Also for stats report which repo and which job number use our setup

[neurodebian.git] / tools / nd-vmsetupwizard

diff --git a/tools/nd-vmsetupwizard b/tools/nd-vmsetupwizard
index 539fb350a09c0afc2f8af42ec984c5cca219d37c..43a58809fe4f174d36b5b5c4a40d9f74b64fa576 100755 (executable)
--- a/tools/nd-vmsetupwizard
+++ b/tools/nd-vmsetupwizard
@@ -32,17 +32,38 @@ Do you want to proceed with updating the system?
 fi
 
 # initialize apt
-update-manager -c
+#
+# 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
 
-if [ ! -e /etc/popularity-contest.conf ]; then
+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
+               nd-autoinstall popularity-contest /etc/popularity-contest.conf || true
+       fi
 fi
 
 # install custom filter for synaptics
@@ -77,10 +98,32 @@ EOT
        sudo bash -c "mkdir -p $cfg_dir && touch $success_flag"
 fi
 
-# create symlink to shared folder into homedir
-[ ! -e $HOME/host ] && ln -s /mnt/host $HOME/host
+if ! grep -q '/etc/fsl/fsl.sh' $HOME/.profile && \
+   zenity --question $icon_opt --title="FSL/AFNI Environments" \
+--text="Packages, such as AFNI and FSL, provide large collections of command line tools which are available from their private directories, and require custom environment variables to be set for proper functioning.  Usually you need to source /etc/fsl/fsl.sh or /etc/afni/afni.sh in your environments.
+
+Do you want to get those files, if available, sourced automatically for your environment?
+"; then
+   for t in fsl afni cmtk freesurfer; do
+       cf="/etc/$t/$t.sh"
+       grep -q -e "$cf" $HOME/.profile || \
+               echo "[ -e \"$cf\" ] && . $cf" >> $HOME/.profile
+   done
+fi
 
-packages=$(zenity --list $icon_opt --checklist --column="Install" --column="Description" \
+# 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 $HOME/host
+
+# Figure out which version of IPython is available
+ipython_version=$(apt-cache policy ipython 2>/dev/null | sed -ne '/Version table:/ { n;s,^[ \*]*\(.*\) .*,\1,gp}')
+dpkg --compare-versions $ipython_version lt 0.13.1 && ipython=ipython01x || ipython=ipython,ipython-notebook,ipython-qtconsole
+
+# TODO: add PyMVPA:
+#   FALSE "PyMVPA" "python-mvpa2,python-mvpa2-doc,python-mvpa2-tutorial-data" \
+# needs -doc and -tutorial-data package
+packages=$(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.
 
@@ -88,12 +131,16 @@ Please note that this selection will not affect packages already installed
 on the system. No installed packages will be reinstalled or removed, only
 additional components will be installed." \
 FALSE "Emacs" "emacs" \
-FALSE "GNU Image Manipulation Program (Gimp)" "gimp" \
+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