Impilo Central - en:install

apache_config_impilo

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Apache virtual host for Impilo Ideally, all documentation created for Impilo will be put in a centralized, Web-delivered resource. To allow this, I created a virtual host profile with the following content: * First, let's copy the default host settings to an impilo-specific file:

archeopteryx_4104

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Archeopteryx 4.1.04 Additional libraries Java, already installed. Procedure here is the procedure to install de Archeopteryx: * The application is contained in a JAR archive named forester.jar. After downloading it, create a folder named

archeopteryx

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Archeopteryx Web site: http://www.phylosoft.org/archaeopteryx/ License: GNU LGPL v.3 Installed version Impilo 8.04 H10 v.4.1.04

artemis_11

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Artemis 11 Additional libraries Java, already installed. Procedure Here is the procedure to install Artemis: * After downloading the TAR archive and decompressing it into /home/bioubuntu, move the newly created artemis folder under

artemis

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Artemis General informations * Web site: http://www.sanger.ac.uk/Software/Artemis/ * License: GNU GPL v.3 Installation instructions Installed version Impilo 8.04 H10 11 Impilo 10.04 A10 12 Usage instructions

beast_153

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of BEAST 1.5 Additional librairies Java, already installed. Procedure Here is the procedure to install BEAST: * After downloading the archive from the web in /home/bioubuntu, decompressed it and move the newly created folder in /opt/bio/sources

beast

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

BEAST Web site: http://beast.bio.ed.ac.uk/Main_Page License: GNU LGPL v.2.1 Installed version Impilo 8.04 H10 v.1.5.3

bin_app_select

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation instructions for building the bioinformatics apps in Impilo As its first goal, Impilo provides on a single server the largest number of bioinformatics applications while also providing the most pertinent documentation on their uses for teaching and academic purposes.

bioc_25

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Bioconductor 2.5 Additional libraries At system level: * libxml2-dev * libcurl4-openssl-dev % sudo apt-get install libxml2 libcurl4-openssl-dev R will take care of everything else ;-) Procedure Bioconductor having an absolute requirement of having R

bioconductor

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Bioconductor General informations * Web site: http://www.bioconductor.org * Licence: vary according to the modules, but a mix of Artistic 2.0, GPL v.2 and BSD Installation instructions Installed version Impilo 8.04 H10 2.5 Impilo 10.04 A10

blast_2222

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of BLAST 2.2.22 Additional libraries None needed Procedure For the past couple of years, there has been two versions of NCBI BLAST in the wild: BLAST and BLAST+, a complete rewrite of BLAST in C++. Although it has many advantages (easier to use and faster among other things), BLAST+ has this big problem: it consumes a hell of lot more space than BLAST, which is a problem for a VM-based distro like Impilo which has as a goal to keep its footprint small. Because of that, I chose t…

blast

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

NCBI BLAST General informations * Web site: ftp://ftp.ncbi.nlm.nih.gov/blast/executables * License: public domain software, freely accessible Installation instructions Installed Version Impilo 12.04 A12 2.2.26+ Basic usage * More to come

build_cycle

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Impilo construction cycle Each year, there are two dates in my calendar that can't be ignored, which I use as flags in my process to build Impilo: * St-Swithin day, July 15th, which also correspond to the yearly major update of the EMBOSS suite; * 15 September, which more or less the beginning of my Fall trimester teaching cycle at the

clustalw

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

CLUSTALW General informations * Web site : http://www.clustal.org * License: free to use for non-commercial purposes. Details are available here Installation instructions Impilo Version Installed version Impilo 10.04 A10 2.0.12 Impilo 11.04 A11

clustalx

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

CLUSTALX General informations * Web site: http://www.clustal.org * License: free to use for non-commercial purposes. Details are available here Installation instructions Impilo versions Installed version Impilo 10.04 A10 2.0.12 Impilo 11.04 A11

