_Compilation

Step:

1. Move to src directory

2. Make an executable file

3. Test

---

Move to src directory

Type cd (UNIX or Linux) or dir (Windows) command.

cd (target directory)
dir (target directory)

For example, if ParasoR folder is at /home/carushi/Downloads/ParasoR/,

cd /home/carushi/Downloads/ParasoR/

Because ParasoR continuously needs several files in that directory even after compilation, please move ParasoR folder first to an appropriate location for maintenance.

---

Make an executable file

Type make (and make install) command

./configure
make
make install    

A variable VAR alternates a float precision.

make VAR=LONG
# use long double.
make VAR=SHORT
# use float.

During this compilation, ParasoR determines a home directory.

If you would like to change the location of ParasoR folder, please recompile ParasoR.

In addition, if you fail to compile by above-mentioned processes, you can also try a primitive makefile (stored as "_Makefile") as follows.

cd src/
make -f _Makefile
make install -f _Makefile

Or

autoreconf -ivf
./configure
make

---

Test

Run a test script.

cd script/
sh check.sh

Then, ParasoR creates test outputs to the doc folder.

• doc/pre.txt

  • stem probability

• doc/pre_r.txt

  • stem probability for an anti-sense sequence

• doc/stem.txt

  • stem probability for an anti-sense sequence by parallel calculation

• doc/stem_mem.txt

  • stem probability for an anti-sense sequence by parallel calculation with memory-saving mode

• doc/struct.txt

  • centroid structure with a reliability of base pairing probability

In prob folder, you can find sample structure images.

• prob/Sample0__stem_0_se=0_1748_gamma=1.ps
• prob/Sample0__prof_0_se=0_1748_gamma=1.ps