Recent changes to install

install modified by Wei Li

Wei Li — Mon, 11 Sep 2023 20:24:01 -0000

--- v69
+++ v70
@@ -7,14 +7,14 @@
 To install MAGeCK through bioconda channel, first download and install the Python 3 variant of the [Miniconda Python distribution](http://conda.pydata.org/miniconda.html). Then, in the command line, type

     ::bash
-    conda install -c bioconda mageck
+    conda install -c bioconda -c conda-forge mageck

  That's it!

 An optional step (but recommended) is, you can create an isolated software environment for mageck by executing

     ::bash
-    conda create -c bioconda -n mageckenv mageck
+    conda create -c bioconda -c conda-forge -n mageckenv mageck

 in a terminal. The environment can be activated via

install modified by Wei Li

Wei Li — Tue, 18 Aug 2020 04:13:48 -0000

--- v68
+++ v69
@@ -54,7 +54,7 @@



-Or click the link [here (in cases the button points to a wrong file)](https://sourceforge.net/projects/mageck/files/0.5/mageck-0.5.9.3.tar.gz/download). 
+Or click the link [here (in cases the button points to a wrong file)](https://sourceforge.net/projects/mageck/files/0.5/mageck-0.5.9.4.tar.gz/download). 

 ---------------

install modified by Wei Li

Wei Li — Mon, 13 Apr 2020 03:52:42 -0000

--- v67
+++ v68
@@ -54,7 +54,7 @@



-Or click the link [here (in cases the button points to a wrong file)](https://sourceforge.net/projects/mageck/files/0.5/liulab-mageck-0.5.9.1.tar.gz/download). 
+Or click the link [here (in cases the button points to a wrong file)](https://sourceforge.net/projects/mageck/files/0.5/mageck-0.5.9.3.tar.gz/download). 

 ---------------

install modified by Wei Li

Wei Li — Sun, 12 Apr 2020 20:32:36 -0000

--- v66
+++ v67
@@ -82,14 +82,17 @@

 ### Optional dependencies ###

-Two optional softwares include [R](http://cran.r-project.org/) and [pdflatex](http://www.latex-project.org/). MAGeCK relies on both softwares to generating PDF reports if the **--pdf-report** option is used. If it is not possible to install them, you can also generate PDF reports by copying some MAGeCK output files to another computers with R and pdflatex are properly installed. See [Q and A](https://sourceforge.net/p/mageck/wiki/QA/) for more information. 
+Since version 0.5.9.3, MAGeCK updates the visualization module by generating a R markdown file (.Rmd) for **count** and **test** subcommand. This allows users to easily create a html-based report webpage using [RStudio](https://rstudio.com/). No additional dependencies are needed for running MAGeCK. However, to generate the report webpage, a computer with [Rstudio](https://rstudio.com/) and [rmarkdown](https://rmarkdown.rstudio.com/) are needed.
+
+
+
+
+To use the --pdf-report option, which is mainly used for visualization before 0.5.9.3, two optional softwares include [R](http://cran.r-project.org/) and [pdflatex](http://www.latex-project.org/). MAGeCK relies on both softwares to generating PDF reports if the **--pdf-report** option is used. If it is not possible to install them, you can also generate PDF reports by copying some MAGeCK output files to another computers with R and pdflatex are properly installed. See [Q and A](https://sourceforge.net/p/mageck/wiki/QA/) for more information. 

 If you use the **--pdf-report** option, [xtable](http://cran.r-project.org/web/packages/xtable/index.html) is required, and [gplots](http://cran.r-project.org/web/packages/gplots/index.html) as well as ggplot2 is optional. Use *install.packages("xtable")* and *install.packages(c("gplots","ggplot2"))* in R to install them.  

 You won't get any error messages if you don't have gplots, but you will get a more beautiful clustering figure in the pdf report of the *count* command.

-
-### What if I cannot install these R packages in my machine ###

 You can run MAGeCK without --pdf-report option, and copy some files to another machine with these R packages to generate pdf report. See [Q and A](https://sourceforge.net/p/mageck/wiki/QA/#the-test-or-count-command-is-successful-but-i-have-some-problems-producing-the-pdf-file-how-can-i-generate-the-pdf-file) for more details.

install modified by Wei Li

Wei Li — Thu, 12 Mar 2020 14:49:30 -0000

--- v65
+++ v66
@@ -1,3 +1,4 @@
+[TOC]
 # Installation #
 There are several ways to install MAGeCK.

@@ -44,7 +45,7 @@

 You can also download the software and install it by yourself. See the detailed instructions below. 

-[TOC]
+

 ## Download  ##

install modified by Wei Li

Wei Li — Thu, 12 Mar 2020 14:48:23 -0000

--- v64
+++ v65
@@ -38,7 +38,7 @@

 You can also run MAGeCK via Docker image which is automatically built upon each commit in our [bitbucket](https://bitbucket.org/liulab/mageck) source code. 

-To run through Docker image, install [Docker](https://www.docker.com/) on your own system, and follow the instructions in Tutorials on running Docker images.
+To run through Docker image, install [Docker](https://www.docker.com/) on your own system, and follow the instructions in [tutorials on running Docker images](https://sourceforge.net/p/mageck/wiki/demo/#tutorial-3-run-mageck-on-docker-image).

 ## Method 3: through source code ##

install modified by Wei Li

Wei Li — Tue, 04 Feb 2020 21:18:44 -0000

--- v63
+++ v64
@@ -38,7 +38,7 @@

 You can also run MAGeCK via Docker image which is automatically built upon each commit in our [bitbucket](https://bitbucket.org/liulab/mageck) source code. 

-To run through Docker image, install [Docker](https://www.docker.com/) on your own system, and follow instructions below on running Docker images.
+To run through Docker image, install [Docker](https://www.docker.com/) on your own system, and follow the instructions in Tutorials on running Docker images.

 ## Method 3: through source code ##

install modified by Wei Li

Wei Li — Tue, 04 Feb 2020 21:02:16 -0000

--- v62
+++ v63
@@ -34,7 +34,13 @@

 You can install MAGeCK-VISPR (which includes MAGeCK) using conda, a commonly used package management softare. The instructions to install MAGeCK-VISPR can be found on [MAGeCK-VISPR manual](https://bitbucket.org/liulab/mageck-vispr).

-## Method 2: through source code ##
+## Method 2: through Docker Image ##
+
+You can also run MAGeCK via Docker image which is automatically built upon each commit in our [bitbucket](https://bitbucket.org/liulab/mageck) source code. 
+
+To run through Docker image, install [Docker](https://www.docker.com/) on your own system, and follow instructions below on running Docker images.
+
+## Method 3: through source code ##

 You can also download the software and install it by yourself. See the detailed instructions below.

install modified by Wei Li

Wei Li — Sun, 18 Aug 2019 03:04:55 -0000

--- v61
+++ v62
@@ -22,15 +22,15 @@

 To update mageck, run

-     ::bash
-     conda update mageck
+    ::bash
+    conda update mageck

 from within the environment.

 This environment can be deactivated via

-     ::bash
-     source deactivate
+    ::bash
+    source deactivate

 You can install MAGeCK-VISPR (which includes MAGeCK) using conda, a commonly used package management softare. The instructions to install MAGeCK-VISPR can be found on [MAGeCK-VISPR manual](https://bitbucket.org/liulab/mageck-vispr).

install modified by Wei Li

Wei Li — Sun, 18 Aug 2019 03:03:10 -0000

--- v60
+++ v61
@@ -22,8 +22,8 @@

 To update mageck, run

-    ::bash
-    conda update mageck
+     ::bash
+     conda update mageck

 from within the environment.