cas install

.gitignore

@@ -37,3 +37,4 @@ jupyter-book/data
 
 **/data/*
 **/figures/*
+jupyter-book/cellular_structure/KPTracer-Data.tar.gz\?download=1

jupyter-book/cellular_structure/lineage_tracing.ipynb

@@ -100,7 +100,12 @@
     "1. preprocessing sequencing reads into character matrices. \n",
     "2. reconstructing phylogenies from these character matrices.\n",
     "3. providing analysis tools for deriving insights from these phylogenies. \n",
-    "For more details and installation guidelines see [here](https://cassiopeia-lineage.readthedocs.io/en/latest/index.html)"
+    "For more details and installation guidelines see [here](https://cassiopeia-lineage.readthedocs.io/en/latest/index.html)\n",
+    "\n",
+    "\\ZP{maybe add the lines for short installations, e.g.}\n",
+    "\n",
+    "### Installation for users\n",
+    "`pip install git+https://github.com/YosefLab/Cassiopeia@master#egg=cassiopeia-lineage`"
    ]
   },
   {
@@ -119,7 +124,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "id": "2d279b26",
    "metadata": {
     "pycharm": {
@@ -201,21 +206,39 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "id": "55121557",
    "metadata": {
     "pycharm": {
      "name": "#%%\n"
     }
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "--2022-06-27 19:05:52--  https://zenodo.org/record/5847462/files/KPTracer-Data.tar.gz?download=1\n",
+      "Resolving zenodo.org (zenodo.org)... 137.138.76.77\n",
+      "Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.\n",
+      "HTTP request sent, awaiting response... 200 OK\n",
+      "Length: 1304975216 (1.2G) [application/octet-stream]\n",
+      "Saving to: 'KPTracer-Data.tar.gz?download=1'\n",
+      "\n",
+      "KPTracer-Data.tar.g 100%[===================>]   1.21G  7.65MB/s    in 1m 56s  \n",
+      "\n",
+      "2022-06-27 19:07:51 (10.7 MB/s) - 'KPTracer-Data.tar.gz?download=1' saved [1304975216/1304975216]\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
-    "!wget https://zenodo.org/record/5847462/files/KPTracer-Data.tar.gz?download=1"
+    "!wget \"https://zenodo.org/record/5847462/files/KPTracer-Data.tar.gz?download=1\""
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "id": "d3eaf116",
    "metadata": {
     "pycharm": {
@@ -957,9 +980,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "cas3.7",
+   "display_name": "python39",
    "language": "python",
-   "name": "cas3.7"
+   "name": "python39"
   },
   "language_info": {
    "codemirror_mode": {
@@ -971,7 +994,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,