I'm using Ubuntu 1604 in Oracle VM VirtualBox. Try to follow http://staff.um.edu.mt/jebej02/blog/2016/05/23/installing-cufflinks-rnaseq-on-ubuntu/ to install Cufflinks in Ubuntu. But have issue when I install Tophat:
$ tar xzvf tophat-2.1.1.tar.gz
$ cd tophat-2.1.1
$ ./configure --prefix /opt/tophat-2.1.1 --with-boost=/opt/boost_1_61_0
after I type "./configure --prefix /opt/tophat-2.1.1 --with-boost=/opt/boost_1_61_0", I see
checking for boostlib >= 1.38.0... configure: error: We could not detect the boost libraries (version 1.38 or higher). If you have a staged boost library (still not installed) please specify $BOOST_ROOT in your environment and do not give a PATH to --with-boost option. If you are sure you have boost installed, then check your version number looking in <boost version.hpp="">. See http://randspringer.de/boost for more documentation.
Then I type
dpkg -s libboost-dev | grep 'Version'
Version: 1.58.0.1ubuntu1
**Why the version is still 1.58 but not 1.61?
**How do I know I already successfully install boost 1.61?
How to solve "configure: error: We could not detect the boost libraries (version 1.38 or higher)." problem? Thanks!!**
Is there a reason not to use the pre-compiled tophat linux binary? That should avoid all these issues.
I know I can use "apt-get" to install Tophat directly.
But the goal is install Cufflinks, to follow the http://staff.um.edu.mt/jebej02/blog/2016/05/23/installing-cufflinks-rnaseq-on-ubuntu/ step by step, I'm not sure if I skip Tophat in the link will cause problem.
There is no guarantee that apt-get will install the latest binaries. You can adjust $PATH once you download the pre-compiled binaries.
Even for cufflinks you can get a pre-compiled linux binary here.
I need to install boost 1.61, do I need to completely remove boost 1.58 to make 1.61 work?
You don't need to install or uninstall either of them. Ignore the instructions you found on that blog. Download this, extract it, move the executables to somewhere in your path and you're done. Why the person who wrote that blog wasted so much time is beyond me.
lol, I gonna try it soon.
I downloaded cufflink from this link as you mention above: :http://cole-trapnell lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz
But when I am running cammand: /home/yog/software/cufflinks-2.2.1.Linux_x86_64/gffread
it do not run.