container versiion -> latest on staging branch

Author: tdudgeon

Dockerfile-dmpk

@@ -16,7 +16,7 @@ ENV PYTHONPATH=/code
 ENV HOME=/code
 WORKDIR ${HOME}
 
-RUN pip install matplotlib==3.7.1 im-data-manager-job-utilities==1.2.0
+RUN pip install numpy==1.26.* matplotlib==3.7.1 im-data-manager-job-utilities==1.2.0
 
 COPY utils.py ./
 COPY dmpk/*.py ./dmpk/

Dockerfile-prep

@@ -16,7 +16,8 @@ ENV HOME=/code
 WORKDIR ${HOME}
 
 # install our requirements. RDKit is present in base container, OBabel is apt installed earlier
-RUN pip install scikit-learn==1.2.2\
+RUN pip install sigfig==1.3.2\
+  scikit-learn==1.2.2\
   pdb2pqr==3.6.1\
   im-standardize-molecule==0.1.0\
   im-data-manager-job-utilities==1.2.0

Dockerfile-rdkit-base

@@ -13,6 +13,6 @@ RUN apt-get -y update &&\
 ENV PYTHONUNBUFFERED=1
 
 # pip install RDKit
-RUN pip install rdkit==2023.3.2 sigfig==1.3.2
+RUN pip install rdkit==2023.3.2 numpy==1.26.*
 
 

moldb/enumerate_mols.nf

@@ -56,7 +56,7 @@ workflow enumerate_forms {
     extract_need_enum(specification)
     split_txt(extract_need_enum.out)
     enumerate(split_txt.out.flatten())
-    load_enum(enumerate.out)
+    load_enum(enumerate.out[0])
 
     extract_need_enum.out.subscribe {
         now = dateFormat.format(new java.util.Date())
@@ -73,7 +73,7 @@ workflow enumerate_forms {
     }
 
     enumerate_count = 0
-    enumerate.out.subscribe {
+    enumerate.out[1].subscribe {
         now = dateFormat.format(new java.util.Date())
         enumerate_count++
         log.info("$now # PROGRESS -DONE- $wrkflw:enumerate $enumerate_count")

nf-processes/file/concatenate_files.nf

@@ -6,7 +6,7 @@ params.optional = false
 
 process concatenate_files {
 
-    container 'informaticsmatters/vs-prep:stable'
+    container 'informaticsmatters/vs-prep:latest'
     if (params.publish_dir) { publishDir params.publish_dir, mode: params.publish_dir_mode }
 
     input:

nf-processes/file/split_sdf.nf

@@ -17,7 +17,7 @@ params.chunk_size = 1000
 
 process split_sdf {
 
-    container 'informaticsmatters/vs-rdock:stable'
+    container 'informaticsmatters/vs-rdock:latest'
 
     input:
     path molecules

nf-processes/file/split_txt.nf

@@ -19,9 +19,11 @@ params.suffix = '.txt'
 params.header = false // if true then skip the first line
 params.chunk_size = 1000
 
+tag = 'latest'
+
 process split_txt {
 
-    container 'informaticsmatters/vs-prep:stable'
+    container 'informaticsmatters/vs-prep:latest'
 
     input:
     file inputs

nf-processes/moldb/calc_molprops.nf

@@ -5,7 +5,7 @@ params.interval = 10000
 
 process calc_molprops {
 
-    container 'informaticsmatters/vs-moldb:stable'
+    container 'informaticsmatters/vs-moldb:latest'
     if (params.publish_dir) { publishDir params.publish_dir, mode: params.publish_dir_mode }
 
     input:

nf-processes/moldb/db_extract.nf

@@ -3,7 +3,7 @@ params.outfile = 'outputs.smi'
 
 process extract_molprops {
 
-    container 'informaticsmatters/vs-moldb:stable'
+    container 'informaticsmatters/vs-moldb:latest'
 
     output:
     file params.outfile

nf-processes/moldb/db_load.nf

@@ -5,7 +5,7 @@ params.library_name = 'no_name'
 
 process load_standardized {
 
-    container 'informaticsmatters/vs-moldb:stable'
+    container 'informaticsmatters/vs-moldb:latest'
     maxForks 1
     errorStrategy { sleep(Math.pow(2, task.attempt) * 1000 as long); return 'retry' }
     maxRetries 3
@@ -20,7 +20,7 @@ process load_standardized {
 
 process load_molprops {
 
-    container 'informaticsmatters/vs-moldb:stable'
+    container 'informaticsmatters/vs-moldb:latest'
     maxForks 1
     errorStrategy { sleep(Math.pow(2, task.attempt) * 1000 as long); return 'retry' }
     maxRetries 3
@@ -41,7 +41,7 @@ process load_molprops {
 
 process load_enum {
 
-    container 'informaticsmatters/vs-moldb:stable'
+    container 'informaticsmatters/vs-moldb:latest'
     maxForks 1
     errorStrategy { sleep(Math.pow(2, task.attempt) * 1000 as long); return 'retry' }
     maxRetries 3
@@ -63,7 +63,7 @@ process load_enum {
 
 process load_conf {
 
-    container 'informaticsmatters/vs-moldb:stable'
+    container 'informaticsmatters/vs-moldb:latest'
     maxForks 1
     errorStrategy { sleep(Math.pow(2, task.attempt) * 1000 as long); return 'retry' }
     maxRetries 3