clarified readme

Jigyasa3 · Jul 20, 2016 · 40b24be · 40b24be
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diff --git a/README.md b/README.md
@@ -6,10 +6,12 @@ This is an interactive tutorial teaching the principles of next-generation data
 
 You can launch it by clicling on the "Launch Binder" badge above. This will launch Binder and build a virutal environment (takes a few minutes), after which you can interactively analyze data.
 
-Alternatively, you can clone the repository and install the environment using the [Miniconda](http://conda.pydata.org/miniconda.html)  package manager from within the repo folder.
+Alternatively, on Mac and Linux you can clone the repository by `git clone https://github.com/mikheyev/phage-lab.git && cd phage-lab` and install the environment using the [Miniconda](http://conda.pydata.org/miniconda.html) package manager from within the repo folder.
 
 	conda install jupyter ipython
 	conda env create -f environment.yml
 	jupyter notebook
 
-This should open the same environment, but locally.
+This should open the same environment, but locally.
+
+If you ever need to reload the environment later, you can run `source activate phage-lab` and
diff --git a/custom.css → css/custom.css b/custom.css → css/custom.css
diff --git a/index.ipynb b/index.ipynb
@@ -34,7 +34,7 @@
        "    }\n",
        "    .text_cell_render h1 {\n",
        "        font-weight: 200;\n",
-       "        font-size: 40pt;\n",
+       "        font-size: 20pt;\n",
        "        line-height: 100%;\n",
        "        color:#447adb;\n",
        "        margin-bottom: 0em;\n",
@@ -247,7 +247,7 @@
    "source": [
     "# CSS styling within IPython notebook\n",
     "from IPython.display import display, HTML\n",
-    "display(HTML(open('custom.css').read()))"
+    "display(HTML(open('css/custom.css').read()))"
    ]
   }
  ],

diff --git a/1. Raw data.ipynb → notebooks/1. Raw data.ipynb b/1. Raw data.ipynb → notebooks/1. Raw data.ipynb
@@ -86,7 +86,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 1,
    "metadata": {
     "collapsed": false
    },
@@ -95,32 +95,32 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Started analysis of mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 5% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 10% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 15% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 20% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 25% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 30% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 35% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 40% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 45% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 50% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 55% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 60% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 65% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 70% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 75% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 80% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 85% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 90% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Approx 95% complete for mutant1_OIST-2015-03-28.fq.gz\n",
-      "Analysis complete for mutant1_OIST-2015-03-28.fq.gz\n"
+      "Started analysis of mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 5% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 10% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 15% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 20% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 25% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 30% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 35% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 40% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 45% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 50% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 55% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 60% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 65% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 70% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 75% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 80% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 85% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 90% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Approx 95% complete for mutant2_OIST-2015-03-28.fq.gz\n",
+      "Analysis complete for mutant2_OIST-2015-03-28.fq.gz\n"
      ]
     }
    ],
    "source": [
-    "!fastqc reads/mutant1_OIST-2015-03-28.fq.gz"
+    "!fastqc reads/mutant2_OIST-2015-03-28.fq.gz"
    ]
   },
   {