Orca setup notes

orca-setup.md

Install

Burn ubuntu-14.04-desktop-amd64.iso to DVD and boot from it and choose "Try Ubuntu".

Run "GParted Partition Editor" and set up the following primary partitions:

/dev/sda1   ntfs    windows  92160 MiB /   90.00 GiB
/dev/sda2   ext2    boot      1024 MiB /    1.00 GiB
/dev/sda3   ext4    ubuntu  143360 MiB /  140.00 GiB
/dev/sda4   fat32   shared  240395 MiB /  234.76 GiB

Boot from "Microsoft Windows 7 SP1 ENG Professional" DVD. Install Windows to "Disk 0 Partition 1: windows".

Boot from "Ubuntu 14.04 Desktop 64 bit" DVD and choose "Try Ubuntu".

Create a LUKS container:

sudo cryptsetup luksFormat /dev/sda3
sudo cryptsetup luksOpen /dev/sda3 cryptorca

Create LVM physical volume, volume group and logical volumes:

sudo pvcreate /dev/mapper/cryptorca
sudo vgcreate vgorca /dev/mapper/cryptorca
sudo lvcreate -n lvorcaswap -L 10G vgorca
sudo lvcreate -n lvorcaroot -l 100%FREE vgorca

Run "Install Ubuntu 14.04 LTS". Choose "Something else" for "Installation type".

Use /dev/mapper/vgorca-lvorcaroot as ext4 mounted at / and use /dev/mapper/vgorca-lvorcaswap as swap.

Use /dev/sda1 as ntfs mounted at /windows and /dev/sda2 as ext2 mounted at /boot and /dev/sda4 as fat32 mounted at /shared.

After installation, choose "Continue Testing" not "Restart Now".

Mount and chroot into new installation:

sudo mount /dev/mapper/vgorca-lvorcaroot /mnt
sudo mount /dev/sda2 /mnt/boot
sudo mount --bind /dev /mnt/dev
sudo chroot /mnt
mount -t proc proc /proc
mount -t sysfs sys /sys
mount -t devpts devpts /dev/pts

Create /etc/crypttab:

echo -n "cryptorca UUID=" > /etc/crypttab
echo -n `blkid -o value -s UUID /dev/sda3` >> /etc/crypttab
echo " none luks,retry=1,lvm=vgorca" >> /etc/crypttab

Create /etc/initramfs-tools/conf.d/cryptroot:

echo -n "CRYPTROOT=target=cryptorca,source=/dev/disk/by-uuid/" > /etc/initramfs-tools/conf.d/cryptroot
echo `blkid -o value -s UUID /dev/sda3` >> /etc/initramfs-tools/conf.d/cryptroot

Update initramfs images:

update-initramfs -k all -c

Update grub config:

cp -p /etc/default/grub /etc/default/grub.orig
perl -spi -e 's!GRUB_CMDLINE_LINUX=""!print "GRUB_CMDLINE_LINUX=\"cryptopts=target=cryptorca,source=/dev/disk/by-uuid/", `blkid -o value -s UUID /dev/sda3 | tr -d "\n"`, ",lvm=vgorca\""!e' /etc/default/grub
update-grub

Reboot.