cndsrc_20091117

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Mercator Additional libraries Some of Mercator's functions depend on some otehr applications that are not present in a basic Impilo install. \\Taken from the README file: PREREQUISITES ------------- In order to successfully compile the programs in this package, you must have a couple of external packages installed. These are: - Optik: http://optik.sourceforge.net/ - Only required if your version of python is < 2.3. This python library must be installed system-wide or …

cytoscape_263

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Cytoscape 2.6.3 Additional libraries Java, already installed. Procedure Here is the procedure to install Cytoscape: * Cytoscape is distributed as a JAR archive ready to use. Download the archive version (not the one with a JRE with it: we already have a functioning Java installation), decompressed under

cytoscape

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Cytoscape Web site: http://www.cytoscape.org License: GNU LGPL v.2.1 Installed version Impilo 8.04 H10 v.2.6.3

dev_app_select

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of software development environments in Impilo Although the courses we teach do not require that students to know how to program, we strongly advise them to get their acts together and learn at least one programming language. In addition, some minimal components are require to compile bioinformatics applications from source code. For Impilo, I decided to install the necessary tools to exploit the three most used toolboxes in bioinformatics:

develop_impilo_8.04

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Software Development Environments selected for Impilo Here is the content of the file named develop_module.txt used to build Impilo 8.04. # # Developer's tools for Impilo # build-essential sun-java6-jdk bioperl python-biopython php5-cli php5-gd php-pear

dotter

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Dotter General informations * Web site: http://www.sanger.ac.uk/resources/software/seqtools/ * License: The original license is unknown but the SeqTools package which now contains Dotter is using the GPL v.3 license. Installation instructions Installed Version Impilo 11.04 A11

draw_app_select

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Image Manipulation Applications in Impilo Because so much of the data coming into bioinformatics these days is image-based (i.e.: high-throughput sequencing and cell-based screening), Impilo needs to provide its users som tools to create and edit images. This is also necessary to put images in context for presentation and publication. For this, we need to provide the best we can find in their field.

emboss

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

EMBOSS General informations * Web site: http://www.emboss.org * License: AJAX and NUCLEUS librairies are under GNU LGPL v.3; the EMBOSS applications are under GNU GPL v.3 Installation instructions Impilo version Installed version Impilo 10.04 A10

erpin_55

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Erpin 5.5 Additional libraries No additional library is necessary. Procedure Here is the procedure to install Erpin from its source code: * The archive is downloaded in /home/bioubuntu, decompressed and the resulting folder is moved to

erpin

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Erpin Web site: http://tagc.univ-mrs.fr/erpin/ License: Unknown Installed version Impilo 8.04 H10 5.5

exonerate_22

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Exonerate 2.20 Additional libraries No additional library is necessary. Procedure Here is the procedure to install Exonerate from source code: * The source code archive has been downloaded from its web location, decompressed in

fasta_3548

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of FASTA 35.4.8 Additional libraries None required Procedure Here is the procedure followed to install FASTA from its source code: * The source code archive was downloaded and put under /home/bioubuntu, decompressed and the created folder is moved toward

fasta

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

FASTA 35 General informations * Web site : http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml * License: free to use for non-commercial purposes Installation instructions Installed version Impilo 8.04 H10 35.4.8 Basic usage * More to come... References * More to come...

figtree_131

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of FigTree 1.3.1 Additional libraries Java, already installed. Procedure Here is the procedure to install FigTree: * After downloading the archive the FigTree files, yo uhave to decompressed it in /home/bioubuntu and move the newly created folder in

figtree

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

FigTree Web site: http://beast.bio.ed.ac.uk/FigTree License: GNU GPL v.3 (???) Installed version Impilo 8.04 H10 v.1.3.1

fsa_1152

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of FSA 1.15.2 Additionnal libraries Aucune en tant que tel mais certaines des fonctions d'alignement de génome dépendent du trio MUMmer/Exonerate/Mercator. Assurez-vous de les avoir installés :-) Procedure Here is the procedure for installing FSA from source code:

fsa

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

FSA General information * Web site: http://fsa.sourceforge.net * License: GNU GPL v.3 Installation instructions Installed version Impilo 8.04 H10 1.15.2 Usage instructions * More to come... References * More to come...

