Configurar la cuenta de email del CSIC para usarla desde GMAIL

Hola,

aquí pongo las instrucciones a seguir para poder recibir los correos del CSIC en GMAIL, y poder escribir los correos desde GMAIL para que se envíen como correos escritos desde la cuenta del CSIC. Además, se puede configurar para que al responder correos se haga automáticamente utilizando la cuenta original receptora del mensaje o no. También se puede decidir si los emails recibidos a través del CSIC vayan directamente con una etiqueta concreta a GMAIL e incluso que se archiven directamente. No voy a entrar en detalle en todas estas opciones, porque me ha parecido que están muy claras. Sí voy a comentar lo que pueda ser menos claro.

1. Enviar correos como cuenta del CSIC desde GMAIL.

Entrar en la cuenta de GMAIL.
Ir al icono del engranaje y pinchar en Configuración.
Ir a la pestaña Cuentas e Importación.
En "Enviar mensajes como:" añadir la cuenta del CSIC.
Seguir las instrucciones de activación, etc y configurar las opciones.

2. Recibir los correos del CSIC en la cuenta de GMAIL.

Entrar en la cuenta de GMAIL.

Ir al icono del engranaje y pinchar en Configuración.
Ir a la pestaña Cuentas e Importación.
En "Comprobar el correo de otras cuentas (mediante POP3):" pichar en "Añadir una cuenta de correo POP3 tuya".
Escribir la cuenta del CSIC.
Cambiar el nombre de usuario al que usamos en el CSIC.
Poner el password de la cuenta del CSIC.
En "Servidores POP:" poner "correo.csic.es".
Ahora el puerto:
- Si no marcamos la opción de "Utilizar siempre una conexión SSL..." poner puerto 110.
- Si sí la marcamos poner el puerto 995.
Cambiar las opciones de etiquetas, etc.

HECHO!

The quest to install Biopieces

This is my own experience installing Biopieces on Ubuntu 10.04 Lucid Lynx LTS.

sudo apt-get install subversion
sudo perl -MCPAN -e 'install inline'
sudo perl -MCPAN -e 'install JSON::XS'
sudo apt-get install curl
bash -s stable < <(curl -s https://raw.github.com/wayneeseguin/rvm/master/binscripts/rvm-installer)
source ~/.rvm/scripts/rvm
rvm install 1.9.3
sudo gem install rubygems-update
cd /var/lib/gems/1.9.1/bin
sudo ./update_rybygems
sudo gem install gnuplot
sudo apt-get install ruby1.9.3-dev
sudo gem install narray
sudo gem install RubyInline
sudo bash biopieces_install....sh

Warnings: blastall, blat, bwa, bowtie, formatdb, gnuplot, idba, mummer, mysql, prodigal, ray, scan_for_matches, usearch, velveth, velvetg, vmatch

Does biopieces deserve its own Linux distribution?

Some notes about profiles, bash and PATH variable Ubuntu 10.04 LTS

It seems there are 4 places one could edit to get PATH updated permanently.

I. /etc/profile

And the directory for scripts:
/etc/profile.d/*.sh

I could add something like: "export PATH=$PATH:/whatever"

in /etc/profile file using, for instance, pico program.

This file should be running all the .sh files in /etc/profile.d/

And it seems that includes /etc/bash.bashrc

II. /etc/bash.bashrc

# System-wide .bashrc file for interactive bash(1) shells.

III. ~/.profile


Lets take a look at the file ~/.profile:


# ~/.profile: executed by the command interpreter for login shells.
# This file is not read by bash(1), if ~/.bash_profile or ~/.bash_login
# exists.
# see /usr/share/doc/bash/examples/startup-files for examples.
# the files are located in the bash-doc package.

# the default umask is set in /etc/profile
#umask 022

# if running bash
if [ -n "$BASH_VERSION" ]; then
    # include .bashrc if it exists
    if [ -f "$HOME/.bashrc" ]; then
. "$HOME/.bashrc"
    fi
fi

# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/bin" ] ; then
    PATH="$HOME/bin:$PATH"
fi

It seems that includes ~/.bashrc
and adds ~/bin if it exists.
But no words about /etc/profile.d

IV. ~/bashrc

# ~/.bashrc: executed by bash(1) for non-login shells.

We can add lines to the end of the file like:

export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/usr/games:$PATH

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

From bash man page:

"When bash is invoked as an interactive login shell, or as a non-interactive shell with the --login option, it first reads and executes commands from the file /etc/profile, if that file exists.

After reading that file, it looks for (~/.bash_profile, ~/.bash_login and ~/.profile) in that order, and reads and executes commands from the first one that exists and is readable.

[...]

When an interactive shell that is not a login shell is started, bash reads and executes commands from /etc/bash.bashrc and ~/.bashrc, if these files exist.

[...]

