To install the environnement and the related software and data, follow this procedure.


Install RNAspace environment

1. Create directories

First we recommand to create the following directories where you want to store RNAspace environnement:

2. Download environment

Access the RNAspace download page at http://sourceforge.net/projects/rnaspace/files/.
Download the latest version file in the rnaspace_sources directory.

In a terminal, go to the directory where the file is, then execute:
tar xzvf rnaspace-1.2.tar.gz

3. Install Linux packages

Install required software using Linux package distribution: Python 2.6, Cherrypy (version 3.1.2), Cheetah (version 2.0.1).


Install related programs

Install them in rnaspace_softwares directory.

4. Install blastall, bl2seq

Install the corresponding Linux package (blast2 package on Ubuntu 11.04 with blastall 2.2.21).

5. Install clustalw

Install the corresponding Linux package (clustalw package on Ubuntu 11.04 with clustalw 2.1).

6. Install Vienna RNA package

It is possible to download the version tested in RNAspace or to download the software from the Vienna RNA site.

In a terminal, execute the following commands:
tar xzvf ViennaRNA-1.8.4.tar.gz
cd ViennaRNA-1.8.4
configure
make

Depending on your compiler, some errors can occured. See faq for possible solution.

7. Install UNAFold

It is possible to download the version tested in RNAspace or to download the software from the UNAFold site.

In a terminal, execute the following commands:
tar xzvf unafold-3.8.tar.gz
cd unafold-3.8
configure

Then modify the source code to avoid to use the environment variable UNAFOLDDAT not suitable for running on a cluster.
So in src/energy.c file, replace the following lines (68 to 72):
  if (!file && getenv("UNAFOLDDAT"))
     {
       buffer = xmalloc(strlen(getenv("UNAFOLDDAT")) + strlen(name) + 2);
       strcpy(buffer, getenv("UNAFOLDDAT"));
 by
  if (!file)
     {
       buffer = xmalloc(strlen("<local path>/unafold-3.8/data") + strlen(name) + 2);
       strcpy(buffer, "<local path>/unafold-3.8/data");
In src/extinction.h file, replace the following lines (10 to 14) :
   if (!file && getenv("UNAFOLDDAT"))
     {
       buffer = xmalloc(strlen(getenv("UNAFOLDDAT")) + 16);
       strcpy(buffer, getenv("UNAFOLDDAT"));
 by
  if (!file)
     {
       buffer = xmalloc(strlen("<local path>/unafold-3.8/data") + 16);
       strcpy(buffer, "<local path>/unafold-3.8/data");

 Finally compile the software.
Make

8. Install RNAshapes

It is possible to download the version tested in RNAspace or to download the software from the RNAshapes site.

In a terminal, execute the following commands:
tar xzvf RNAshapes-2.1.6.tar.gz
cd RNAshapes-2.1.6
configure
make

9. Install RNAz

RNAz is used for RNA predictions alignment and is then required even when the comparative approach is not wished.
It is possible to download the version tested in RNAspace or to download the software from the RNAz site.
RNAz requires g++ to compile.

In a terminal, execute the following commands:
tar xzvf RNAz-1.0.tar.gz
cd RNAz-1.0
./configure
make

Install non-coding RNA gene finders


Homology search based gene finders

10. BLAST based (optional)

BLAST is yet installed.
RNA databases have to be installed.

Install Rfam

Note that we removed SSU_rRNA_5 from the fasta file to avoid excessive running time in particular with E. coli genome. You can download this file here.

We also make available Rfam 10.0 seed database. You can download this file here.

Install frnadb

NOTE: During the conversion of frnadb, some family names will be converted to the RFAM ones according to the file rfam_families.txt. You can add some RFAM family ids in the file excluded_families.txt to avoid the conversion of these ids.

Install miRBase

11. Install Darn (optional)

It is possible to download the version tested in RNAspace or to download the software from the Darn site.
Darn requires the following programs: makedepend (xutils-dev Ubuntu package) , make, g++.

In a terminal, execute the following commands:
tar xzvf darn-1.0.tar.gz
cd darn-1.0
In the file common.h, add the absolute path for costs.dat file
static const char costFile[] = "/save/rnaspace/rnaspace_softwares/darn-1.0/costs.dat";
Only to compile on a 64 bits computer, cd lib/ViennaLib, make clean, then return to darn-1.0 directory
make

12. Install ERPIN (optional)

It is possible to download the version tested in RNAspace or to download the software from the ERPIN site.
ERPIN requires Perl.

In a terminal, execute the following commands:
tar xzvf ErpinBatch.9.1.tar.gz
cd ErpinBatch.9.1
Modify paths in epnscan.pl and readerpin.pl

13. Install Infernal (optional)

It is possible to download the version tested in RNAspace or to download the software from the Infernal site.

