Cufflink installation problem for Linux

[DrD2009]

Hey Guys,
I am trying to install "Cufflink" in Linux machine but it is throwing an error "Cannot execute.exe file" every time, I try to execute Cufflinks.exe or any other exe files.

Please help me if anyone know how to handle this..

Thank you.

[hdchen]

I think .exe file is for windows, not Linux. I'm not a Linux guy and I'm not sure.

[drio]

Hey Guys,
I am trying to install "Cufflink" in Linux machine but it is throwing an error "Cannot execute.exe file" every time, I try to execute Cufflinks.exe or any other exe files.

Please help me if anyone know how to handle this..

Thank you.

Make sure you get the Linux binary:

http://cufflinks.cbcb.umd.edu/downloads/cufflinks-0.8.1.Linux_x86_64.tar.gz

[BioTalk]

It's a Linux Binary but it is not working.

Can someone please write step wise commands/procedure to make it work!!

Thank you

[Boel]

step wise

Download cufflinks-0.8.1.Linux_x86_64.tar.gz
Untar it: tar xvfz cufflinks-0.8.1.Linux_x86_64.tar.gz
Move cufflinks and cuffcompare to your PATH.

[Xi Wang]

It's a Linux Binary but it is not working.

Can someone please write step wise commands/procedure to make it work!!

Thank you

How do you know it's a Linux Binary? Where did you get it?

[BioTalk]

Download cufflinks-0.8.1.Linux_x86_64.tar.gz
Untar it: tar xvfz cufflinks-0.8.1.Linux_x86_64.tar.gz
Move cufflinks and cuffcompare to your PATH.

Here is the step wise method what I did :

1. I downloaded Cufflinks-0.8.1.Linux_x86_64.tar.gz
2. Untar Cufflinks-0.8.1.Linux_x86_64.tar.gz
3. Moved cufflinks and cuffcompare to the path
4. tried to execute Cufflinks and cuffcompare with ./cufflinks and ./cuffcompare respectively.
5. Also I tried to give input of sam file with the command cuffliinks test_data.sam

But it is throwing the error "Cannot execute binary file" every time I write any command. Please let me know if there are some other commands to work with it.

Thank you

[Xi Wang]

Here is the step wise method what I did :

1. I downloaded Cufflinks-0.8.1.Linux_x86_64.tar.gz
2. Untar Cufflinks-0.8.1.Linux_x86_64.tar.gz
3. Moved cufflinks and cuffcompare to the path
4. tried to execute Cufflinks and cuffcompare with ./cufflinks and ./cuffcompare respectively.
5. Also I tried to give input of sam file with the command cuffliinks test_data.sam

But it is throwing the error "Cannot execute binary file" every time I write any command. Please let me know if there are some other commands to work with it.

Thank you

EDIT: you may use the 32-bit system. I just tried a 32 bit system, it threw this error.
you should download the source code, and compile it yourself.

[BioTalk]

You need to change the files executable by the command chmod.

With the command Chmod I came to know that the file is executable, but I dont know the exact command, I should write to execute it.

[BioTalk]

32- Bit system..How can I try it?

Thank you

[Xi Wang]

32- Bit system..How can I try it?

Thank you

* Download this package:

http://cufflinks.cbcb.umd.edu/downloads/cufflinks-0.8.1.tar.gz

* Untar the package
* cd the dir cufflinks-0.8.1
* type ./configure
* type make
* type make install

If no error, it is installed successfully.

[BioTalk]

* Download this package:

http://cufflinks.cbcb.umd.edu/downloads/cufflinks-0.8.1.tar.gz

* Untar the package
* cd the dir cufflinks-0.8.1
* type ./configure
* type make
* type make install

If no error, it is installed successfully.

Thanks Xi Wang. Looks like it is working but I got an error in the middle of installation that "We could not detect the boost lib with version 1.38 or higher."

So I tried to find Boost library for Linux, but it looks like there isn't any or probably any spececific out of the list.

http://sourceforge.net/projects/boost/files/

Thank you.

[Xi Wang]

For boost, download this file

http://sourceforge.net/projects/boost/files/boost/1.42.0/boost_1_42_0.tar.gz/download

And follow the instruction in the dir after untar the package.

[BioTalk]

Hey Guys,

I am still not able to configure cufflinks. It is constantly throwing me an error eventhough I downloaded and latest version of boost and tryed to add it to its path:

The error is: "We could not detect the boost library(version1.38 or higher). If you have a stages boost library(still not installed) please specify $boost_root in your envireonment and do not give a PATH to --with-bost option. IF you are sure you have boost installed, then check 7youe version number looking in<boost/version.hpp>"

I think I am doing some silly mistake but don't know what? PLease write stepwise command so that my cufflinks starts working...!!

[drio]

Hey Guys,

I am still not able to configure cufflinks. It is constantly throwing me an error eventhough I downloaded and latest version of boost and tryed to add it to its path:

The error is: "We could not detect the boost library(version1.38 or higher). If you have a stages boost library(still not installed) please specify $boost_root in your envireonment and do not give a PATH to --with-bost option. IF you are sure you have boost installed, then check 7youe version number looking in<boost/version.hpp>"

I think I am doing some silly mistake but don't know what? PLease write stepwise command so that my cufflinks starts working...!!

The software requires the Boost library (C++). Did you download the library prior to try to configure the software?