Add CCMpred and mmseqs pkgs for msaselect service.

THU-ATOM · Jul 2, 2024 · 25a499e · 25a499e
1 parent 894b699
commit 25a499e
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Showing 6 changed files with 39 additions and 5 deletions.
diff --git a/README.md b/README.md
@@ -48,7 +48,6 @@ Please follow these steps:
 
 5.  Interact with AIRFold via Web page or RESTful API:
     - Submit page: http://127.0.0.1
-    - RESTful API URL: http://127.0.0.1:8081
     - API document page: http://127.0.0.1:8081/docs
     - Tasks monitor page: http://127.0.0.1:5555
 

diff --git a/batch_run.py b/batch_run.py
@@ -124,14 +124,17 @@ def main():
     # json_file = argv.input_path
     # with open("./tmp/temp_5000_128_1_mmseqs.json", 'r') as jf:
     #     request_dict = json.load(jf)
-    with open("./tmp/temp_6000_64_1_seqentropy_mmseqs.json", 'r') as jf:
+    # with open("./tmp/temp_6000_64_1_seqentropy_mmseqs.json", 'r') as jf:
+    # with open("./tmp/temp_6000_64_1_plmsim_mmseqs.json", 'r') as jf:
+    # with open("./tmp/temp_6000_64_1_seqentropy.json", 'r') as jf:
+    with open("./tmp/temp_6000_64_1_seqentropy_nodq.json", 'r') as jf:
         request_dict = json.load(jf)
 
     # weeks = ['2024.02.17', '2024.02.24', '2024.03.02', '2024.03.09', 
     #          '2024.03.16', '2024.03.23', '2024.03.30', '2024.04.06']
 
     # new weeks: 2024.05.04  2024.05.11  2024.05.18  2024.05.25
-    cameo_dir = "/data/protein/datasets_2024/experiment/modeling/2024.05.11/"
+    cameo_dir = "/data/protein/datasets_2024/experiment/modeling/2024.05.25/"
     data_suffix = "2024-06-05"
     # case_suffix = "base_deepmsa_mmseqs"
     case_suffix = "bdm"

diff --git a/gui/stats.html b/gui/stats.html
diff --git a/lib/conf/msa_search/search.yaml b/lib/conf/msa_search/search.yaml
@@ -44,5 +44,5 @@ mmseqs:
   sensitivity: 8
   align_eval: 10
   diff: 3000
-  qsc": -20.0
+  qsc: -20.0
 
diff --git a/lib/strategy/af2_select.py b/lib/strategy/af2_select.py
diff --git a/services/selectmsa/Dockerfile b/services/selectmsa/Dockerfile
@@ -25,6 +25,38 @@ RUN pip install --no-cache-dir \
 # Install ESM
 RUN pip install git+https://github.com/facebookresearch/esm.git
 
+# Install cmake
+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 CCMpred
+RUN git clone --recursive https://github.com/soedinglab/CCMpred.git /tmp/CCMpred \
+&& mkdir /tmp/CCMpred/build \
+&& cd /tmp/CCMpred/build \
+&& cmake -DCMAKE_INSTALL_PREFIX=/usr/local .. \
+&& make \
+&& make install\
+&& rm -rf /tmp/CCMpred
+
+# Install MMseqs2
+#RUN git clone https://github.com/soedinglab/MMseqs2.git /tmp/MMseqs2 \
+#    && mkdir /tmp/MMseqs2/build \
+#    && cd /tmp/MMseqs2/build \
+#    && cmake -DHAVE_AVX2=1 -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=/usr/local .. \
+#    && make \
+#    && make install\
+#    && rm -rf /tmp/MMseqs2
+RUN cd /tmp \
+    && wget https://mmseqs.com/latest/mmseqs-linux-avx2.tar.gz \
+    && tar xvfz mmseqs-linux-avx2.tar.gz \
+    && 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} \