update docker

linnabrown · Apr 19, 2024 · 8097053 · 8097053
1 parent 1f06c84
commit 8097053
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Showing 3 changed files with 7 additions and 16 deletions.
diff --git a/.gitignore b/.gitignore
@@ -131,4 +131,6 @@ Hotpep_bkp*
 EscheriaColiK12MG1655.*
 
 
-34*
+34*
+
+output*
diff --git a/Dockerfile b/Dockerfile
@@ -11,21 +11,7 @@ RUN echo "source activate run_dbcan" > ~/.bashrc
 ENV PATH /opt/conda/envs/run_dbcan/bin:$PATH
 
 # download and make the databases
-RUN test -d db || mkdir db
-RUN cd db \
-    && wget http://bcb.unl.edu/dbCAN2/download/Databases/fam-substrate-mapping-08252022.tsv \
-	&& wget http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN-PUL_07-01-2022.xlsx && wget http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN-PUL_07-01-2022.txt \
-	&& wget http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN-PUL.tar.gz && tar xvf dbCAN-PUL.tar.gz \
-    && wget http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN_sub.hmm && hmmpress dbCAN_sub.hmm \
-    && wget http://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fa && diamond makedb --in CAZyDB.08062022.fa -d CAZy \
-    && wget https://bcb.unl.edu/dbCAN2/download/Databases/V11/dbCAN-HMMdb-V11.txt && mv dbCAN-HMMdb-V11.txt dbCAN.txt && hmmpress dbCAN.txt \
-    && wget https://bcb.unl.edu/dbCAN2/download/Databases/V11/tcdb.fa && diamond makedb --in tcdb.fa -d tcdb \
-    && wget http://bcb.unl.edu/dbCAN2/download/Databases/V11/tf-1.hmm && hmmpress tf-1.hmm \
-    && wget http://bcb.unl.edu/dbCAN2/download/Databases/V11/tf-2.hmm && hmmpress tf-2.hmm \
-    && wget https://bcb.unl.edu/dbCAN2/download/Databases/V11/stp.hmm && hmmpress stp.hmm \
-    && cd ../ && wget http://bcb.unl.edu/dbCAN2/download/Samples/EscheriaColiK12MG1655.fna \
-    && wget http://bcb.unl.edu/dbCAN2/download/Samples/EscheriaColiK12MG1655.faa \
-    && wget http://bcb.unl.edu/dbCAN2/download/Samples/EscheriaColiK12MG1655.gff
+RUN dbcan_build --cpus 1 --db-dir db --clean
 
 
 ENTRYPOINT ["run_dbcan"]

diff --git a/docker/cazyme_annotation/Dockerfile b/docker/cazyme_annotation/Dockerfile
@@ -11,4 +11,7 @@ RUN conda env create -f dbcan.yml && conda clean -ya
 RUN echo "source activate CAZyme_annotation" > ~/.bashrc
 ENV PATH /opt/conda/envs/CAZyme_annotation/bin:$PATH
 
+# download and make the databases
+RUN dbcan_build --cpus 1 --db-dir db --clean
+
 CMD [ "run_dbcan -h" ]