Recent changes to Install

WikiPage Install modified by Vincent WALTER

Vincent WALTER — Tue, 26 Feb 2013 13:55:09 -0000

--- v21
+++ v22
@@ -41,11 +41,15 @@

 ####Graphical mode####

-Go into the folder containing the downloaded file:
+Go into the folder containing the downloaded file :

-Open the deb files with GDebi by double-clicking:
+![alternate "Go into the folder"](http://lbgi.igbmc.fr/~walterv/gepetto/sourceforge/images/00010.png)

-Click "Install Package":
+Open the deb files with GDebi by double-clicking :
+![alternate "Click Install Package"](http://lbgi.igbmc.fr/~walterv/gepetto/sourceforge/images/00011.png)
+
+
+Click "Install Package".

 ####Console mode####

WikiPage Install modified by Vincent WALTER

Vincent WALTER — Tue, 26 Feb 2013 13:21:49 -0000

--- v20
+++ v21
@@ -29,7 +29,7 @@
 * **biolo** : to install in /biolo dir or in the $HOME dir
 * **any** : to install according to the FHS (Filesystem Hierarchy Standard)

-You can also find the latest snapshot release [here](https://sourceforge.net/projects/gepetto/files/ Download):
+You can also find the latest snapshot release [here](https://sourceforge.net/projects/gepetto/files/ "Download"):

 Install

WikiPage Install modified by Vincent WALTER

Vincent WALTER — Fri, 22 Feb 2013 16:14:27 -0000

--- v19
+++ v20
@@ -54,7 +54,7 @@
 Run the following command:

 ~~~~~~
-sudo dpkg --force-depends -i 
+sudo dpkg --force-depends -i 
 ~~~~~~

 or
@@ -137,19 +137,17 @@
 gpgcheck=1
 ~~~~~~

-Then install Blast using the follwoing command :
+Then install Blast using the following command :

 ~~~~~~
 sudo yum install ncbi-blast
 ~~~~~~

-After install and configure script execution (see below), please check the value of GEPETTO 
-properties into the biolo/gepetto/bin/gepetto.properties and modify the path of
-dependencies if its wrong.
+After install and configure script execution (see below), please check the value of [GEPETTO ] properties into the _biolo/gepetto/bin/gepetto.properties_ and modify the path of dependencies if its wrong.

 #####GEPETTO Install#####

-Choose a GEPETTO destination directory __ and put the .tar.gz file
+Choose a [GEPETTO] destination directory __ and put the .tar.gz file

 ~~~~~~
 cd  && tar -xzvf 
@@ -157,12 +155,17 @@
 sh ./configure
 ~~~~~~

-This will add aliases to read GEPETTO man pages using 
+This will add aliases to read [GEPETTO] man pages using 

