From 40b24be23b8da462c4f51a768558a6a4241d4619 Mon Sep 17 00:00:00 2001 From: Sasha Mikheyev Date: Wed, 20 Jul 2016 09:25:14 +0900 Subject: [PATCH] clarified readme --- README.md | 6 ++- custom.css => css/custom.css | 0 index.ipynb | 4 +- .../1. Raw data.ipynb | 46 +++++++++---------- 4 files changed, 29 insertions(+), 27 deletions(-) rename custom.css => css/custom.css (100%) rename 1. Raw data.ipynb => notebooks/1. Raw data.ipynb (86%) diff --git a/README.md b/README.md index ac60586..c6476ee 100644 --- 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. \ No newline at end of file +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 \ No newline at end of file diff --git a/custom.css b/css/custom.css similarity index 100% rename from custom.css rename to css/custom.css diff --git a/index.ipynb b/index.ipynb index 061d3af..dea4046 100644 --- 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 b/notebooks/1. Raw data.ipynb similarity index 86% rename from 1. Raw data.ipynb rename to notebooks/1. Raw data.ipynb index ff1c6ac..316a4cf 100644 --- a/1. Raw data.ipynb +++ b/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" ] }, {