Packages installed

• nautilus-dropbox
• keepassx
• lynx-cur
• links
• indicator-multiload
• classicmenu-indicator
• ubuntu-restricted-extras
• libavcodec-extra
• build-essential
• vlc
• ssh
• git
• gimp
• myrepos
• terminator
• xwrits
• clementine
• clamz
• python-pip
• python3-pip
• beets
• freerdp-x11
• screen
• focuswriter
• libdbi-perl
• libdbd-mysql-perl
• perl-doc
• libdist-zilla-perl
• libdist-zilla-plugin-podweaver-perl
• libdist-zilla-plugin-test-perl-critic-perl
• libtest-exception-perl
• libtest-warn-perl
• libtest-databaserow-perl
• libtest-mockobject-perl
• libreadonly-perl
• libreadonly-xs-perl
• libclass-insideout-perl
• libfile-readbackwards-perl
• libdata-compare-perl
• libsort-naturally-perl
• libtext-csv-perl
• libtext-csv-xs-perl
• exonerate
• samtools
• libbam-dev
• gmap
• liblocal-lib-perl
• ack-grep
• perltidy
• libperl-critic-perl
• libtest-perl-critic-perl
• libtest-tester-perl
• libcpan-meta-check-perl
• libtest-minimumversion-perl
• libtest-warnings-perl
• libexporter-lite-perl
• libhash-merge-perl
• libyaml-perl
• libprobe-perl-perl
• libstatistics-descriptive-perl
• libtest-pod-coverage-perl
• libpod-coverage-trustpod-perl
• openjdk-6-jdk
• cifs-utils
• sshfs
• libswitch-perl
• libmoosex-strictconstructor-perl
• libspreadsheet-writeexcel-perl
• python-numpy
• python3-numpy
• python-dev
• pwgen
• libdbd-sqlite3-perl
• liferea
• dos2unix
• whois
• mysql-client
• python-xlrd
• python-dateutil
• python-sqlalchemy
• python-openpyxl
• python-dbf
• flpsed
• youtube-dl
• offlineimap
• bzr
• devscripts
• ipython-notebook
• ipython3-notebook
• python-scipy
• python3-scipy
• python-matplotlib
• python3-matplotlib
• python-pandas
• python3-pandas
• libimage-info-perl
• libnumber-format-perl
• htop
• iotop
• dkms
• python-biom-format
• pyqi
• python-html2text
• python3-html2text
• python3-sqlalchemy
• python-thrift
• ruby
• kpcli
• gparted
• unetbootin
• squashfs-tools
• acpitool
• abcde
• python-flake8
• python3-flake8
• pylint
• python3-astroid
• python3-logilab-common
• python-virtualenv
• virtualenvwrapper
• libmime-types-perl
• libpod-pom-perl
• libmodule-build-perl
• libppi-html-perl
• libberkeleydb-perl
• libsearch-queryparser-perl
• libplack-perl
• libtemplate-perl
• libtemplate-tiny-perl
• libconfig-any-perl
• libreturn-multilevel-perl
• libsafe-isa-perl
• liblwp-protocol-psgi-perl
• libtest-fatal-perl
• libtest-memory-cycle-perl
• libtest-mocktime-perl
• libtest-script-perl
• scratch
• python3-networkx
• subversion
• sqlite3
• wavemon
• libcurl4-openssl-dev
• catdoc
• libfile-chdir-perl
• libdevel-cover-perl
• pandoc
• curl
• libdevel-nytprof-perl
• filezilla
• rdfind
• libgmp3-dev
• libdbix-connector-perl

Configuration

Normal scroll bars:

gsettings set com.canonical.desktop.interface scrollbar-mode normal

Remove unwanted places:

cp -p ~/.config/user-dirs.dirs ~/.config/user-dirs.dirs.orig
cat /dev/null > ~/.config/user-dirs.dirs
echo "enabled=False" > ~/.config/user-dirs.conf
nautilus --quit

Install libdvdcss:

sudo /usr/share/doc/libdvdread4/install-css.sh

Configure git:

git config --global user.name 'Ian Sealy'
git config --global user.email 'github@iansealy.com'
git config --global core.editor nano

In Sanger repositories:

git config user.email 'ian.sealy@sanger.ac.uk'

Configure CPAN:

perl -MCPAN -e shell
o conf prerequisites_policy ask
o conf commit

Prevent Recently Used being default place when choosing files:

perl -spi -e 's/StartupMode=recent/StartupMode=cwd/' ~/.config/gtk-2.0/gtkfilechooser.ini

Make Live CD

Download and extract ISO:

mkdir ~/livecd
cd ~/livecd
wget http://releases.ubuntu.com/14.04.1/ubuntu-14.04.1-desktop-amd64.iso
mkdir mnt
sudo mount -o loop ubuntu-14.04.1-desktop-amd64.iso mnt
mkdir extract-cd
sudo rsync --exclude=/casper/filesystem.squashfs -a mnt/ extract-cd
sudo unsquashfs mnt/casper/filesystem.squashfs
sudo mv squashfs-root edit
sudo umount mnt
rmdir mnt

Enter chroot:

sudo mount --bind /dev/ edit/dev
sudo mount --bind /run/ edit/run
sudo chroot edit
mount -t proc none /proc
mount -t sysfs none /sys
mount -t devpts none /dev/pts
export HOME=/root
export LC_ALL=C

Install Google Chrome:

wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
dpkg -i google-chrome-stable_current_amd64.deb
apt-get install libindicator7 libappindicator1
rm google-chrome-stable_current_amd64.deb

Exit chroot:

umount /proc || umount -lf /proc
umount /sys
umount /dev/pts
exit
sudo umount edit/dev
sudo umount edit/run

