--text="Welcome to the NeuroDebian virtual machine!
This is the first time you have started this virtual machine. We will now perform a few simple steps to finalize its configuration. This includes upgrading the system to the latest available versions and installing additional software packages upon your request."
+fi
+
+if ! zenity --question $icon_opt --title="NeuroDebian Setup Wizard" \
+--text="The setup procedure requires network access to download packages from the Debian archive. If you do not have network access right now, you can re-start this wizard at any time from the NeuroDebian menu. If you proceed you may have to enter the superuser password with is by default 'neurodebian'.
+
+Do you want to proceed with updating the system?
+"; then
+ exit 0
+fi
+
+# initialize apt
+#
+# update-manager (from update-manager-gnome) and
+# update-software-center (from software-center)
+# are present only in wheezy
+if which update-manager > /dev/null; then update-manager -c; fi
+
+if which update-software-center > /dev/null; then
+ sudo update-software-center --debug 2>&1 | \
+ zenity $icon_opt --title="Updating Software Center Repository" \
+ --progress --pulsate --auto-close --auto-kill;
+else
+ sudo apt-get update 2>&1 | \
+ zenity $icon_opt --title="Running apt-get update" \
+ --progress --pulsate --auto-close --auto-kill;
+fi
+
+popconf=/etc/popularity-contest.conf
+if [ ! -e "$popconf" ] || grep -q -e '^PARTICIPATE.*no' "$popconf" ;
+then
+ zenity --info $icon_opt --title="NeuroDebian Setup Wizard" \
+ --text="You will now be given the choice to participate in the package survey. If enabled, a list of installed packages will be anonymously sent to Debian (http://popcon.debian.org). Your participation is important for two reasons:
+
+1) Popular packages receive more attention from developers, bugs are fixed faster and updates are provided quicker.
+2) User statistics can help research software developers to acquire funding for continued development."
+
+ if [ -e "$popconf" ] ; then
+ # just reconfigure so user could get a chance to participate
+ sudo DEBIAN_FRONTEND=gnome dpkg-reconfigure popularity-contest
+ else
+ # install, but do not fail if something goes wrong
+ nd-autoinstall popularity-contest /etc/popularity-contest.conf || true
+ fi
+fi
# install custom filter for synaptics
-sudo mkdir -p /root/.synaptic
-sudo cat << EOT >> /root/.synaptic/filters
+if [ $first_run -eq 1 ]; then
+ sudo mkdir -p /root/.synaptic
+ sudo bash -c 'cat << EOT >> /root/.synaptic/filters
filter "NeuroDebian" {
section {
inclusive false;
};
};
EOT
+'
+ # essential things are done -- let's mark sucess
+ sudo bash -c "mkdir -p $cfg_dir && touch $success_flag"
fi
-if ! zenity --question $icon_opt --title="NeuroDebian Setup Wizard" \
---text="The setup procedure requires network access to download packages from the Debian archive. If you do not have network access right now, you can re-start this wizard at any time from the NeuroDebian menu.
+if ! grep -q '/etc/fsl/fsl.sh' $HOME/.profile && \
+ zenity --question $icon_opt --title="FSL/AFNI Environments" \
+--text="Packages, such as AFNI and FSL, provide large collections of command line tools which are available from their private directories, and require custom environment variables to be set for proper functioning. Usually you need to source /etc/fsl/fsl.sh or /etc/afni/afni.sh in your environments.
-Do you want to proceed with updating the system?
+Do you want to get those files, if available, sourced automatically for your environment?
"; then
- exit 0
+ for t in fsl afni cmtk freesurfer; do
+ cf="/etc/$t/$t.sh"
+ grep -q -e "$cf" $HOME/.profile || \
+ echo "[ -e \"$cf\" ] && . $cf" >> $HOME/.profile
+ done
fi
-# initialize apt
-update-manager -c
+# create symlink to shared folder into homedir
+# note: -e check would exit 1 if link is broken
+# ln -f is used for further robustness
+[ ! -L $HOME/host ] && ln -sf /media/sf_host $HOME/host
-if [ ! -e /etc/popularity-contest.conf ]; then
- zenity --info $icon_opt --title="NeuroDebian Setup Wizard" \
- --text="You will now be given the choice to participate in the package survey. If enabled, a list of installed packages will be anonymously sent to Debian (http://popcon.debian.org). Your participation is important for two reasons:
+# Figure out which version of IPython is available
+ipython_version=$(apt-cache policy ipython 2>/dev/null | sed -ne '/Version table:/ { n;s,^[ \*]*\(.*\) .*,\1,gp}')
+dpkg --compare-versions $ipython_version lt 0.13.1 && ipython=ipython01x || ipython=ipython,ipython-notebook,ipython-qtconsole
-1) Popular packages receive more attention from developers, bugs are fixed faster and updates are provided quicker.
-2) User statistics can help research software developers to acquire funding for continued development."
-
- # install, but do not fail if something goes wrong
- nd-autoinstall popularity-contest /etc/popularity-contest.conf || true
-fi
-
-# essential things are done -- let's mark sucess
-if [ $first_run -eq 1 ]; then
- sudo bash -c "mkdir -p $cfg_dir && touch $success_flag"
-fi
-
-packages=$(zenity --list --checklist --column="Install" --column="Description" \
+# TODO: add PyMVPA:
+# FALSE "PyMVPA" "python-mvpa2,python-mvpa2-doc,python-mvpa2-tutorial-data" \
+# needs -doc and -tutorial-data package
+packages=$(zenity --height 450 --list $icon_opt --checklist --column="Install" --column="Description" \
--column="Package Name" --print-column=3 --hide-column=3 --hide-header \
--separator=' ' --text="Please select any additional component that shall be installed.
on the system. No installed packages will be reinstalled or removed, only
additional components will be installed." \
FALSE "Emacs" "emacs" \
+FALSE "Graphics (e.g. GIMP, Inscape)" "gimp,inkscape,svgtune,xzgv,vym" \
+FALSE "Octave" "qtoctave" \
FALSE "OpenOffice.org" "openoffice.org" \
-FALSE "Scientific Python" "ipython,python-numpy,python-matplotlib" \
+FALSE "PyMVPA Tutorial" "$ipython,python-mvpa2,python-mvpa2-doc,python-mvpa2-tutorialdata,spyder" \
+FALSE "Python: Electrophysiology & Modeling" "python-brian,python-pynn,python-pyentropy,stimfit" \
+FALSE "Python: Neuroimaging" "$ipython,spyder,nipy-suite,python-mvpa2" \
+FALSE "Python: Scientific stack" "$ipython,spyder,python-matplotlib,python-pandas,python-sympy,python-statsmodels,python-skimage" \
+FALSE "R" "r-recommended" \
FALSE "TeX Live" "texlive" \
FALSE "Adobe Flash browser plugin" "flashplugin-nonfree" \
-FALSE "Sun Java browser plugin" "sun-java6-plugin" \
|| true)
if [ -n "$packages" ]; then
done
fi
+# some sane ending
+zenity --info $icon_opt --text="Wizard has finished."
+
# and start greeter
x-www-browser http://neuro.debian.net/vm_welcome.html &
projects / neurodebian.git / blobdiff