gblocks_091b

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Gblocks Additional libraries The ia32-libs package is necessary to run Gblocks on a x86_64 operating system. This should be covered if you start a server from scratch with these instructions. If you are installing on another Ubuntu server, do this:

gblocks

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

GBlocks Web site: http://molevol.cmima.csic.es/castresana/Gblocks.html License: Unknown... Installed version Impilo 8.04 H10 0.91b

graphics_impilo_8.04

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Image Manipulation Applications in Impilo 8.04 Here is the content of graphics_module.txt used in building Impilo 8.04. # # Graphics tools for Impilo # gimp gimp-data gimp-dcraw gimp-helpbrowser gimp-help-common gimp-help-fr gimp-help-en gimp-data-extras gimp-gutenprint gimp-plugin-registry ghostscript inkscape imagemagick xfmedia xfmedia-remote-plugin xsane xsane-doc

gui_select

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installing the graphical user interface Rationale I chose the Xfce graphical environment for the following reasons: * It needs less resources than GNOME or KDE, which makes it a perfect solution for a virtual machine. * It includes nearly everything that one needs for a desktop environment, providing a user experience quite similar to Mac

imagej_143b

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of ImageJ 1.43b Additional libraries Java, already installed. Procedure here is the procedure to install ImageJ: * ImageJ is contained in a JAR archive, all ready to execute via a script called run found in the folder created after decompressing the Zip archive. The whole ImageJ folder has to be moved to

imagej

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

ImageJ General informations * Web site: http://rsb.info.nih.gov/ij * Licence: Free software in the public domain. Installation instructions Installed Version Impilo 8.04 H10 1.43b Impilo 10.04 A10 1.44d

ingap_201

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of inGAP 2.0.1 Additional libraries Java, already installed. Procedure Here is the procedure to install inGAP: * InGAP is distributed in a *.tar.gz archive. This archive is decompressed into /home/bioubuntu and the resulting folder is moved into

ingap

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

InGAP Web site: http://sites.google.com/site/nextgengenomics/ingap License: GNU LGPL v.3 Installed version Impilo 8.04 H10 2.0.1 ATTENTION! InGAP is only found in Impilo 64-bit editions since there is no packages for 32-bits systems.

internet_app_select

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Internet Applications in Impilo Let's face it: without the internet, bioinformatics would never work as it does =) Therefore, IMpilo has to provide the necessary applications to communicate and acquire the necessary day-to-day information needed by a bioinformatician. As always, to keep Impilo focused on its main task, no chat application for us!

internet_impilo_8.04

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Internet Applications selected for Impilo 8.04 Here is the content of the file named internet_module.txt used to build Impilo 8.04. # # Minimal Internet utilities for Impilo # firefox firefox-3.0-gnome-support thunderbird thunderbird-gnome-support thunderbird-locale-fr filezilla filezilla-locales sshfs

jalview_24

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Jalview 2.4 Additional libraries Java, which is already installed. Procedure Here is the procedure to install Jalview: * Jalview is distributed as a binary installer. Create a folder in /home/bioubuntu to put ut in and move it to

jalview

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Jalview General informations * Web site: http://www.jalview.org * License: GNU GPL v2 Installation instructions Installed version Impilo 8.04 H10 2.4 Basic usage * More to come... References * More to come...

jchempaint_310

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of JChemPaint 3.1.0 Additional libraries Java, already installed. Procedure Here is the procedure to install JChemPaint: * JChemPaint is distributed as a JAR archive, ready to execute. Create a folder under /home/bioubuntu to put the archive in and move this folder to

jchempaint

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

JChemPaint General informations * Web site: http://sourceforge.net/apps/mediawiki/cdk/index.php?title=JChemPaint * License: GNU LGPL v.2.1 Installation instructions Installed version Impilo 8.04 H10 3.1.0 Impilo 10.04 A10 3.1.2 Usage instructions

jmol_11746

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Jmol 11.7.46 Additional libraries Java, already installed. Procedure Here is the procedure to install Jmol: * Jmol is distributed as a JAR archive, ready to execute through a startup script. Create a folder under /home/bioubuntu

jmol

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Jmol General informations * Web site: http://jmol.sourceforge.net * License: GNU LGPL Installation instructions Installed version Impilo 8.04 H10 11.7.46 Impilo 10.04 A10 12.0.2 Usage instructions

kalign

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

KAlign 2 General informations * Web site: http://msa.sbc.su.se/cgi-bin/msa.cgi * License: GNU GPL v2 Installation instructions Installed version Impilo 8.04 H10 2.0.4 Basic usage * More to come... References * More to come...