Make manifest:

sudo chmod +w extract-cd/casper/filesystem.manifest
sudo chroot edit dpkg-query -W --showformat='${Package} ${Version}\n' | sudo tee extract-cd/casper/filesystem.manifest > /dev/null
sudo cp extract-cd/casper/filesystem.manifest extract-cd/casper/filesystem.manifest-desktop
sudo sed -i '/ubiquity/d' extract-cd/casper/filesystem.manifest-desktop
sudo sed -i '/casper/d' extract-cd/casper/filesystem.manifest-desktop

Compress filesystem, recalculate checksums and make ISO:

sudo mksquashfs edit extract-cd/casper/filesystem.squashfs
printf $(sudo du -sx --block-size=1 edit | cut -f1) | sudo tee extract-cd/casper/filesystem.size > /dev/null
cd extract-cd
sudo rm md5sum.txt
find -type f -print0 | sudo xargs -0 md5sum | grep -v isolinux/boot.cat | sudo tee md5sum.txt
sudo mkisofs -D -r -V "Ubuntu 14.04.1 Custom" -cache-inodes -J -l -b isolinux/isolinux.bin -c isolinux/boot.cat -no-emul-boot -boot-load-size 4 -boot-info-table -o ../ubuntu-14.04.1-desktop-amd64-custom.iso .
cd ..

Burn to DVD:

cdrecord dev=/dev/cdrom ubuntu-14.04.1-desktop-amd64-custom.iso

Tidy:

sudo rm -rf edit extract-cd

Software installed

Install Komodo Edit to /opt/Komodo-Edit-8.

Install Pipelight:

sudo add-apt-repository ppa:pipelight/stable
sudo apt-get update
sudo apt-get install pipelight-multi
sudo pipelight-plugin --update
sudo pipelight-plugin --enable silverlight5.0
sudo pipelight-plugin --enable silverlight5.1
sudo pipelight-plugin --enable flash

Install TrueCrypt and add to ~/.bash_aliases:

alias  mnt-truecrypt='sudo /usr/bin/truecrypt --text --keyfiles="" --protect-hidden=no /shared/truecrypt.tc /truecrypt'
alias umnt-truecrypt='sudo /usr/bin/truecrypt --dismount /shared/truecrypt.tc && touch /shared/truecrypt.tc'

Install Pine:

mkdir -p ~/src ~/bin
sudo apt-get install libpam0g-dev libssl-dev libncurses5-dev libldap2-dev
cd ~/src
mkdir pine
cd pine
wget ftp://ftp.cac.washington.edu/pine/pine4.64.tar.bz2
wget http://patches.freeiz.com/pine/patches/pine4.64/maildir.patch.gz
wget http://patches.freeiz.com/pine/patches/pine4.64/rules.patch.gz
wget http://patches.freeiz.com/pine/patches/pine4.64/incoming.patch.gz
wget http://patches.freeiz.com/pine/patches/pine4.64/fromheader.patch.gz
wget http://patches.freeiz.com/pine/patches/pine4.64/searchheader.patch.gz
gzip -d *.patch.gz
tar jxf pine4.64.tar.bz2
patch -p0 < rules.patch
patch -p0 < incoming.patch
patch -p0 < fromheader.patch
patch -p0 < searchheader.patch
patch -p0 < maildir.patch
cd pine4.64
./build SSLLIB=/usr/lib ldb
cp bin/pine ~/bin
cd ..
rm -rf pine4.64

Add to ~/.bash_aliases:

alias pine='~/bin/pine -p {mail.messagingengine.com/user=iansealy@fastmail.fm/ssl}inbox.remote_pinerc'
alias copypinerc='~/bin/pine -copy_pinerc ~/.pinerc {mail.messagingengine.com/user=iansealy@fastmail.fm/ssl}inbox.remote_pinerc'

Install get_iplayer:

sudo apt-add-repository ppa:jon-hedgerows/get-iplayer
sudo apt-get update
sudo apt-get install get-iplayer
sudo apt-get install mplayer

Install Skype:

sudo apt-get install skype
sudo cp /usr/share/applications/skype.desktop /usr/share/applications/skype.desktop.orig
sudo perl -spi -e 's/PULSE_LATENCY_MSEC=60/PULSE_LATENCY_MSEC=30/' /usr/share/applications/skype.desktop

