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ubccr / software-layer

CCR Software Layer
GNU General Public License v2.0
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intaRNA #276

Closed eau829 closed 1 month ago

eau829 commented 2 months ago

Hi, I'd like to request installation of intaRNA- more info here https://github.com/BackofenLab/IntaRNA

dsajdak commented 1 month ago

This software is now available in the ccrsoft/2023.01 software release. To run it, load its dependencies along with the module, then specify the $EBROOTINTARNA variable to access the packages. For example:

$ module load gcc/11.2.0  openmpi/4.1.1 intarna/3.4.0
$ $EBROOTINTARNA/bin/IntaRNA --help

IntaRNA predicts RNA-RNA interactions.

The following basic program arguments are supported:

Query:
  -q [ --query ] arg            either an RNA sequence or the stream/file name
                                from where to read the query sequences (should
                                be the shorter sequences to increase
                                efficiency); use 'STDIN' to read from standard
                                input stream; sequences have to use IUPAC
                                nucleotide encoding; output alias is [seq2]

Target:
  -t [ --target ] arg           either an RNA sequence or the stream/file name
                                from where to read the target sequences (should
                                be the longer sequences to increase
                                efficiency); use 'STDIN' to read from standard
                                input stream; sequences have to use IUPAC
                                nucleotide encoding; output alias is [seq1]

To see other executables, you can use the $EBROOTINTARNA variable to cd into the software installation directory:

$ cd $EBROOTINTARNA
$ /cvmfs/soft.ccr.buffalo.edu/versions/2023.01/easybuild/software/avx512/MPI/gcc/11.2.0/openmpi/4.1.1/intarna/3.4.0 $ ls -al
total 28
drwxr-xr-x 6 cvmfs cvmfs 4096 Apr 18 13:44 .
drwxr-xr-x 3 cvmfs cvmfs 4096 Apr 18 13:44 ..
drwxr-xr-x 3 cvmfs cvmfs 4096 Apr 18 13:44 bin
drwxr-xr-x 3 cvmfs cvmfs 4096 Apr 18 13:44 easybuild
drwxr-xr-x 3 cvmfs cvmfs 4096 Apr 18 13:44 include
drwxr-xr-x 3 cvmfs cvmfs 4096 Apr 18 13:44 lib
lrwxrwxrwx 1 cvmfs cvmfs    3 Apr 10 13:32 lib64 -> lib

$/cvmfs/soft.ccr.buffalo.edu/versions/2023.01/easybuild/software/avx512/MPI/gcc/11.2.0/openmpi/4.1.1/intarna/3.4.0 $ cd bin
$/cvmfs/soft.ccr.buffalo.edu/versions/2023.01/easybuild/software/avx512/MPI/gcc/11.2.0/openmpi/4.1.1/intarna/3.4.0/bin $ ls -al
total 5165
drwxr-xr-x 3 cvmfs cvmfs    4096 Apr 18 13:44 .
drwxr-xr-x 6 cvmfs cvmfs    4096 Apr 18 13:44 ..
-rwxr-xr-x 1 cvmfs cvmfs   10805 Apr 10 13:32 CopomuS.py
-rwxr-xr-x 1 cvmfs cvmfs 5246960 Apr 10 13:32 IntaRNA
lrwxrwxrwx 1 cvmfs cvmfs       7 Apr 10 13:32 IntaRNA1 -> IntaRNA
lrwxrwxrwx 1 cvmfs cvmfs       7 Apr 10 13:32 IntaRNA2 -> IntaRNA
lrwxrwxrwx 1 cvmfs cvmfs       7 Apr 10 13:32 IntaRNA3 -> IntaRNA
-rwxr-xr-x 1 cvmfs cvmfs    4991 Apr 10 13:32 IntaRNA_CSV_p-value.R
-rwxr-xr-x 1 cvmfs cvmfs    6464 Apr 10 13:32 IntaRNA_plotRegions.R
lrwxrwxrwx 1 cvmfs cvmfs       7 Apr 10 13:32 IntaRNAduplex -> IntaRNA
lrwxrwxrwx 1 cvmfs cvmfs       7 Apr 10 13:32 IntaRNAens -> IntaRNA
lrwxrwxrwx 1 cvmfs cvmfs       7 Apr 10 13:32 IntaRNAexact -> IntaRNA
lrwxrwxrwx 1 cvmfs cvmfs       7 Apr 10 13:32 IntaRNAhelix -> IntaRNA
lrwxrwxrwx 1 cvmfs cvmfs       7 Apr 10 13:32 IntaRNAsTar -> IntaRNA
lrwxrwxrwx 1 cvmfs cvmfs       7 Apr 10 13:32 IntaRNAseed -> IntaRNA
drwxr-xr-x 2 cvmfs cvmfs    4096 Apr 18 13:44 copomus