fixed bugs for analysis, submit and tplfeature service.

THU-ATOM · Mar 8, 2024 · 6686ea4 · 6686ea4
1 parent 7a5eb41
commit 6686ea4
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Showing 16 changed files with 113 additions and 23 deletions.
diff --git a/docker-compose.yaml b/docker-compose.yaml
@@ -5,6 +5,12 @@ services:
     build:
       context: ./gui
       dockerfile: Dockerfile
+      args:
+        - http_proxy=${http_proxy}
+        - https_proxy=${https_proxy}
+        - USER_ID=${UID}
+        - GROUP_ID=${GID}
+        - USER_NAME=${USER_NAME}
     ports:
       - "80:4173"
     volumes:
@@ -19,6 +25,12 @@ services:
     build:
       context: ./api
       dockerfile: Dockerfile
+      args:
+        - http_proxy=${http_proxy}
+        - https_proxy=${https_proxy}
+        - USER_ID=${UID}
+        - GROUP_ID=${GID}
+        - USER_NAME=${USER_NAME}
     ports:
       - "8081:8081"
     depends_on:
@@ -181,7 +193,6 @@ services:
       - ./lib:/worker/lib
     command: celery -A worker worker --loglevel=info -Q queue_selecttpl --concurrency=4
 
-
   worker_tplfeature:
     build:
       context: ./services/tplfeature
@@ -295,6 +306,12 @@ services:
     build:
       context: ./services/submit
       dockerfile: Dockerfile
+      args:
+        - http_proxy=${http_proxy}
+        - https_proxy=${https_proxy}
+        - USER_ID=${UID}
+        - GROUP_ID=${GID}
+        - USER_NAME=${USER_NAME}
     depends_on:
       - rabbitmq
     environment:

diff --git a/gui/stats.html b/gui/stats.html
diff --git a/services/analysis/Dockerfile b/services/analysis/Dockerfile
@@ -15,6 +15,17 @@ RUN pip install -U setuptools pip
 RUN pip install --no-cache-dir -r /tmp/requirements.txt
 
 
+# add user
+RUN if [ $USER_NAME != "root" ] ; \
+    then addgroup --gid ${GROUP_ID} ${USER_NAME} \
+    && adduser --disabled-password --gecos '' --uid $USER_ID --gid $GROUP_ID ${USER_NAME} \
+    && usermod -aG sudo ${USER_NAME} \
+    && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers ; fi
+
+# Switch to the created user
+USER ${USER_NAME}
+
+
 WORKDIR /worker
 
 # Specify the command to run on container start

diff --git a/services/analysis/requirements.txt b/services/analysis/requirements.txt
@@ -10,6 +10,6 @@ psutil
 gpustat
 absl-py
 scipy
-tensorflow
 ray
-dm-tree
+dm-tree
+tensorflow-gpu==2.6.0
diff --git a/services/analysis/worker.py b/services/analysis/worker.py
@@ -270,7 +270,7 @@ def rerank_relaxed_plddts(self, dirname):
             )
             os.system(f"cp {src_path} {tgt_path}")
 
-    def run(self, *args, dry=False, **kwargs):
+    def run(self):
         ptree = get_pathtree(request=self.requests[0])
         num_res = len(self.requests[0]["sequence"])
         dirname = str(ptree.alphafold.root)
@@ -300,4 +300,4 @@ def run(self, *args, dry=False, **kwargs):
         )
         result_path = os.path.join(dirname, "plddt_results.json")
         dtool.write_json(result_path, data=model2plddts)
-        # return True
+        return str(result_path)
diff --git a/services/blast/Dockerfile b/services/blast/Dockerfile
@@ -22,6 +22,16 @@ RUN mkdir /tmp/blast \
     && cp ncbi-blast-2.13.0+/bin/* /usr/local/bin/ \
     && rm -rf /tmp/blast
 