From http://askubuntu.com:

edit .bashrc in your home directory and add the following line:

export PATH=/path/to/dir:$PATH

A path set in .bash_profile will only be set in a bash login shell (bash -l). If you put your path in .profile it will be available to your complete desktop session. That means even metacity will use it.

For example ~/.profile:

if [ -d "$HOME/bin" ] ; then
  PATH="$PATH:$HOME/bin"
fi

Btw, you can check the PATH variable of a process by looking at its environment in/proc/[pid]/environ. (replace [pid] with the number from ps axf)

Further explanations:
http://stefaanlippens.net/bashrc_and_others
http://www.linux-migration.org/ch02s03.html
http://www.admon.org/difference-between-login-shell-and-non-login-shell/

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

So, IMO, I should change /etc files when I have an application installed for all the system. When my application is installed at /home I should instead use the ~/.profile (for login shells) or ~/.bashrc (for non-login shells).

The question then is What the heck are login and non-login shells? As far as I know, a non-login shell is when I open my shell from Ubuntu using the icon in the X-Windows system. But I need more deep on this topic.

Finally, a good patient friend told me to think it this way: what I want to have in my /home in case I am moving to another place? Well, I want to have my clothes, my personal stuff but as I want to save money I want the heating to be central. As everybody in the building needs the heating, I can change the /etc files. As only I want to manage my clothes, photos, etc. this will be on ~/. files. At last, if I want to get everything since I log in, I will change "profile" files. If I just want to use somethings from a bash shell, I change "bashrc" files.

coda: the question that remains for me is Why when I changed the /etc/profile.d/ adding a *.sh file with something like "export PATH=$PATH:/kakakakakakak" didn't seem to work? I will continue researching on this later.

O.,o

Installing 454 Data Analysis v2.6 on Ubuntu 10.04 LTS

This is a backup text about the problems I had when installing that software, the solution I finally achieved and the opened questions remaining.

- First of all, I tried to execute like this

./setup.sh

with the following result:

export: 9: software/DataAnalysis_2.6_All/setup.sh: bad variable name

- Then, I tried to execute from a copy I burned into a CD. The result was:

i) on the awful white backgrounded installing window:

/sbin/lspci: not found

ii) window with the text

Cannot execute command: type rocks2&gt;&amp;1

- On SeqAnwers it was the solution for me. But as well some strange advices.
First, some people was telling to try:

sudo ln -s /bin/true ~/bin/rocks
sudo ./setup.sh

Since /bin/true returns true, we are cheating the install program. I didn't want to do that and moreover some people was being able to install but getting some errors afterwards.

- Son on SeqAnwers.com I found a solution, altough really long. I actually would like to resolve the errors I am describing above, to get a fast forward install process but... meanwhile:


I am trying the first one.
pico .bashrc

On the pico editor, at the end of the file, type:

"export PATH=$PATH:/opt/454/bin"

Then, create directories:

cd /opt
sudo mkdir 454
sudo mkdir 454/apps
sudo mkdir 454/apps/jre

cd user_directory_at_home/454soft/DataAnalysis_All/packages
cp newbler_CLI-2.6.i686.tgz /opt/454

(Here I had another problem. I first did copy the 64 bits package and I found I could not execute sfffile and similar SFFtools, stil wondering why...)

cp assembly_GUI_2.6.noarch.tgz /opt/454/apps
cp (the same with mapper)
cp (the same with amplicon)

cd opt/454
sudo tar -xzvf newbler...tgz
cd apps
sudo tar -xzvf assembly...tgz
sudo (the same with mapper)
sudo (the same with amplicon)

sudo rm -r .*tgz
cd ..
sudo rm -r .*tgz

ls /opt/454

apps bin config

ls /opt/454/apps

amplicons assembly jre mapper

Now that everything is ready, we have to create the symbolic linnks:
(if you create a link by error, you can erase it with # sudo unlink name_of_link)

cd /opt/454/apps/jre
sudo ln -s /usr/lib/jvm/java-6-openjdk jre1.6.0_13

cd ..
cd assembly/jre
sudo ln -s ../../jre/jre1.6.0_13 jre1.6.0_13
cd ../amplicon/jre
sudo ln (exactly the same)
cd ../mapper/jre
sudo ln (exactly the same)

finally:

cd /opt/454/bin
sudo ln -s ../apps/assembly/bin/gsAssembler gsAssembler
sudo ln -s ../apps/mapper/bin/gsMapper gsMapper
sudo ln -s ../apps/amplicons/bin/gsAmplicon gsAmplicon
sudo ln -s ../apps/amplicons/bin/doAmplicon doAmplicon


TEST! Thank you to WaltL from SeqAnswers.com forum: http://seqanswers.com/forums/showthread.php?t=8944

Finally, I hope to find the anwers to the initial problems, to can get an easier installation.

best wishes!