miRDeep on Bio Linux

Question

[quintanamaster]

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!

[Michael]

sudo make install

should work for the last step

Answer 1

[Raony Guimarães]

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 install (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

[quintanamaster]

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.