+# add user
+RUN if [ $USER_NAME != "root" ] ; \
+    then addgroup --gid ${GROUP_ID} ${USER_NAME} \
+    && adduser --disabled-password --gecos '' --uid $USER_ID --gid $GROUP_ID ${USER_NAME} \
+    && usermod -aG sudo ${USER_NAME} \
+    && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers ; fi
+
+# Switch to the created user
+USER ${USER_NAME}
+
 WORKDIR /worker
 
 # Specify the command to run on container start

diff --git a/services/hhblits/Dockerfile b/services/hhblits/Dockerfile
@@ -15,18 +15,13 @@ RUN pip install -U setuptools pip
 RUN pip install --no-cache-dir -r /tmp/requirements.txt
 
 # install cmake
-# RUN apt-get update && apt-get -y install cmake protobuf-compiler
-RUN apt-get update \
-  && apt-get -y install build-essential \
-  && apt-get install -y wget \
-  && rm -rf /var/lib/apt/lists/* \
-  && wget https://github.com/Kitware/CMake/releases/download/v3.24.1/cmake-3.24.1-Linux-x86_64.sh \
-      -q -O /tmp/cmake-install.sh \
-      && chmod u+x /tmp/cmake-install.sh \
-      && mkdir /opt/cmake-3.24.1 \
-      && /tmp/cmake-install.sh --skip-license --prefix=/opt/cmake-3.24.1 \
-      && rm /tmp/cmake-install.sh \
-      && ln -s /opt/cmake-3.24.1/bin/* /usr/local/bin
+RUN wget -O cmake-3.22.5-linux-x86_64.tar.gz https://github.com/Kitware/CMake/releases/download/v3.22.5/cmake-3.22.5-linux-x86_64.tar.gz \
+    && tar zxvf cmake-3.22.5-linux-x86_64.tar.gz \
+    && cd cmake-3.22.5-linux-x86_64 \
+    && cp -r bin/ /usr/local \
+    && cp -r share/ /usr/local \
+    && rm -rf /tmp/cmake-3.22.5-linux-x86_64 \
+    && rm -rf /tmp/cmake-3.22.5-linux-x86_64.tar.gz
 
 # Install HH-suite3
 RUN git clone --recursive https://github.com/soedinglab/hh-suite.git /tmp/hhsuite \

diff --git a/services/jackhmmer/Dockerfile b/services/jackhmmer/Dockerfile
@@ -24,6 +24,16 @@ RUN mkdir /tmp/hmmer \
     && make \
     && make install \
     && rm -rf /tmp/hmmer
+
+# add user
+RUN if [ $USER_NAME != "root" ] ; \
+    then addgroup --gid ${GROUP_ID} ${USER_NAME} \
+    && adduser --disabled-password --gecos '' --uid $USER_ID --gid $GROUP_ID ${USER_NAME} \
+    && usermod -aG sudo ${USER_NAME} \
+    && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers ; fi
+
+# Switch to the created user
+USER ${USER_NAME}
 
 WORKDIR /worker
 

diff --git a/services/mergemsa/Dockerfile b/services/mergemsa/Dockerfile
@@ -14,6 +14,17 @@ RUN pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple
 RUN pip install -U setuptools pip
 RUN pip install --no-cache-dir -r /tmp/requirements.txt
 
+
+# add user
+RUN if [ $USER_NAME != "root" ] ; \
+    then addgroup --gid ${GROUP_ID} ${USER_NAME} \
+    && adduser --disabled-password --gecos '' --uid $USER_ID --gid $GROUP_ID ${USER_NAME} \
+    && usermod -aG sudo ${USER_NAME} \
+    && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers ; fi
+
+# Switch to the created user
+USER ${USER_NAME}
+
 WORKDIR /worker
 
 # Specify the command to run on container start

diff --git a/services/mmseqs/Dockerfile b/services/mmseqs/Dockerfile
@@ -28,6 +28,16 @@ RUN cd /tmp \
     && cp -r mmseqs/bin/* /usr/local/bin/ \
     && rm -rf /tmp/mmseqs
 
