image build fixes, update job-utils

InformaticsMatters · Jul 26, 2024 · d1a57ba · d1a57ba
1 parent d6e2cb5
commit d1a57ba
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Showing 15 changed files with 20 additions and 16 deletions.
diff --git a/Dockerfile-dmpk b/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==1.0.1
+RUN pip install matplotlib==3.7.1 im-data-manager-job-utilities==1.2.0
 
 COPY utils.py ./
 COPY dmpk/*.py ./dmpk/
diff --git a/Dockerfile-fns b/Dockerfile-fns
@@ -14,7 +14,7 @@ WORKDIR ${HOME}
 RUN pip install \
   neo4j-driver==4.4.11 \
   im-standardize-molecule==0.1.0 \
-  im-data-manager-job-utilities==1.1.1
+  im-data-manager-job-utilities==1.2.0
 
 COPY fn_*.py utils.py ./
 
diff --git a/Dockerfile-jaqpot b/Dockerfile-jaqpot
@@ -4,7 +4,7 @@ RUN apt-get -y update &&\
   apt-get -y install procps &&\
   apt-get clean
 
-RUN pip install im-data-manager-job-utilities==1.0.1
+RUN pip install im-data-manager-job-utilities==1.2.0
 
 ENV HOME=/code
 WORKDIR ${HOME}

diff --git a/Dockerfile-moldb b/Dockerfile-moldb
@@ -17,7 +17,7 @@ RUN apt-get update && apt-get install -y gcc libpq-dev &&\
 RUN pip install sqlalchemy==1.4.49\
     psycopg2-binary==2.9.6\
     im-standardize-molecule==0.1.0\
-    im-data-manager-job-utilities==1.0.1
+    im-data-manager-job-utilities==1.2.0
 
 COPY *.py site_substructures.smarts ./
 COPY moldb/* ./moldb/
diff --git a/Dockerfile-mordred b/Dockerfile-mordred
@@ -13,7 +13,7 @@ WORKDIR ${HOME}
 # install our requirements. RDKit is present in base container
 RUN pip install mordredcommunity==2.0.4 \
   im-standardize-molecule==0.1.0 \
-  im-data-manager-job-utilities==1.1.1
+  im-data-manager-job-utilities==1.2.0
 
 COPY im_mordred/descriptor_generator.py ./im_mordred/
 COPY utils.py rdkit_utils.py ./
diff --git a/Dockerfile-oddt b/Dockerfile-oddt
@@ -14,7 +14,7 @@ ENV HOME=/code
 WORKDIR ${HOME}
 
 RUN pip install wheel six &&\
-  pip install im-data-manager-job-utilities==1.1.1\
+  pip install im-data-manager-job-utilities==1.2.0\
   git+https://github.com/oddt/oddt.git@master
 
 COPY *.py ./
diff --git a/Dockerfile-plants b/Dockerfile-plants
@@ -16,4 +16,4 @@ RUN apt-get update &&\
 COPY pharmacophore.py utils.py /code/
 
 RUN chmod a+x /code/*.py &&\
-    pip install im-data-manager-job-utilities==1.1.1
+    pip install im-data-manager-job-utilities==1.2.0
diff --git a/Dockerfile-prep b/Dockerfile-prep
@@ -19,7 +19,7 @@ WORKDIR ${HOME}
 RUN pip install scikit-learn==1.2.2\
   pdb2pqr==3.6.1\
   im-standardize-molecule==0.1.0\
-  im-data-manager-job-utilities==1.1.1
+  im-data-manager-job-utilities==1.2.0
 
 COPY *.py fpscores.pkl.gz site_substructures.smarts ./
 COPY moldb/* ./moldb/
diff --git a/Dockerfile-rdock b/Dockerfile-rdock
@@ -1,11 +1,15 @@
 FROM informaticsmatters/rdock:2013.1
 LABEL maintainer="Tim Dudgeon<tdudgeon@informaticsmatters.com>"
 
+USER 0
+
 RUN yum -y update &&\
-    yum -y install python-jinja2 &&\
+    yum -y install python-devel python-jinja2 &&\
     yum clean all
 
-RUN pip install im-data-manager-job-utilities==1.0.1
+RUN pip install --trusted-host pypi.org --trusted-host pypi.python.org im-data-manager-job-utilities==1.2.0
 
 COPY prepare_rdock.py rdock_*.sh /code/
 RUN chmod 755 /code/prepare_rdock.py
+
+USER rdock
diff --git a/environment-im-fns.yaml b/environment-im-fns.yaml
@@ -7,4 +7,4 @@ dependencies:
   - neo4j-python-driver=4.4.1
   - pip:
     - im-standardize-molecule==0.1.0
-    - im-data-manager-job-utilities==1.0.1
+    - im-data-manager-job-utilities==1.2.0
diff --git a/environment-im-jote.yaml b/environment-im-jote.yaml
@@ -12,4 +12,4 @@ dependencies:
   - nextflow == 21.10.6
   - pip:
     - im-jote
-    - im-data-manager-job-utilities==1.0.1
+    - im-data-manager-job-utilities==1.2.0
diff --git a/environment-im-mordred.yaml b/environment-im-mordred.yaml
@@ -9,4 +9,4 @@ dependencies:
   - mordredcommunity=2.0.4
   - pip:
     - im-standardize-molecule==0.1.0
-    - im-data-manager-job-utilities==1.1.1
+    - im-data-manager-job-utilities==1.2.0
diff --git a/environment-im-oddt.yaml b/environment-im-oddt.yaml
@@ -10,5 +10,5 @@ dependencies:
   - six=1.16.0
   #- oddt
   - pip:
-    - im-data-manager-job-utilities==1.0.1
+    - im-data-manager-job-utilities==1.2.0
     #- git+https://github.com/oddt/oddt.git@master
diff --git a/environment-im-vs-prep.yaml b/environment-im-vs-prep.yaml
@@ -13,4 +13,4 @@ dependencies:
   - pytest=8.0.0
   - pip:
     - im-standardize-molecule==0.1.0
-    - im-data-manager-job-utilities==1.1.1
+    - im-data-manager-job-utilities==1.2.0
diff --git a/environment-moldb.yaml b/environment-moldb.yaml
@@ -9,4 +9,4 @@ dependencies:
 - rdkit=2021.03.5
 - pip:
   - im-standardize-molecule==0.1.0
-  - im-data-manager-job-utilities==1.1.0
+  - im-data-manager-job-utilities==1.2.0