Update docker

Author: yitzchak

02-thermodynamic-integration-demo.ipynb

@@ -32,9 +32,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "dd1a249487534983c373305a14a64df4",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "A Jupyter Widget"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "(tirun-jupyter:workspace)"
    ]
@@ -53,9 +69,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "2087b84ee55f48e9639e63d12fa3c252",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "A Jupyter Widget"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "(tirun-jupyter:load-receptor)"
    ]
@@ -74,9 +106,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "5f88f956d7a94f58498457ac679a942f",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "A Jupyter Widget"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "(tirun-jupyter:load-ligands)"
    ]
@@ -92,9 +140,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "2a6cde23d2b6454de194af6dd07c27a6",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "A Jupyter Widget"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "(tirun-jupyter:select-ligands)"
    ]
@@ -115,9 +179,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "6501c2fac1ff4cdd21f50a49606f43a1",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "A Jupyter Widget"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "(tirun-jupyter:lomap)"
    ]
@@ -137,9 +217,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "544237bcceb34f25a2eeec62431b0716",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "A Jupyter Widget"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "(tirun-jupyter:jobs)"
    ]
@@ -157,7 +253,7 @@
    "mimetype": "text/x-common-lisp",
    "name": "common-lisp",
    "pygments_lexer": "common-lisp",
-   "version": "eclasp-boehmprecise-2.0.0-109-gec9d2b05f-gfe7de2ae-cst"
+   "version": "eclasp-boehmprecise-2.0.0-110-g0f095ce09-ga4471677-cst"
   }
  },
  "nbformat": 4,

Dockerfile

@@ -8,7 +8,7 @@ ARG NB_UID=1000
 ENV DEBIAN_FRONTEND=noninteractive
 ENV USER ${NB_USER}
 ENV HOME /home/${NB_USER}
-ENV PATH "${HOME}/.local/bin:${PATH}"
+ENV PATH "${HOME}/.local/bin:${HOME}/miniconda3/bin:${PATH}"
 
 RUN apt-get update && \
     apt-get upgrade -y && \
@@ -32,5 +32,10 @@ RUN chown -R ${NB_UID} demos/ && \
 WORKDIR ${HOME}/demos/
 USER ${NB_USER}
 
-RUN pip install notebook jupyterlab && \
-    cando-user-install
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+RUN chmod +x Miniconda3-latest-Linux-x86_64.sh && \
+    ./Miniconda3-latest-Linux-x86_64.sh -b && \
+    rm -f Miniconda3-latest-Linux-x86_64.sh
+
+RUN conda install -y -c conda-forge jupyterlab ambertools && \
+   cando-user-install