mafft_6707

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of MAFFT 6.707 Additional libraries No additional library is required. Procedure Follow this procedure to install MAFFT from its source code: * The archive with the soource code is downloaded from its web site in /home/bioubuntu, decompressed and the created folder is moved into

mafft

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

MAFFT General informations * Web site: http://align.bmr.kyushu-u.ac.jp/mafft/software/ * License: open source if license description file is kept and made accessible. Some of the components are free for academic, educational and/or commercial uses as long as no fee is asked (except media cost).

mesquite_272

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Mesquite 2.72 Additional libraries Java, already installed. Procedure Here is the procedure to install Mesquite: * After downloading the Mesquite archive from the web, it is decompressed in /home/bioubuntu and moved in /opt/bio/sources

mesquite

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Mesquite Web site: http://www.mesquite.org License: GNU LGPL v.2.1 Installed version Impilo 8.04 H10 2.72

mev_451

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of TM4 MeV 4.5.1 Additional libraries Java, already installed. Procedure Here is the procedure to install MeV: * MeV is distributed as a startup script that encapsulated a collection of JAR files with the application and auxiliaries. In Linux, MeV is distributed wither in a 32-bit or 64-bit version since a local R install is installed (as of version 4.5, there is an internal dependency between MeV and R which makes MeV dependant on a specific verion of R); download the right …

mev

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

TM4 MeV Web site: http://www.tm4.org/mev/ License: Artistic License v.2 Installed version Impilo 8.04 H10 v.4.5.1

midas_221

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of TM4 MIDAS 2.21 Additional libraries Java, already installed. Procedure Here is the procedure to install MIDAS: * MIDAS is distributed as a JAR archive (Midas.jar) and a collection of auxiliary JAR files. Download and decompress the ZIP archive in

midas

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

TM4 MIDAS Web site: http://www.tm4.org/midas.html License: Artistic License v.2 Installed version Impilo 8.04 H10 v.2.21

mira_3rc4

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of MIRA 3.0RC4 Additional libraries If you start from source code, you will need libboost-dev: % sudo apt-get -y install libboost-dev However, take note that the Ubuntu 8.04 version of this package is too old (1.34) compared to the required version needed to compile MIRA from source ( should be >1.35).

mira

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

MIRA General informations * Web site: http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Page * License: GNU GPL v.2 Installation instructions Installed version Impilo 8.04 H10 3.0RC4 Impilo 10.04 A10 3.2.0RC2 Usage instructions

mrbayes_312

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of MrBayes 3.1.2 Additional libraries No additional library is necessary. Procedure Here is the procedure to install MrBayes from source code: * The archive with the source code is downloaded from the web in /home/bioubuntu, decompressed and the created folder is moved in

mrbayes

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

MrBayes Web site: http://mrbayes.csit.fsu.edu/ License: GNU GPL v.2 Installed version Impilo 8.04 H10 3.1.2

mummer_321

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of MUMmer 3.21 Additional libraries No additional library is necessary. Procedure Here is the procedure to install MUMmer from source code: * The archive with the source code has been downloaded from its web location, decompressed into

muscle_37

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of MUSCLE 3.7 Additional libraries No additional library is required. Procedure This is the procedure to follow to install MUSCLE from source code: * The archive with the source code is downloaded from its web location in /home/bioubuntu

muscle3

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

MUSCLE 3 General informations * Web site: http://www.drive5.com * License: Public domain Installation instructions Installed Version Impilo 8.04 H10 3.7 Basic usage * More to come... References * More to come