Install BioPerl:

cd ~/checkouts
git clone git://github.com/bioperl/bioperl-live.git
sudo mkdir /opt/bioperl
sudo chown iansealy: /opt/bioperl
cd /opt/bioperl
git clone ~/checkouts/bioperl-live bioperl-1-2-3
cd bioperl-1-2-3
git checkout bioperl-release-1-2-3
cd ..
git clone ~/checkouts/bioperl-live bioperl-1-6-9
cd bioperl-1-6-9
git checkout bioperl-release-1-6-9

Install Ensembl:

mkdir ~/checkouts/ensembl
cd ~/checkouts/ensembl
for module in ensembl ensembl-compara ensembl-variation ensembl-tools ensembl-hive ensembl-analysis ensembl-pipeline ensembl-doc ensembl-webcode public-plugins ensembl-rest
do
git clone -b master git@github.com:Ensembl/$module.git
cd $module
for remote in `git branch -r | grep release | grep -v HEAD`
do
git checkout --track $remote
done
git checkout master
cd ..
mr register $module
done
sudo mkdir /opt/ensembl
sudo chown iansealy: /opt/ensembl
cd /opt/ensembl
for version in 38 45 53 59 60 61 62 63
do
mkdir ensembl-$version
cd ensembl-$version
for module in ensembl ensembl-compara ensembl-variation
do
git clone ~/checkouts/ensembl/$module
cd $module
git checkout release/$version
cd ..
done
cd ..
done
for version in 64 65 66 67 68 69 70 71 72 73 74 75
do
mkdir ensembl-$version
cd ensembl-$version
for module in ensembl ensembl-compara ensembl-variation ensembl-tools
do
git clone ~/checkouts/ensembl/$module
cd $module
git checkout release/$version
cd ..
done
cd ..
done

Update Ensembl:

version=76
cd ~/checkouts/ensembl
for module in ensembl ensembl-compara ensembl-variation ensembl-tools ensembl-hive ensembl-analysis ensembl-pipeline ensembl-doc ensembl-webcode public-plugins ensembl-rest
do
cd $module
git checkout --track origin/release/$version
git checkout master
cd ..
done
cd /opt/ensembl
mkdir ensembl-$version
cd ensembl-$version
for module in ensembl ensembl-compara ensembl-variation ensembl-tools
do
git clone ~/checkouts/ensembl/$module
cd $module
git checkout release/$version
cd ..
done

version=77
cd ~/checkouts/ensembl
for module in ensembl ensembl-compara ensembl-variation ensembl-tools ensembl-hive ensembl-analysis ensembl-pipeline ensembl-doc ensembl-webcode public-plugins ensembl-rest
do
cd $module
git checkout --track origin/release/$version
git checkout master
cd ..
done
cd /opt/ensembl
mkdir ensembl-$version
cd ensembl-$version
for module in ensembl ensembl-compara ensembl-variation ensembl-tools
do
git clone ~/checkouts/ensembl/$module
cd $module
git checkout release/$version
cd ..
done

version=78
cd ~/checkouts/ensembl
for module in ensembl ensembl-compara ensembl-variation ensembl-tools ensembl-hive ensembl-analysis ensembl-pipeline ensembl-doc ensembl-webcode public-plugins ensembl-rest
do
cd $module
git checkout --track origin/release/$version
git checkout master
cd ..
done
cd /opt/ensembl
mkdir ensembl-$version
cd ensembl-$version
for module in ensembl ensembl-compara ensembl-variation ensembl-tools
do
git clone ~/checkouts/ensembl/$module
cd $module
git checkout release/$version
cd ..
done

version=79
cd ~/checkouts/ensembl
for module in ensembl ensembl-compara ensembl-variation ensembl-tools ensembl-hive ensembl-analysis ensembl-pipeline ensembl-doc ensembl-webcode public-plugins ensembl-rest
do
cd $module
git checkout --track origin/release/$version
git checkout master
cd ..
done
cd /opt/ensembl
mkdir ensembl-$version
cd ensembl-$version
for module in ensembl ensembl-compara ensembl-variation ensembl-tools
do
git clone ~/checkouts/ensembl/$module
cd $module
git checkout release/$version
cd ..
done

version=80
cd ~/checkouts/ensembl
for module in ensembl ensembl-compara ensembl-variation ensembl-tools ensembl-hive ensembl-analysis ensembl-pipeline ensembl-doc ensembl-webcode public-plugins ensembl-rest
do
cd $module
git checkout --track origin/release/$version
git checkout master
cd ..
done
cd /opt/ensembl
mkdir ensembl-$version
cd ensembl-$version
for module in ensembl ensembl-compara ensembl-variation ensembl-tools
do
git clone ~/checkouts/ensembl/$module
cd $module
git checkout release/$version
cd ..
done