In a terminal, execute the following commands:
tar xzvf infernal-1.0.2.tar.gz
cd infernal-1.0.2
configure
make

It is also necessary to download the Rfam models: the version tested in RNAspace or from the Rfam site .
In a terminal, execute the following commands:
gunzip Rfam-10.0.cm.gz
mkdir Rfam-10.0
python rnaspace/rnaspace/util/infernal_utils.py Rfam-10.0.cm Rfam-10.0/
rm rfam_list.txt rfam_families.txt (non useful to only run RNAspace)
Make a link to Rfam descriptors in the infernal directory
cd infernal-1.0.2
ln -s ../Rfam-10.0 Rfam

14. Install RNAmmer (optional)

In order to install RNAmmer you have to require a version on the RNAmmer site. It is also necessary to download hmmer: the version tested in RNAspace or from the hmmer site.
hmmer requires the following programs: perl, XML:Simple.pm pour rnammer, gcc.
First the XML/Simple.pm is required (can be found in libxml-simple-perl Ubuntu package).
Second, in a terminal, execute the following commands:
tar xzvf hmmer-2.3.2.tar.gz
cd hmmer-2.3.2
configure
make
Finally install rnammer. mkdir rnammer
cd rnammer
tar xzvf Rnammer-1,2,Linux.tar.gz
Into the rnammer file, edit $INSTALL_PATH and $HMMSEARCH_BINARY variables
Edit core-rnammer and delete twice « --cpu 1 »

15. Install tRNAscan-SE (optional)

It is possible to download the version tested in RNAspace or download the software from the tRNAscan-SE site.
tRNAscan-SE requires gcc to compile.

In a terminal, execute the following commands:
tar xzvf tRNAscan-SE-1.23.tar.gz
cd tRNAscan-SE-1.23
Modify paths in Makefile
BINDIR = <absolute path>rnaspace_softwares/bin
LIBDIR = <absolute path>rnaspace_softwares/lib
MANDIR = <absolute path>rnaspace_softwares/man
make install

Depending on your compiler, some errors can occured. See faq for possible solution.

16. Install YASS based (optional)

It is possible to download the version tested in RNAspace or download the software from the YASS site.
YASS requires gcc to compile.

In a terminal, execute the following commands:
tar xzvf yass-1.14.tar.gz
cd yass-1.14
./configure
make
If the BLAST based gene finder has been installed, available databases are yet installed.


Comparative based approach (optional)

BLAST and RNAz are required and yet installed.
YASS is also required. See above desciption if the gene finder YASS based has not be installed.

17. Install arnica

It is possible to directly download the version tested in RNAspace
arnica requires the folowing programs: needle (EMBOSS package version 6.0.1), clustalw, perl (v5.8.8 built for x86_64-linux-thread-multi), flex (version 2.5.4), yacc/bison (GNU Bison, version 2.3), make (GNU Make version 3.81), gcc (version 4.1.2).

In a terminal, execute the following commands:
tar xzvf arnica-0.31-sans-gmp-ni-mpfr.tar.gz
cd arnica-0.31
./configure
make

18. Install matt_ygraph

It is possible to directly download the version tested in RNAspace
matt_ygraph requires te following programs: flex, yacc/bison, make, gcc.

In a terminal, execute the following commands:
tar xzvf matt_ygraph-1.022.tar.gz
cd matt_ygraph-1.022
./configure
make

19. Install genomes

Genomes for comparative analysis have to be structured following this structure:
<genomes_dir>/Bacteria/current/fasta/<organism_name>/*.fna
The directory <genomes_dir> is specified in rnaspace.cfg configuration file.

To accelerate comparative analysis, it is recommended to mask coding regions, that is replace the nucleotides of the regions by ''N'. A Perl procedure is provided in the util directory to do so. Beware that .gbk files are required next to the .fna files to have the annotation of coding regions.
cd rnaspace_sources/rnaspace/rnaspace/util/
perl generate_masked_genomes.pl --indir /bank/ncbi/genomes --outdir /home/rnaspace/save/rnaspace_masked_genomes --except Eukaryotes --except Archaea --mode 0


ab initio approach

20. Install atypicalGC (optional)

Download the version tested in RNAspace

In a terminal, execute the following commands:
tar xzvf atypicalGC.tar.gz

Install visualization tool

21. Install required program/library for JBrowse

JBrowse is provided with RNAspace environment.
Just be sure that the following programs/librairies are available on your system or install them.

22. Install CGview

It is possible to download the version tested in RNAspace or download the software from the CGview site.

In a terminal, execute the following commands:
unzip cgview.zip

Configure the environment

23. Configure local files

Configuration have to be done only in .cfg files in the rnaspace_sources/rnaspace/cfg directory:

and in the subdirectory predictors for the installed gene finders:


Launch the web site and/or use the environment in command line

Execute the following commands:
cd rnaspace/rnaspace
python rnaspace_on_web.py