RUN pip3 install --no-cache-dir Cython==0.29.0
 RUN pip3 install --no-cache-dir macs2==2.2.4
 
+# Install genomic python packages (python2)
+RUN pip2 install --no-cache-dir Cython==0.29.0 versioneer setuptools==44.1.1
+RUN pip2 install --no-cache-dir pybedtools==0.6.9
+RUN pip2 install --no-cache-dir metaseq==0.5.6
+RUN pip2 install --no-cache-dir gffutils==0.10.1
+
 # Install UCSC tools (v377)
 RUN git clone https://github.com/ENCODE-DCC/kentUtils_bin_v377
 ENV PATH=${PATH}:/software/kentUtils_bin_v377/bin