version=81
cd ~/checkouts/ensembl
for module in ensembl ensembl-compara ensembl-variation ensembl-tools ensembl-hive ensembl-analysis ensembl-pipeline ensembl-doc ensembl-webcode public-plugins ensembl-rest
do
cd $module
git checkout --track origin/release/$version
git checkout master
cd ..
done
cd /opt/ensembl
mkdir ensembl-$version
cd ensembl-$version
for module in ensembl ensembl-compara ensembl-variation ensembl-tools
do
git clone ~/checkouts/ensembl/$module
cd $module
git checkout release/$version
cd ..
done

Install HPeak:

mkdir -p ~/src ~/bin
cd ~/src
wget http://www.sph.umich.edu/csg/qin/HPeak/HPeak-2.1.LINUX.tar.gz
tar zxf HPeak-2.1.LINUX.tar.gz
cd HPeak-2.1
perl -spi -e 's/^using namespace std/#include <cstdlib>\nusing namespace std/' chiphmmnew.cpp
g++ -o ~/bin/chiphmmnew chiphmmnew.cpp
cd ..
rm -rf HPeak-2.1

Install Bio-SamTools:

bioperl 1-6-9
local-lib-on
SAMTOOLS=/usr/include/samtools perl -MCPAN -e 'install Bio::DB::Bam'
local-lib-off

Install libstree:

cd ~/src
wget http://www.icir.org/christian/downloads/libstree-0.4.2.tar.gz
tar zxf libstree-0.4.2.tar.gz
cd libstree-0.4.2
./configure
make
sudo make install

Install Perl modules:

local-lib-on
perl -MCPAN -e 'install Test::Filename'
perl -MCPAN -e 'install Path::Iterator::Rule'
perl -MCPAN -e 'install Dist::Zilla::Plugin::PerlTidy'
perl -MCPAN -e 'install Test::Deep::JSON'
perl -MCPAN -e 'install Dist::Zilla::Plugin::Test::Compile'
perl -MCPAN -e "CPAN::Shell->notest('install', 'OBO::Core::Ontology')"
perl -MCPAN -e 'install Set::IntervalTree'
perl -MCPAN -e 'install Alien::GvaScript'
perl -MCPAN -e 'install Pod::POM::Web'
perl -MCPAN -e 'install Search::Indexer'
perl -MCPAN -e 'install Dancer2'
perl -MCPAN -e 'install Dist::Zilla::App::Command::cover'
perl -MCPAN -e 'install Tree::Suffix'
perl -MCPAN -e 'install Math::Combinatorics'
perl -MCPAN -e 'install Algorithm::Combinatorics'
local-lib-off

Install Biopython:

sudo pip install biopython
sudo pip3 install biopython

Install Wine:

sudo apt-get install wine
winecfg

Install Evernote:

Set default Windows Version to Windows 7 using winecfg.

wine Evernote_5.4.1.3962.exe
rm ~/Desktop/Evernote.*
echo 'env WINEPREFIX="/home/iansealy/.wine" wine C:\\windows\\command\\start.exe /Unix /home/iansealy/.wine/dosdevices/c:/users/iansealy/Start\ Menu/Programs/Evernote/Evernote.lnk
sleep 10
killall EvernoteTray.exe EvernoteClipper.exe' > ~/bin/evernote.sh
chmod 775 ~/bin/evernote.sh
cp -p ~/.local/share/applications/wine/Programs/Evernote/Evernote.desktop ~/.local/share/applications/wine/Programs/Evernote/Evernote.desktop.orig
echo "StartupWMClass=Evernote.exe" >> ~/.local/share/applications/wine/Programs/Evernote/Evernote.desktop
perl -spi -e 's!^Exec=.*!Exec=/home/iansealy/bin/evernote.sh!' ~/.local/share/applications/wine/Programs/Evernote/Evernote.desktop
echo '[HKEY_CLASSES_ROOT\.pdf]
@="PDFfile"
"Content Type"="application/pdf"
[HKEY_CLASSES_ROOT\PDFfile\Shell\Open\command]
@="C:\\windows\\system32\\winebrowser.exe \"%1\""' > pdf.reg
regedit pdf.reg
rm pdf.reg

