Merge pull request #372 from ENCODE-DCC/PIPE-48_fix-broken-conda-dependency

Pipe 48 fix broken conda dependency

Author: leepc12

atac.wdl

@@ -7,10 +7,10 @@ struct RuntimeEnvironment {
 }
 
 workflow atac {
-    String pipeline_ver = 'v2.1.1'
+    String pipeline_ver = 'v2.1.2'
 
     meta {
-        version: 'v2.1.1'
+        version: 'v2.1.2'
 
         author: 'Jin wook Lee'
         email: 'leepc12@gmail.com'
@@ -19,8 +19,8 @@ workflow atac {
 
         specification_document: 'https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit?usp=sharing'
 
-        default_docker: 'encodedcc/atac-seq-pipeline:v2.1.1'
-        default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.1.1.sif'
+        default_docker: 'encodedcc/atac-seq-pipeline:v2.1.2'
+        default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.1.2.sif'
         default_conda: 'encode-atac-seq-pipeline'
         croo_out_def: 'https://storage.googleapis.com/encode-pipeline-output-definition/atac.croo.v5.json'
 
@@ -72,8 +72,8 @@ workflow atac {
     }
     input {
         # group: runtime_environment
-        String docker = 'encodedcc/atac-seq-pipeline:v2.1.1'
-        String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.1.1.sif'
+        String docker = 'encodedcc/atac-seq-pipeline:v2.1.2'
+        String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.1.2.sif'
         String conda = 'encode-atac-seq-pipeline'
         String conda_macs2 = 'encode-atac-seq-pipeline-macs2'
         String conda_spp = 'encode-atac-seq-pipeline-spp'

scripts/install_conda_env.sh

@@ -14,9 +14,12 @@ conda create -n encode-atac-seq-pipeline-macs2 --file ${SH_SCRIPT_DIR}/requireme
 conda create -n encode-atac-seq-pipeline-spp --file ${SH_SCRIPT_DIR}/requirements.spp.txt \
   --override-channels -c r -c bioconda -c defaults -y
 
-# 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-atac-seq-pipeline-spp --no-deps --no-update-deps -y readline==6.2 -c conda-forge
+# adhoc fix for the following issues:
+# - https://github.com/ENCODE-DCC/chip-seq-pipeline2/issues/259
+# - https://github.com/ENCODE-DCC/chip-seq-pipeline2/issues/265
+# force-install readline 6.2, ncurses 5.9 from conda-forge (ignoring dependencies)
+conda install -n encode-atac-seq-pipeline-spp --no-deps --no-update-deps -y \
+  readline==6.2 ncurses==5.9 -c conda-forge
 
 conda create -n encode-atac-seq-pipeline-python2 --file ${SH_SCRIPT_DIR}/requirements.python2.txt \
   --override-channels -c conda-forge -c bioconda -c defaults -y