+# add user
+RUN if [ $USER_NAME != "root" ] ; \
+    then addgroup --gid ${GROUP_ID} ${USER_NAME} \
+    && adduser --disabled-password --gecos '' --uid $USER_ID --gid $GROUP_ID ${USER_NAME} \
+    && usermod -aG sudo ${USER_NAME} \
+    && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers ; fi
+
+# Switch to the created user
+USER ${USER_NAME}
+
 WORKDIR /worker
 
 # Specify the command to run on container start

diff --git a/services/selecttpl/Dockerfile b/services/selecttpl/Dockerfile
@@ -14,6 +14,16 @@ RUN pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple
 RUN pip install -U setuptools pip
 RUN pip install --no-cache-dir -r /tmp/requirements.txt
 
+# add user
+RUN if [ $USER_NAME != "root" ] ; \
+    then addgroup --gid ${GROUP_ID} ${USER_NAME} \
+    && adduser --disabled-password --gecos '' --uid $USER_ID --gid $GROUP_ID ${USER_NAME} \
+    && usermod -aG sudo ${USER_NAME} \
+    && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers ; fi
+
+# Switch to the created user
+USER ${USER_NAME}
+
 WORKDIR /worker
 
 # Specify the command to run on container start

diff --git a/services/submit/Dockerfile b/services/submit/Dockerfile
@@ -4,13 +4,26 @@ ENV CELERY_BROKER_URL pyamqp://guest:guest@localhost:5672/
 ENV CELERY_RESULT_BACKEND rpc://
 ENV C_FORCE_ROOT true
 
-# RUN apk add build-base linux-headers   # very slow
+ARG USER_ID=1011
+ARG GROUP_ID=1011
+ARG USER_NAME=docker
+
 COPY requirements.txt /tmp/requirements.txt
 
 RUN pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple
 RUN pip install -U setuptools pip
 RUN pip install --no-cache-dir -r /tmp/requirements.txt
 
+# add user
+RUN if [ $USER_NAME != "root" ] ; \
+    then addgroup --gid ${GROUP_ID} ${USER_NAME} \
+    && adduser --disabled-password --gecos '' --uid $USER_ID --gid $GROUP_ID ${USER_NAME} \
+    && usermod -aG sudo ${USER_NAME} \
+    && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers ; fi
+
+# Switch to the created user
+USER ${USER_NAME}
+
 WORKDIR /worker
 
 # Specify the command to run on container start

diff --git a/services/submit/requirements.txt b/services/submit/requirements.txt
@@ -13,4 +13,5 @@ gpustat
 absl-py
 scikit-learn
 ray
-dm-tree
+dm-tree
+numpy==1.23
diff --git a/services/submit/worker.py b/services/submit/worker.py
@@ -333,7 +333,7 @@ def init_runners(self, groups):
             self.add_runner(f"submit_{sender}", submit)
         return runners
 
-    def run(self, dry=False, *args, **kwargs):
+    def run(self, dry=False):
         for runner in self.runners:
             runner.run(dry=dry)
-        # return True
+        return "submitted!"
diff --git a/services/tplfeature/requirements.txt b/services/tplfeature/requirements.txt
@@ -11,4 +11,5 @@ gpustat
 absl-py
 docker
 ray
-dm-tree
+dm-tree
+numpy==1.23
diff --git a/services/tplfeature/worker.py b/services/tplfeature/worker.py
@@ -78,6 +78,7 @@ def run(self):
         # get template hits
         ptree = get_pathtree(request=self.requests[0])
         template_hits_path = str(ptree.search.template_hits)
+        logger.info(f"template_hits_path: {template_hits_path}")
         template_hits = dtool.read_pickle(template_hits_path)
 
         output_path = str(ptree.alphafold.template_feat)
-Original file line number
+Diff line change
@@ Expand Up / @@ -10,6 +10,6 @@ psutil @@
     gpustat
     absl-py
     scipy
-    tensorflow
     ray
-    dm-tree
+    dm-tree
+    tensorflow-gpu==2.6.0