Question: miRDeep on Bio Linux
0
gravatar for quintanamaster
5.2 years ago by
United Kingdom
quintanamaster0 wrote:

Hi,

I've been trying to install miRDeep on Bio Linux but it keeps showing the following error message: 

--2014-07-26 15:10:17--  http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.8.4.tar.gz
Resolving www.tbi.univie.ac.at www.tbi.univie.ac.at)... 131.130.44.61
Connecting to www.tbi.univie.ac.at www.tbi.univie.ac.at)|131.130.44.61|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://www.tbi.univie.ac.at/RNA/ViennaRNA-1.8.4.tar.gz [following]
--2014-07-26 15:10:17--  http://www.tbi.univie.ac.at/RNA/ViennaRNA-1.8.4.tar.gz
Reusing existing connection to www.tbi.univie.ac.at:80.
HTTP request sent, awaiting response... 404 Not Found
2014-07-26 15:10:17 ERROR 404: Not Found.

Download of Vienna package not successful

I've also tried to run the manual installation (that is, not running the perl Installation script). This requires the pre-installation of several packages like ViennaRNA. This is what I'm doing and the error message that it retrieves: 

cd ViennaRNA-1.8.4

./configure

make

make install

make[1]: Entering directory `/home/manager/mirdeep2/ViennaRNA-1.8.4/lib'
make[2]: Entering directory `/home/manager/mirdeep2/ViennaRNA-1.8.4/lib'
test -z "/usr/local/lib" || /bin/mkdir -p "/usr/local/lib"
 /usr/bin/install -c -m 644  libRNA.a '/usr/local/lib'
/usr/bin/install: cannot create regular file `/usr/local/lib/libRNA.a': Permission denied
make[2]: *** [install-libLIBRARIES] Error 1
make[2]: Leaving directory `/home/manager/mirdeep2/ViennaRNA-1.8.4/lib'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/home/manager/mirdeep2/ViennaRNA-1.8.4/lib'
make: *** [install-recursive] Error 1
manager@bl7vbox[ViennaRNA-1.8.4]      

I don't have an IT background (more of a self-learner) so any comments/suggestions would be greatly appreciated!

Thanks!

 

 

 

 

sequencing rna-seq next-gen • 2.6k views
ADD COMMENTlink modified 5.2 years ago by Raony Guimarães1.0k • written 5.2 years ago by quintanamaster0
2

sudo make install

should work for the last step

ADD REPLYlink written 5.2 years ago by Michael Dondrup46k
2
gravatar for Raony Guimarães
5.2 years ago by
Dublin / Ireland
Raony Guimarães1.0k wrote:

There are several mirrors for this file:
http://www.filewatcher.com/m/ViennaRNA-1.8.4.tar.gz.1397733-0.html

Which version of biolinux are you using (6, 7 or 8) ?

The second error is because you don't have the right permissions to install this software globally, you have two alternatives:

sudo make instal (if you have root)

or 

./configure --prefix=$HOME
make
make install

Check this question: http://askubuntu.com/questions/339/how-can-i-install-a-package-without-root-access

There is also a ppa package that you could consider trying:

https://launchpad.net/~j-4/+archive/ubuntu/vienna-rna

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Raony Guimarães1.0k

Hi Raony,

Thanks for the links and info. Will try to run them on my BioLinux (version 7) on my laptop and see if I can overcome issues with permissions. 

 

 

ADD REPLYlink written 5.2 years ago by quintanamaster0
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