njplot_23

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of NJPlot 2.3 Additional libraries * lesstif2 * ncbi-data * libncbi6-dev * libvibrant6-dev % sudo apt-get -y install lesstif2 ncbi-data libncbi6-dev libvibrant6-dev Procedure Here is the procedure to install NJPlot from source code:

njplot

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

NJPlot Web site: http://pbil.univ-lyon1.fr/software/njplot.html License: Artistic License Installed version Impilo 8.04 H10 v.2.3

office_app_select

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Office/Productivity Applications in Impilo Impilo needs to provide to its users tools to manipulate text files as well as matrix-based formatted files (i.e. Excel). However, one of the goals of the distro is to keep it as small as possible to work at its best in a virtual machine environment. OpenOffice, however good it might be, is not optimal

office_impilo_8.04

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Office-like Applications in Impilo 8.04 Here is the content of the file named office_module.txt used in Impilo. # # Office-like applications for Impilo # abiword abiword-help abiword-plugins aspell-en aspell-fr gnumeric gnumeric-plugins-extra gnumeric-doc latex-xft-fonts

pathvisio_201

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation de PathVisio 2.0.1 Libraries additionnelles Java, already installed. Procédure Here is the procedure for installing PathVisio: * PathVisio is distributed as a Java Web Start file. Create a folder under /home/bioubuntu and move the

pathvisio

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

PathVisio Web site: http://www.pathvisio.org License: Apache License v.2 Installed version Impilo 8.04 H10 v.2.0.1

phylip_368

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of PHYLIP 3.68 Additional libraries See this link Procedure PHYLIP is a part of the EMBASSY application packages that are installed with EMBOSS in Impilo. Therefore, there is no need to install it as a standalone. The various PHYLIP programs are accessible through the appropriate EMBOSS wrappers, which start with the letter

phylip

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

PHYLIP Web site: http://evolution.genetics.washington.edu/phylip.html License: no explicit license beside the fact that it should never be sold as is or as part of a commercial product. Installed version Impilo 8.04 H10 3.68

phylobayes_2.3

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of PhyloBayes 2.3 Additional libraries * gsl-bin * libgsl0-dev % sudo apt-get -y install gsl-bin libgsl0-dev Procedure Here is the procedure to install PhyloBayes from source code: * The archive with the source code is downloaded from the web in

phylobayes

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

PhyloBayes Web site: http://www.atgc-montpellier.fr/phylobayes/ License: free to use/free to own for academics usages. Installed version Impilo 8.04 H10 2.3

phyml

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of PhyML 3.0 Additional libraries No additional library is required. Procedure You have to register on the website to get access to the executables and/or the source code (by contacting the author). Here is the procedure to install PhyML using the executable:

primer3

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Primer3 General informations * Web site: http://primer3.sourceforge.net * License: GNU GPL v.2 Installation instructions Installed version Impilo 10.04 A10 2.2.2-beta Impilo 11.04 A11 2.2.3 Basic usage Informations and tutorial provided by the application.

primer3plus_100

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Primer3Plus 1.0.0 Additional Libraries No additional libraries are necessary. Procedure Primer3Plus is not an application per se but rather a web interface to interact with Primer3. There is no compilation to be performed but you need to make sure that it is available to a local web browser using these instructions:

primer3plus

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Primer3Plus Web site: http://primer3.sourceforge.net License: GNU GPL v.2 Installed version Impilo 8.04 H10 1.0.0

pymol_123

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Pymol 1.2r3pre Additional libraries Many... Procedure Still again, the dilemma: package vs source code... Pymol has lots of dependencies which make compiling quite a work. However, it is popular enough in the community that a quite recent Ubuntu package exists. To install Pymol the Impilo way, I did the following:

pymol

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Pymol General informations * Web site: http://www.pymol.org * License: Free and open as long as original copyright notices not removed or changed Installation instructions Installed version Impilo 8.04 H10 1.2r3pre Impilo 10.04 A10 1.3 Usage instructions