Install csvkit:

sudo pip install csvkit

Install google-drive-ocamlfuse:

sudo add-apt-repository ppa:alessandro-strada/ppa
sudo apt-get update
sudo apt-get install google-drive-ocamlfuse
google-drive-ocamlfuse -id XXX -secret XXX

Install Jungle Disk Desktop:

sudo dpkg -i junglediskdesktop_316-0_amd64.deb
sudo ln -s /usr/lib/x86_64-linux-gnu/libnotify.so.4 /usr/lib/libnotify.so.1

Patch Unity (to whitelist Jungle Disk Desktop tray icon):

sudo apt-get build-dep unity
mkdir -p ~/packaging/unity
cd ~/packaging/unity
bzr branch lp:unity/7.2
cd 7.2
perl -spi -e 's/2> WHITELIST {{ "JavaEmbeddedFrame", "Wine"/3> WHITELIST {{ "JavaEmbeddedFrame", "Wine", "junglediskdesktop"/' panel/PanelTray.cpp
perl -spi -e 's/7.2.1\+14.04.20140513-0ubuntu2/7.2.1+14.04.20140513-0ubuntu2+traywhitelist/' debian/changelog
debuild -i -us -uc -b
cd ..
sudo dpkg -i \
unity_7.2.1+14.04.20140513-0ubuntu2+traywhitelist_amd64.deb \
libunity-core-6.0-9_7.2.1+14.04.20140513-0ubuntu2+traywhitelist_amd64.deb \
unity-services_7.2.1+14.04.20140513-0ubuntu2+traywhitelist_amd64.deb

Patch Unity (to whitelist Jungle Disk Desktop tray icon) after update:

cd ~/packaging/unity/7.2
bzr pull
bzr revert debian/changelog po/unity.pot
perl -spi -e 's/7.2.2\+14.04.20140714-0ubuntu1/7.2.2+14.04.20140714-0ubuntu1+traywhitelist/' debian/changelog
debuild -i -us -uc -b
cd ..
sudo dpkg -i \
unity_7.2.2+14.04.20140714-0ubuntu1+traywhitelist_amd64.deb \
libunity-core-6.0-9_7.2.2+14.04.20140714-0ubuntu1+traywhitelist_amd64.deb \
unity-services_7.2.2+14.04.20140714-0ubuntu1+traywhitelist_amd64.deb

Patch Unity (to whitelist Jungle Disk Desktop tray icon) after update:

cd ~/packaging/unity/7.2
bzr pull
bzr revert debian/changelog po/unity.pot po/*.po
perl -spi -e 's/7.2.2\+14.04.20140714-0ubuntu1.1/7.2.2+14.04.20140714-0ubuntu1.1+traywhitelist/' debian/changelog
debuild -i -us -uc -b
cd ..
sudo dpkg -i \
unity_7.2.2+14.04.20140714-0ubuntu1.1+traywhitelist_amd64.deb \
libunity-core-6.0-9_7.2.2+14.04.20140714-0ubuntu1.1+traywhitelist_amd64.deb \
unity-services_7.2.2+14.04.20140714-0ubuntu1.1+traywhitelist_amd64.deb

Install scikit-bio:

sudo pip install scikit-bio
sudo pip3 install scikit-bio

Install Primer3:

mkdir -p ~/src ~/bin
cd ~/src
wget -O primer3-src-2.3.6.tar.gz http://sourceforge.net/projects/primer3/files/primer3/2.3.6/primer3-src-2.3.6.tar.gz/download
tar zxf primer3-src-2.3.6.tar.gz
cd primer3-2.3.6/src
make all
make test
cp primer3_core oligotm ~/bin
sudo cp -r primer3_config /opt
cd ../..
rm -rf primer3-2.3.6

Install Spotify:

sudo add-apt-repository "deb http://repository.spotify.com stable non-free"
sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 94558F59
sudo apt-get update
sudo apt-get install spotify-client

Install VirtualBox:

sudo add-apt-repository "deb http://download.virtualbox.org/virtualbox/debian trusty contrib"
wget -q http://download.virtualbox.org/virtualbox/debian/oracle_vbox.asc -O- | sudo apt-key add -
sudo apt-get update
sudo apt-get install virtualbox-4.3

