From bff7881e4f8f73a2d4523d897e1abb585b61d7ac Mon Sep 17 00:00:00 2001 From: Hong-Rui Lin Date: Tue, 9 Apr 2024 18:17:08 +0800 Subject: [PATCH 1/3] [feature] unidock tools add required dependencies --- unidock_tools/Dockerfile | 4 +--- unidock_tools/pyproject.toml | 4 ++++ 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/unidock_tools/Dockerfile b/unidock_tools/Dockerfile index 7323652..a42062f 100644 --- a/unidock_tools/Dockerfile +++ b/unidock_tools/Dockerfile @@ -20,9 +20,7 @@ RUN wget --quiet -O CDPKit.sh https://github.com/molinfo-vienna/CDPKit/releases/ rm CDPKit.sh WORKDIR /opt -RUN mamba install -y ipython requests openbabel pandas -c conda-forge -RUN mamba create -y -n mgltools mgltools autogrid -c bioconda -ENV PATH $PATH:/opt/conda/envs/mgltools/bin +RUN mamba install -y ipython tqdm requests numpy pathos networkx ambertools rdkit openbabel openmm mdanalysis pandas -c conda-forge COPY . /opt/unidock_tools RUN cd /opt/unidock_tools && \ diff --git a/unidock_tools/pyproject.toml b/unidock_tools/pyproject.toml index 8b821bd..a2517aa 100644 --- a/unidock_tools/pyproject.toml +++ b/unidock_tools/pyproject.toml @@ -15,7 +15,11 @@ description = "Several docking-related applications based on Uni-Dock." readme = "README.md" requires-python = ">=3.8" dependencies = [ + "ambertools", "rdkit", + "mdanalysis", + "openmm", + "openbabel", "networkx", "tqdm", "numpy", From 0cad635d676ca25ee0f9a586aa0d3f1123a3c96a Mon Sep 17 00:00:00 2001 From: dp-yuanyn Date: Tue, 9 Apr 2024 18:34:26 +0800 Subject: [PATCH 2/3] modify dockerfile package and pip package --- unidock_tools/Dockerfile | 2 +- unidock_tools/pyproject.toml | 7 ++----- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/unidock_tools/Dockerfile b/unidock_tools/Dockerfile index a42062f..8298a8d 100644 --- a/unidock_tools/Dockerfile +++ b/unidock_tools/Dockerfile @@ -20,7 +20,7 @@ RUN wget --quiet -O CDPKit.sh https://github.com/molinfo-vienna/CDPKit/releases/ rm CDPKit.sh WORKDIR /opt -RUN mamba install -y ipython tqdm requests numpy pathos networkx ambertools rdkit openbabel openmm mdanalysis pandas -c conda-forge +RUN mamba install -y ipython requests tqdm lmdb openbabel ambertools openmm -c conda-forge COPY . /opt/unidock_tools RUN cd /opt/unidock_tools && \ diff --git a/unidock_tools/pyproject.toml b/unidock_tools/pyproject.toml index a2517aa..272d3f8 100644 --- a/unidock_tools/pyproject.toml +++ b/unidock_tools/pyproject.toml @@ -15,14 +15,11 @@ description = "Several docking-related applications based on Uni-Dock." readme = "README.md" requires-python = ">=3.8" dependencies = [ - "ambertools", "rdkit", - "mdanalysis", - "openmm", - "openbabel", + "MDAnalysis", "networkx", - "tqdm", "numpy", + "pandas", "pathos", ] From e0463887bb0eb7ddce3c4f65bc9d85849bc2abf1 Mon Sep 17 00:00:00 2001 From: dp-yuanyn Date: Tue, 9 Apr 2024 18:36:52 +0800 Subject: [PATCH 3/3] fix:lmdb package name --- unidock_tools/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unidock_tools/Dockerfile b/unidock_tools/Dockerfile index 8298a8d..95127f2 100644 --- a/unidock_tools/Dockerfile +++ b/unidock_tools/Dockerfile @@ -20,7 +20,7 @@ RUN wget --quiet -O CDPKit.sh https://github.com/molinfo-vienna/CDPKit/releases/ rm CDPKit.sh WORKDIR /opt -RUN mamba install -y ipython requests tqdm lmdb openbabel ambertools openmm -c conda-forge +RUN mamba install -y ipython requests tqdm python-lmdb openbabel ambertools openmm -c conda-forge COPY . /opt/unidock_tools RUN cd /opt/unidock_tools && \