r

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

R General informations * Web site: http://www.r-project.org * Licence: GNU GPL v.2 Installation instructions Installed version Impilo 8.04 H10 2.10 Impilo 10.04 A10 2.11.1 Usage instructions It is possible to get help informations on various methods and classes by two different procedures:

raxml_704

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation de RAxML 7.0.4 Additional libraries No additional library is required. Procedure Here is the procedure to install RAxML from source code: * The archive with the source code is downloaded from the web in /home/bioubuntu, decompressed and the newly created folder is moved to

raxml

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

RAxML Web site: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm License: GNU GPL v.2 Installed version Impilo 8.04 H10 7.0.4

readseq_2119

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of ReadSeq 2.1.19 Additional libraries Java, already installed. Procedure Here is the procedure to install ReadSeq: * ReadSeq is distributed as a JAR archive, ready for execution. Create a folder in /home/bioubuntu to put the archive in and move this folder to

readseq

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

ReadSeq General informations * Web site: http://iubio.bio.indiana.edu/soft/molbio/readseq/java/ * License: software in the public domain, open to all. Installation instructions Installed version Impilo 8.04 H10 2.1.19 Impilo 10.04 A10

rmaexpress_104

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of RMAExpress 1.0.4 Additional libraries * libwxgtk2.8-dev % sudo apt-get -y install libwxgtk2.8-dev Procedure Here is the procedure to install RMAExpress from its source code: * The archive with the source code is downloaded from its web site in

rmaexpress

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

RMAExpress Web site: http://rmaexpress.bmbolstad.com License: GNU GPL v.2 Installed version Impilo 8.04 H10 1.0.4

rnamotif_305

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of RNAMotif 3.0.5 Additional librairies The following libraries are necessary to successfully compile RNAmotif: * bison * byacc * flex % sudo apt-get -y install bison byacc flex Procedure Here is the procedure to install RNAMotif from its source code:

rnamotif

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

RNAMotif Web site: http://casegroup.rutgers.edu/ License: GNU GPL v.2 Installed version Impilo 8.04 H10 3.0.5

rproject_210

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of R 2.10 Additional libraries No additional library is necessary. Procedure Installing R * Source or package? In this case, it is a really good question to ask oneself... Impilo's principal philosophy is to install from source as much as possible but for R, I decided to start from the packages that are found on R's web site. Many of the applications found in Impilo are dependent on a correct R install so let's save ourselves from a mighty headache!

samtools

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

SAMtools General informations * Site web:http://samtools.sourceforge.net/ * License: License BSD and License MIT Installation instructions Installed versions Impilo 10.04 A10 0.1.8 Usage instructions * More to come... References * More to come

sirius_12

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Sirius 1.2 Additional libraries Java, already installed. Procedure Here is the procedure for installing de Sirius: * Sirius is distributed as a Java installer which take care of everything :-) After downloading it in /home/bioubuntu

sirius

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Sirius Web site: http://sirius.sdsc.edu Licence: Free use for academic or non-commercial applications Installed version Impilo 8.04 H10 1.2

spotfinder_321

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of TM4 Spotfinder 3.2.1 Additional libraries None with this procedure. If you decide to start from source code, you will need an old version of the Qt library (no more than 3.3.8) as well as libtiff4-dev and libgsl0-dev (already installed for

spotfinder

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

TM4 Spotfinder Web site: http://www.tm4.org/spotfinder.html License: Artistic License v.2 Version installé Impilo 8.04 H10 3.2.1

staden

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Staden package General informations * Web site:http://staden.sourceforge.net/ * License: License BSD Installation instructions Installed versions Impilo 10.04 A10 2.0.0b7 Usage instructions * More to come... References * More to come

starting_point

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Our starting points... We plan on building Impilo from the following rules: * We use the “Virtual Machine” approach. * Rationale: Most of the students are not very comfortable at starting their computers from a CD/DVD and they might not even have this recourse because people running computer labs might have either remove the drives or disable them. A virtual machine is more natural and allows sharing of files between the real and the virtual machines.

