refactoring of rdkit property calcs

InformaticsMatters · Jul 25, 2024 · e621550 · e621550
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commit e621550
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Showing 12 changed files with 315 additions and 167 deletions.
diff --git a/Dockerfile-prep b/Dockerfile-prep
@@ -1,4 +1,4 @@
-FROM informaticsmatters/vs-rdkit-base:stable
+FROM informaticsmatters/vs-rdkit-base:latest
 
 # Note:     When run by the Data Manager the uid and gid
 #           will be set according to the Project we're running against.

diff --git a/data-manager/dmpk.yaml b/data-manager/dmpk.yaml
@@ -18,7 +18,7 @@ jobs:
     - kel
     image:
       name: informaticsmatters/vs-dmpk
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true

diff --git a/data-manager/fragnet-search.yaml b/data-manager/fragnet-search.yaml
@@ -27,7 +27,7 @@ jobs:
     - candidate-selection
     image:
       name: informaticsmatters/vs-fragnet-search
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -145,7 +145,7 @@ jobs:
     - synthons
     image:
       name: informaticsmatters/vs-fragnet-search
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -229,7 +229,7 @@ jobs:
     - candidate-selection
     image:
       name: informaticsmatters/vs-fragnet-search
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true

diff --git a/data-manager/im-virtual-screening.yaml b/data-manager/im-virtual-screening.yaml
@@ -66,7 +66,7 @@ jobs:
     - test
     image:
       name: informaticsmatters/vs-prep
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -143,7 +143,7 @@ jobs:
     - openbabel
     image:
       name: informaticsmatters/vs-prep
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -206,7 +206,7 @@ jobs:
     - 3d
     image:
       name: informaticsmatters/vs-prep
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -294,7 +294,7 @@ jobs:
     - 3d
     image:
       name: informaticsmatters/vs-rdock
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -362,7 +362,7 @@ jobs:
     - 3d
     image:
       name: informaticsmatters/vs-oddt
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -466,7 +466,7 @@ jobs:
     doc-url: im-virtual-screening/rdock-filter-sdf.md
     image:
       name: informaticsmatters/vs-rdock
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -570,7 +570,7 @@ jobs:
     doc-url: im-virtual-screening/rdock-filter-sdf.md
     image:
       name: informaticsmatters/vs-rdock
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -679,7 +679,7 @@ jobs:
     - format
     image:
       name: informaticsmatters/vs-prep
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -735,7 +735,7 @@ jobs:
     - 3d
     image:
       name: informaticsmatters/vs-prep
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -949,7 +949,7 @@ jobs:
     - 3d
     image:
       name: informaticsmatters/vs-nextflow
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: nextflow
@@ -1077,7 +1077,7 @@ jobs:
     - 3d
     image:
       name: informaticsmatters/vs-nextflow
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: nextflow
@@ -1200,7 +1200,7 @@ jobs:
     - 3d
     image:
       name: informaticsmatters/vs-nextflow
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: nextflow
@@ -1268,7 +1268,7 @@ jobs:
     doc-url: im-virtual-screening/ph4-align-to-fragments.md
     image:
       name: informaticsmatters/vs-plants
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -1415,7 +1415,7 @@ jobs:
     doc-url: im-virtual-screening/ph4-align-to-fragments.md
     image:
       name: informaticsmatters/vs-plants
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true
@@ -1534,7 +1534,7 @@ jobs:
     doc-url: im-virtual-screening/ph4-align-to-fragments.md
     image:
       name: informaticsmatters/vs-nextflow
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: nextflow
@@ -1745,7 +1745,7 @@ jobs:
     - nextflow
     image:
       name: informaticsmatters/vs-nextflow
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: nextflow

diff --git a/data-manager/moldb.yaml b/data-manager/moldb.yaml
@@ -29,7 +29,7 @@ jobs:
     - database
     image:
       name: informaticsmatters/vs-moldb
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: simple
@@ -80,7 +80,7 @@ jobs:
     - database
     image:
       name: informaticsmatters/vs-moldb
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: simple
@@ -181,7 +181,7 @@ jobs:
     - library
     image:
       name: informaticsmatters/vs-nextflow
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: nextflow
@@ -307,7 +307,7 @@ jobs:
     - molecular properties
     image:
       name: informaticsmatters/vs-nextflow
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: nextflow
@@ -391,7 +391,7 @@ jobs:
     - stereoisomers
     image:
       name: informaticsmatters/vs-nextflow
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: nextflow
@@ -489,7 +489,7 @@ jobs:
     - conformers
     image:
       name: informaticsmatters/vs-nextflow
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: nextflow
@@ -586,7 +586,7 @@ jobs:
     - database
     image:
       name: informaticsmatters/vs-moldb
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: simple
@@ -691,7 +691,7 @@ jobs:
     - stereoisomers
     image:
       name: informaticsmatters/vs-moldb
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: simple
@@ -820,7 +820,7 @@ jobs:
     - 3d
     image:
       name: informaticsmatters/vs-moldb
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: simple
@@ -947,7 +947,7 @@ jobs:
     - database
     image:
       name: informaticsmatters/vs-moldb
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       type: simple

diff --git a/data-manager/mordred.yaml b/data-manager/mordred.yaml
@@ -17,7 +17,7 @@ jobs:
     - descriptors
     image:
       name: informaticsmatters/mordred
-      tag: 'stable'
+      tag: 'latest'
       project-directory: /data
       working-directory: /data
       fix-permissions: true