Install Windows 7 VM from https://www.modern.ie/en-gb/virtualization-tools:

mkdir vms-archive
wget -i https://az412801.vo.msecnd.net/vhd/VMBuild_20131127/VirtualBox/IE11_Win7/Linux/IE11.Win7.ForLinuxVirtualBox.txt
rm IE11.Win7.ForLinuxVirtualBox.txt
chmod +x IE11.Win7.ForLinuxVirtualBox.part1.sfx
./IE11.Win7.ForLinuxVirtualBox.part1.sfx
rm IE11.Win7.ForLinuxVirtualBox.part*
mv IE11\ -\ Win7.ova vms-archive
open vms-archive/IE11\ -\ Win7.ova

Install within Windows 7 VM:

• Google Chrome
• Firefox
• Opera
• IETester

Install Xenu:

wine Setup.exe
cp -p ~/.local/share/applications/wine/Programs/Xenu\'s\ Link\ Sleuth/Xenu.desktop ~/.local/share/applications/wine/Programs/Xenu\'s\ Link\ Sleuth/Xenu.desktop.orig
echo "StartupWMClass=Xenu.exe" >> ~/.local/share/applications/wine/Programs/Xenu\'s\ Link\ Sleuth/Xenu.desktop

Install bedtools:

mkdir -p ~/src ~/bin
cd ~/src
wget https://github.com/arq5x/bedtools2/releases/download/v2.20.1/bedtools-2.20.1.tar.gz
tar zxf bedtools-2.20.1.tar.gz
cd bedtools2-2.20.1
make
cp bin/bedtools ~/bin
cd ..
rm -rf bedtools2-2.20.1

Install Geeknote:

cd ~/checkouts
git clone git://github.com/VitaliyRodnenko/geeknote.git
cd geeknote
sudo python setup.py install
geeknote login
geeknote settings --editor nano

Install ghi:

gem install --user-install ghi

Install Scrapy:

sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 627220E7
echo 'deb http://archive.scrapy.org/ubuntu scrapy main' | sudo tee /etc/apt/sources.list.d/scrapy.list
sudo apt-get update
sudo apt-get install scrapy-0.24

Install datamash:

mkdir -p ~/src
cd ~/src
wget http://ftp.gnu.org/gnu/datamash/datamash-1.0.6.tar.gz
tar zxf datamash-1.0.6.tar.gz
cd datamash-1.0.6
./configure
make
make check
sudo make install

Install Pylint:

sudo pip3 install pylint

Install Atom:

wget https://github.com/atom/atom/releases/download/v0.135.0/atom-amd64.deb
sudo dpkg -i atom-amd64.deb

Install Kindle for PC:

wine KindleForPC-installer.exe
cp -p ~/.local/share/applications/wine/Programs/Amazon/Amazon\ Kindle/Kindle.desktop ~/.local/share/applications/wine/Programs/Amazon/Amazon\ Kindle/Kindle.desktop.orig
echo "StartupWMClass=Kindle.exe" >> ~/.local/share/applications/wine/Programs/Amazon/Amazon\ Kindle/Kindle.desktop

Install Brackets:

wget https://github.com/adobe/brackets/releases/download/release-0.44-beta2/Brackets.Release.0.44.64-bit.deb
sudo dpkg -i Brackets.Release.0.44.64-bit.deb

Install sta:

cd ~/checkouts
git clone git@github.com:simonccarter/sta.git
cd sta
./autogen.sh
./configure
cp sta ~/bin

Install Aspera Connect:

wget http://download.asperasoft.com/download/sw/connect/3.5/aspera-connect-3.5.1.92523-linux-64.sh
sh aspera-connect-3.5.1.92523-linux-64.sh

Install aws-cli:

sudo pip install awscli
sudo pip3 install awscli

Install RStudio Desktop from http://www.rstudio.com/products/rstudio/download/:

sudo apt-get install libjpeg62
sudo dpkg -i rstudio-0.98.1103-amd64.deb

Install R:

sudo add-apt-repository "deb http://mirrors.ebi.ac.uk/CRAN/bin/linux/ubuntu trusty/"
sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E084DAB9
sudo apt-get update
sudo apt-get install r-base r-base-dev r-recommended

Update and install R packages and Bioconductor packages:

