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Old 02-15-2010, 10:58 AM   #1
DrD2009
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Default Cufflink installation problem for Linux

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.
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Old 02-15-2010, 01:14 PM   #2
hdchen
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I think .exe file is for windows, not Linux. I'm not a Linux guy and I'm not sure.
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Old 02-15-2010, 03:28 PM   #3
drio
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Quote:
Originally Posted by DrD2009 View Post
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/downlo..._x86_64.tar.gz
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Old 02-16-2010, 06:21 AM   #4
BioTalk
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It's a Linux Binary but it is not working.

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

Thank you
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Old 02-16-2010, 06:31 AM   #5
Boel
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Default 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.
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Old 02-16-2010, 06:33 AM   #6
Xi Wang
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Quote:
Originally Posted by BioTalk View Post
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?
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Old 02-16-2010, 06:46 AM   #7
BioTalk
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Quote:
Originally Posted by Boel View Post
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
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Old 02-16-2010, 06:50 AM   #8
Xi Wang
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Quote:
Originally Posted by BioTalk View Post
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.
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Last edited by Xi Wang; 02-16-2010 at 06:56 AM.
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Old 02-16-2010, 06:54 AM   #9
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Quote:
Originally Posted by Xi Wang View Post
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.
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Old 02-16-2010, 06:56 AM   #10
BioTalk
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32- Bit system..How can I try it?

Thank you
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Old 02-16-2010, 07:05 AM   #11
Xi Wang
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Quote:
Originally Posted by BioTalk View Post
32- Bit system..How can I try it?

Thank you
* Download this package:
http://cufflinks.cbcb.umd.edu/downlo...s-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.
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Old 02-16-2010, 07:36 AM   #12
BioTalk
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Quote:
Originally Posted by Xi Wang View Post
* Download this package:
http://cufflinks.cbcb.umd.edu/downlo...s-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.
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Old 02-16-2010, 08:11 AM   #13
Xi Wang
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For boost, download this file
http://sourceforge.net/projects/boos...ar.gz/download

And follow the instruction in the dir after untar the package.
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Old 02-17-2010, 08:48 AM   #14
BioTalk
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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...!!
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Old 02-17-2010, 08:54 AM   #15
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Quote:
Originally Posted by BioTalk View Post
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?
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Old 02-17-2010, 08:56 AM   #16
Xi Wang
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Last time I successfully installed Cufflinks using the option --with-boost=/PATH/TO/BOOST/ROOT when configuring. I give my solution here.

1. get the path to boost root, in which there are at least two dirs: include and lib
2. cd into the dir cufflinks-0.8.1
* type ./configure --with-boost=/PATH/TO/BOOST/ROOT
* type make
* type make install

Let me know if this trial fails.
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Old 02-17-2010, 08:59 AM   #17
BioTalk
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Yes I downloaded boost library and try to add path to it with the command path=<home/path to the boost folder...>.

I do not know if there is anything else I need to do!

Thank you
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Old 02-17-2010, 09:06 AM   #18
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Quote:
Originally Posted by Xi Wang View Post
Last time I successfully installed Cufflinks using the option --with-boost=/PATH/TO/BOOST/ROOT when configuring. I give my solution here.

1. get the path to boost root, in which there are at least two dirs: include and lib
2. cd into the dir cufflinks-0.8.1
* type ./configure --with-boost=/PATH/TO/BOOST/ROOT
* type make
* type make install

Let me know if this trial fails.
Thank you for your prompt reply.

I did not understand how 1st step works? i.e How to get a path to boost root. Also I searched boost folder, I found Lib Directory but can not see include directory in it. PLease let me know how this works.

Thank you.
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Old 02-22-2010, 06:24 AM   #19
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Thank you everyone for the help.
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Old 02-22-2010, 06:27 AM   #20
Xi Wang
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Quote:
Originally Posted by BioTalk View Post
Thank you everyone for the help.
Have you solved this problem? I didn't hear from you any more:-)
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