Merge pull request #262 from ENCODE-DCC/PIP-1667_fix_conda_conflicts

Pip 1667 fix conda conflicts

Author: leepc12

.circleci/config.yml

@@ -7,7 +7,7 @@ defaults: &defaults
 
 machine_defaults: &machine_defaults
   machine: 
-    image: ubuntu-1604:202007-01
+    image: ubuntu-2004:202010-01
   working_directory: ~/chip-seq-pipeline2
 
 make_tag: &make_tag
@@ -22,21 +22,11 @@ commands:
       - run:
           command: |
             sudo apt-get update && sudo apt-get install software-properties-common git wget curl -y
+            sudo apt-get install -y software-properties-common git wget curl python3 python3-pip default-jre
 
-            # install java 11
-            sudo add-apt-repository ppa:openjdk-r/ppa -y
-            sudo apt-get update && sudo apt-get install openjdk-11-jdk -y
-            # automatically set 11 as default java
-            sudo update-java-alternatives -a
-
-            sudo add-apt-repository ppa:deadsnakes/ppa -y
-            sudo apt-get update && sudo apt-get install python3.6 -y
-            sudo wget --no-check-certificate https://bootstrap.pypa.io/get-pip.py
-            sudo python3.6 get-pip.py
-            sudo ln -s /usr/bin/python3.6 /usr/local/bin/python3
-
-            pip3 install --upgrade pip
-            pip3 install caper google-cloud-storage
+            sudo python3 -m pip install --upgrade pip
+            sudo pip3 install PyYAML --ignore-installed
+            sudo pip3 install caper google-cloud-storage
 
   run_workflow_test:
     description: "Run workflow test. This requires an env var INPUT as input JSON's basename."

chip.wdl

@@ -7,10 +7,10 @@ struct RuntimeEnvironment {
 }
 
 workflow chip {
-    String pipeline_ver = 'v2.1.3'
+    String pipeline_ver = 'v2.1.4'
 
     meta {
-        version: 'v2.1.3'
+        version: 'v2.1.4'
 
         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:v2.1.3'
-        default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.3.sif'
+        default_docker: 'encodedcc/chip-seq-pipeline:v2.1.4'
+        default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.4.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:v2.1.3'
-        String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.3.sif'
+        String docker = 'encodedcc/chip-seq-pipeline:v2.1.4'
+        String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/chip-seq-pipeline_v2.1.4.sif'
         String conda = 'encode-chip-seq-pipeline'
         String conda_macs2 = 'encode-chip-seq-pipeline-macs2'
         String conda_spp = 'encode-chip-seq-pipeline-spp'

scripts/install_conda_env.sh

@@ -3,13 +3,21 @@ set -e  # Stop on error
 
 SH_SCRIPT_DIR=$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)
 
-echo "** Installing pipeline's Conda environments..."
+echo "$(date): Installing pipeline's Conda environments..."
+
 conda create -n encode-chip-seq-pipeline --file ${SH_SCRIPT_DIR}/requirements.txt \
   --override-channels -c bioconda -c defaults -y
+
 conda create -n encode-chip-seq-pipeline-macs2 --file ${SH_SCRIPT_DIR}/requirements.macs2.txt \
   --override-channels -c bioconda -c defaults -y
+
 conda create -n encode-chip-seq-pipeline-spp --file ${SH_SCRIPT_DIR}/requirements.spp.txt \
   --override-channels -c r -c bioconda -c defaults -y
-echo "** Done."
+
+# adhoc fix for https://github.com/ENCODE-DCC/chip-seq-pipeline2/issues/259
+# force-install readline 6.2 from conda-forge (ignoring dependencies)
+conda install -n encode-chip-seq-pipeline-spp --no-deps --no-update-deps -y readline==6.2 -c conda-forge
+
+echo "$(date): Done successfully."
 
 bash ${SH_SCRIPT_DIR}/update_conda_env.sh

scripts/update_conda_env.sh

@@ -11,10 +11,10 @@ PIPELINE_CONDA_ENVS=(
 )
 chmod u+rx ${SRC_DIR}/*.py
 
-echo "** Updating WDL task wrappers on each Conda environment..."
+echo "$(date): Updating WDL task wrappers on each Conda environment..."
 for PIPELINE_CONDA_ENV in "${PIPELINE_CONDA_ENVS[@]}"
 do	
   CONDA_BIN=$(dirname $(conda run -n ${PIPELINE_CONDA_ENV} which python))
-  echo -e "** Transferring WDL task wrappers to ${CONDA_BIN}..."
+  echo -e "$(date): Transferring WDL task wrappers to ${CONDA_BIN}..."
   cp -f ${SRC_DIR}/*.py ${CONDA_BIN}/
 done