strap_070809

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of STRAP Compilation 07.08.09 Additional libraries Java, which is already installed. Procedure Here is the procedure to install STRAP: * STRAP is distributed as a JAR archive, with the program ready to run. Create a folder under /home/bioubuntu

strap

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

STRAP General informations * Web site: http://www.3d-alignment.eu * License: GNU GPL v2 Installation instructions Installed version Impilo 8.04 H10 07.08.09 Basic usage * More to come... References * More to come...

tcoffee_806

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of T-COFFEE 8.06 Additional libraries No additional library is necessary. Procedure This is the procedure to install T-COFFEE from source code: * The archive with the source code has been downloaded into /home/bioubuntu, decompressed and the resulting folder moved into

tcoffee

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

T-COFFEE General informations * Web site: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html * License: GNU GPL v3 Installation instructions Installed version Impilo 8.04 H10 8.06 Basic usage * More to come... References * More to come...

tracer_15

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Tracer 1.5 Additional libraries Java, already installed. Procedure Here is the procedure to install Tracer: * After downloading the archive with Tracer from the web, decompressed it in /home/bioubuntu and moved the newly created folder in

tracer

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Tracer Web site: http://beast.bio.ed.ac.uk/Tracer License: GNU LGPL v.3 Installed version Impilo 8.04 H10 v.1.5

tree_structure

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Impilo specific modifications to the base system Base Installation * As starting point, I use a CD-ROM image of Ubuntu's Minimal installer that I want to use; I use this ISO file as boot disk for my newly created VirtualBox's VM. * Use the latest LTS version (as of 06/2-13, it is Ubuntu 12.04).

treefinder_1008

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of Treefinder October 2008 Additional libraries Java, already installed. Procedure Here is the procedure to install Treefinder: * After downloading the archive containing the applications and auxiliary files, decompressed the ZIP archive in

treefinder

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Treefinder Web site: http://www.treefinder.de License: Free for scientific use. Installed version Impilo 8.04 H10 October_2008

treeview

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

TreeviewX Web site: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/ License: GNU GPL v.2 Installed version Impilo 8.04 H10 0.5.1

trnascan_123

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of tRNAscan-SE 1.23 Additional libraries No additional library is necessary. Procedure Here is the procedure for installing tRNAscan-SE from its source code: * The archive is downloaded from the web in /home/bioubuntu, decompressed and the newly created folder is moved into

trnascan

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

tRNAscan-SE Web site: http://lowelab.ucsc.edu/tRNAscan-SE/ License: GNU GPL v.2 Installed version Impilo 8.04 H10 1.23

tv_051

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of TreeviewX 0.5.1 Additional libraries * libwxgtk2.4-dev (libwxgtk2.6-dev ou libwxgtk2.8-dev; voir ci-dessus...) Procedure I have tried my best to compile TreeviewX from source but without much success: I only end up with a bunch of compile errors due to ambiguities in method names that turn the compiler into a moron. If anyone has had success, please let me know. I resigned myself to install from the Ubuntu package

unafold_37

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Installation of UNAFOLD 3.7 Additional libraries No additional library is necessary. Procedure Here is the procedure to install UNAFOLD from source code: * Download the archive with the source code in /home/bioubuntu, decompressed and move this new folder in

unafold

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

UNAFOLD Web site: http://dinamelt.bioinfo.rpi.edu/download.php License: UNAFold 3.x ACADEMIC NON-COMMERCIAL USE LICENSE AGREEMENT, allowing its use but not modifications of the source code, for research purposes only. Installed version Impilo 8.04 H10 3.7

xfcegui_impilo_8.04

Anonymous (anonymous@undisclosed.example.com) — 2021-05-29T19:35:54+00:00

Impilo 8.04 - Xfce Environement Here is the content of the xfcegui_module.txt file use to build Impilo 8.04. # # Packages to create Xfce4-based GUI for Impilo # acpi displays information on ACPI devices acpi-support a collection of useful events for acpi acpid Utilities for using ACPI power management anacron cron-like program that does not go by time apmd Utilities for Advanced Power Management (APM) avahi-daemon Avahi mDNS/DNS-SD daemon bc …