 ~~~~~~
 mangepetto 
 ~~~~~~

-and add GEPETTO commands to the PATH in .bashrc and .cshrc files
+and add [GEPETTO] commands to the PATH in .bashrc and .cshrc files

 To use it, you have to open a new instance of shell in the terminal (csh, tcsh, bash,...)
+
+How to use it?
+--------------
+
+See the [Usage] page. Let's go!

WikiPage Install modified by Vincent WALTER

Vincent WALTER — Fri, 22 Feb 2013 16:11:25 -0000

--- v18
+++ v19
@@ -1,5 +1,7 @@
 INSTALL
 =======
+
+[TOC]

 Prerequisites
 -------------

WikiPage Install modified by Vincent WALTER

Vincent WALTER — Fri, 22 Feb 2013 16:10:14 -0000

--- v17
+++ v18
@@ -145,3 +145,22 @@
 properties into the biolo/gepetto/bin/gepetto.properties and modify the path of
 dependencies if its wrong.

+#####GEPETTO Install#####
+
+Choose a GEPETTO destination directory __ and put the .tar.gz file
+
+~~~~~~
+cd  && tar -xzvf 
+cd /biolo/gepetto
+sh ./configure
+~~~~~~
+
+This will add aliases to read GEPETTO man pages using 
+
+~~~~~~
+mangepetto 
+~~~~~~
+
+and add GEPETTO commands to the PATH in .bashrc and .cshrc files
+
+To use it, you have to open a new instance of shell in the terminal (csh, tcsh, bash,...)

WikiPage Install modified by Vincent WALTER

Vincent WALTER — Fri, 22 Feb 2013 16:06:53 -0000

--- v16
+++ v17
@@ -102,3 +102,46 @@
 manually (due to the absence of .rpm package).

 ######R Install######
+
+~~~~~~
+sudo yum install R
+~~~~~~
+
+
+######RJava install######
+
+~~~~~~
+sudo R
+install.packages('rJava')
+quit()
+~~~~~~
+
+######Python 3 install######
+
+~~~~~~
+sudo yum install python3
+~~~~~~
+
+######Blast install######
+
+Create the /etc/yum.repos.d/rpm-sphere.repo file and put it into it (as sudo user):
+
+~~~~~~
+[rpm-sphere]
+name=RPM Sphere
+baseurl=http://download.opensuse.org/repositories/home:/zhonghuaren/Fedora_17/
+gpgkey=http://download.opensuse.org/repositories/home:/zhonghuaren/Fedora_17/repodata/repomd.xml.key
+enabled=1
+gpgcheck=1
+~~~~~~
+
+Then install Blast using the follwoing command :
+
+~~~~~~
+sudo yum install ncbi-blast
+~~~~~~
+
+After install and configure script execution (see below), please check the value of GEPETTO 
+properties into the biolo/gepetto/bin/gepetto.properties and modify the path of
+dependencies if its wrong.
+

WikiPage Install modified by Vincent WALTER

Vincent WALTER — Fri, 22 Feb 2013 16:03:30 -0000

--- v15
+++ v16
@@ -3,6 +3,7 @@

 Prerequisites
 -------------
+
 The [GEPETTO] installers assume you have Python3, R/RJava and Blast (from NCBI) installed. If you don't, use the following links to download and install them :

 * **Python3**: http://www.python.org/download/
@@ -15,6 +16,7 @@

 Download the installer
 ----------------------
+
 First of all, you need to download the installer. There are different versions :

 * a Red Hat Enterprise Linux based compatible
@@ -64,6 +66,7 @@
 If you don't have user rights, use the _gepetto-all_version-biolo.deb_ version.

 #####Caution#####
+
 If you do not have sudo rights, you must install [GEPETTO] in a directory where you can read write and execute file : for example in your $HOME directory.

 Due to the structure and standards imposed by _.deb_ packages, this practice violates tje FHS (Filesystem Hierarchy Standard). The common procedure applied by __dpkg__ or __gdebi__ can not be applied. You will have to use the command __dpkg -X__ which does not check if dependencies are satisfied on your computer. You have the responsability to check if all of those dependencies necessary for the [GEPETTO] usage are previously installed.
@@ -88,6 +91,14 @@

 ###Fedora-based OS###

+####Console mode####

+#####Prerequisites#####

-####Console mode####
+For Debian-based distributions (Debian, LMDE, Linux Mint, Ubuntu,...), you can 
+download the corresponding .deb package that will resolve and install 
+dependencies but for RedHat-based distributions (Red Hat Enterprise Linux, Fedora, CentOS, 
+Mandriva, openSUSE, SUSE Linux Enterprise,...) you have to install dependencies
+manually (due to the absence of .rpm package).
+
+######R Install######

WikiPage Install modified by Vincent WALTER

Vincent WALTER — Fri, 22 Feb 2013 16:01:39 -0000

--- v14
+++ v15
@@ -61,7 +61,7 @@

 #####As simple user#####

-
+If you don't have user rights, use the _gepetto-all_version-biolo.deb_ version.

 #####Caution#####
 If you do not have sudo rights, you must install [GEPETTO] in a directory where you can read write and execute file : for example in your $HOME directory.

WikiPage Install modified by Vincent WALTER

Vincent WALTER — Fri, 22 Feb 2013 15:59:34 -0000

--- v13
+++ v14
@@ -61,6 +61,8 @@

 #####As simple user#####

+
+
 #####Caution#####
 If you do not have sudo rights, you must install [GEPETTO] in a directory where you can read write and execute file : for example in your $HOME directory.

@@ -76,13 +78,13 @@
 cd  && dpkg -X  
 ~~~~~~

-Go into the GEPETTO directory _biolo/gepetto_ and reconfigure the program :
+Go into the [GEPETTO] directory _biolo/gepetto_ and reconfigure the program :

 ~~~~~~
 cd biolo/gepetto && bash configure
 ~~~~~~

-Use a new terminal instance (bash or tcsh) to ensure that specific commands GEPETTO are recognized by the console
+Use a new terminal instance (with a shell .bashrc or .cshrc compatible) to ensure that specific commands [GEPETTO] are recognized by the console

 ###Fedora-based OS###

WikiPage Install modified by Vincent WALTER

Vincent WALTER — Fri, 22 Feb 2013 15:58:02 -0000

--- v12
+++ v13
@@ -68,6 +68,24 @@

 #####Install#####

+First step to install is the copy of _gepetto-all_version.deb_ file into the __ that you have defined.
+
+Go into this directory and decompress the package :
+
+~~~~~~
+cd  && dpkg -X  
+~~~~~~
+
+Go into the GEPETTO directory _biolo/gepetto_ and reconfigure the program :
+
+~~~~~~
+cd biolo/gepetto && bash configure
+~~~~~~
+
+Use a new terminal instance (bash or tcsh) to ensure that specific commands GEPETTO are recognized by the console
+
 ###Fedora-based OS###

+
+
 ####Console mode####