From 7f3a0cf9a8e1e3127071674440811b831b0d6f0d Mon Sep 17 00:00:00 2001
From: joaomcteixeira <jteixeira@zymvol.com>
Date: Thu, 23 May 2024 19:15:28 +0200
Subject: [PATCH] add docker file

---
 Dockerfile   | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
 compose.yaml |  8 ++++++++
 2 files changed, 56 insertions(+)
 create mode 100644 Dockerfile
 create mode 100644 compose.yaml

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 00000000..2bd359fc
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,48 @@
+FROM ubuntu:22.04
+
+RUN apt update
+RUN apt install python3 python3-pip -y
+
+# This part is copied from DSSP
+# https://github.com/cmbi/dssp/blob/master/Dockerfile
+RUN apt-get install -y make rsync wget
+RUN apt-get install -y git g++ libboost-all-dev libbz2-dev doxygen xsltproc docbook docbook-xsl docbook-xml autoconf automake autotools-dev
+
+RUN mkdir -p /deps
+
+# Install libzeep
+RUN git clone https://github.com/mhekkel/libzeep.git /deps/libzeep ;\
+    cd /deps/libzeep ;\
+    git checkout tags/v3.0.3
+# XXX: Workaround due to bug in libzeep's makefile
+RUN sed -i '71s/.*/\t\$\(CXX\) \-shared \-o \$@ \-Wl,\-soname=\$\(SO_NAME\) \$\(OBJECTS\) \$\(LDFLAGS\)/' /deps/libzeep/makefile
+WORKDIR /deps/libzeep
+# XXX: Run ldconfig manually to work around a bug in libzeep's makefile
+RUN make ; make install ; ldconfig
+
+WORKDIR /deps
+RUN git clone https://github.com/cmbi/dssp dssp
+WORKDIR /deps/dssp
+RUN ./autogen.sh && ./configure && make && make install
+
+RUN mkdir -p /app
+WORKDIR /app
+
+RUN git clone https://github.com/julie-forman-kay-lab/IDPConformerGenerator idpconfgen
+WORKDIR /app/idpconfgen
+
+RUN ./install_miniconda3.sh
+RUN ./miniconda3/bin/pip install -r requirements.txt
+RUN ./miniconda3/bin/python setup.py develop --no-deps
+
+RUN echo 'export PATH="/app/idpconfgen/miniconda3/bin/:$PATH"' >> ~/.bashrc
+
+WORKDIR /deps
+RUN git clone https://github.com/THGLab/MCSCE
+WORKDIR /deps/MCSCE
+RUN /app/idpconfgen/miniconda3/bin/pip install tensorflow tdqm pathos
+RUN /app/idpconfgen/miniconda3/bin/python setup.py develop --no-deps
+
+WORKDIR /app/idpconfgen
+RUN ./miniconda3/bin/python setup.py develop --no-deps
+
diff --git a/compose.yaml b/compose.yaml
new file mode 100644
index 00000000..e7360d4d
--- /dev/null
+++ b/compose.yaml
@@ -0,0 +1,8 @@
+services:
+    idpconfgen:
+        build:
+            context: .
+            dockerfile: Dockerfile
+        command: tail -F anything
+        volumes:
+            - /home/jteixeira/shared/idpconfgen:/shared