R
update.packages(lib.loc=c("/usr/lib/R/library","~/R/x86_64-pc-linux-gnu-library/3.2"), repos="http://mirrors.ebi.ac.uk/CRAN")
source("http://bioconductor.org/biocLite.R")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "DESeq2")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "gplots")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "Mfuzz")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "hopach")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "topGO")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "swirl")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "vcd")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "abd")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "fpc")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "Rgraphviz")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "DEXSeq")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "qvalue")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "sva")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "limma")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "SpikeInSubset")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "BSgenome.Hsapiens.UCSC.hg19")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "SNPlocs.Hsapiens.dbSNP.20120608")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "Homo.sapiens")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "COPDSexualDimorphism.data")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "hgfocus.db")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "R.cache")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "pheatmap")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "ROntoTools")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "bit64")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "gmp")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "getopt")
biocLite(lib.loc="~/R/x86_64-pc-linux-gnu-library/3.2", "devtools")
library(devtools)
install_github("ririzarr/rafalib")
install_github("hadley/lineprof")
install_github("genomicsclass/GSE5859Subset")
install_github("genomicsclass/dagdata")
install_github("genomicsclass/tissuesGeneExpression")
install_github("genomicsclass/ph525x")
install_github("genomicsclass/GSE5859")

Install Java SE Development Kit 8 from http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html:

cd
sudo mkdir /opt/jvm
sudo tar -xzf jdk-8u25-linux-x64.tar.gz -C /opt/jvm

Install Android Studio from http://developer.android.com/sdk/index.html:

cd
unzip android-studio-ide-135.1641136-linux.zip

Add to ~/.bashrc:

# Android Studio
export STUDIO_JDK=/opt/jvm/jdk1.8.0_25 
PATH="$HOME/android-studio/bin:$PATH"

Install querycsv.py:

sudo pip install querycsv

Install xlsx2csv:

sudo pip install xlsx2csv

Install Node.js:

curl -sL https://deb.nodesource.com/setup | sudo bash -
sudo apt-get install nodejs

Install RVM, Ruby and Rails:

gpg --keyserver hkp://keys.gnupg.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3
curl -sSL https://get.rvm.io | bash -s stable --ruby
rm .mkshrc .zshrc .zlogin
source ~/.rvm/scripts/rvm
gem install rails

Install temporary older version of R:

cd ~/src
wget http://mirrors.ebi.ac.uk/CRAN/src/base/R-3/R-3.1.3.tar.gz
tar zxf R-3.1.3.tar.gz
cd R-3.1.3
./configure --prefix=$HOME/packages/R-3.1.3 --enable-R-shlib
make
make check
make install

~/packages/R-3.1.3/bin/R
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("BSgenome.Hsapiens.UCSC.hg19")
biocLite("SNPlocs.Hsapiens.dbSNP.20120608")
biocLite("Homo.sapiens")
biocLite("COPDSexualDimorphism.data")
biocLite("hgfocus.db")
biocLite("BSgenome.Hsapiens.UCSC.hg19.masked")
biocLite("R.utils")
biocLite("Gviz")
biocLite("AnnotationHub")
biocLite("ReportingTools")
biocLite("hgu95acdf")
biocLite("affy")
biocLite("pasillaBamSubset")
biocLite("TxDb.Dmelanogaster.UCSC.dm3.ensGene")
biocLite("SpikeIn")
biocLite("SpikeInSubset")
biocLite("hgu133atagcdf")
biocLite("primeviewcdf")
biocLite("SQN")
biocLite("TxDb.Mmusculus.UCSC.mm9.knownGene")
biocLite("BSgenome.Mmusculus.UCSC.mm9")
biocLite("org.Mm.eg.db")
biocLite("qvalue")
biocLite("GEOquery")
biocLite("TxDb.Celegans.UCSC.ce6.ensGene")
biocLite("org.Ce.eg.db")
biocLite("microbenchmark")
biocLite("RNAseqData.HNRNPC.bam.chr14")
biocLite("harbChIP")
biocLite("yeastCC")
biocLite("gwascat")
biocLite("hugene10sttranscriptcluster.db")
biocLite("dplyr")
biocLite("sva")
biocLite("DEXSeq")
biocLite("pasilla")
biocLite("cummeRbund")
biocLite("devtools")
library(devtools)
install_github("ririzarr/rafalib")
install_github("genomicsclass/ph525x")
install_github("genomicsclass/tissuesGeneExpression")
install_github("genomicsclass/GSE5859")
install_github("genomicsclass/ERBS")
install_github("genomicsclass/GSE5859Subset")
install_github("genomicsclass/maPooling")
install_github("stephaniehicks/mycAffyData")

RSTUDIO_WHICH_R="$HOME/packages/R-3.1.3/bin/R" rstudio