Error in installation of RandFold 2.0

Question

[akshay_ware]

I am trying to install RandFold 2.0, got following error:

fold.o: In function `fill_arrays':
fold.c:(.text+0x115c): undefined reference to `HairpinE'
fold.c:(.text+0x12ca): undefined reference to `LoopEnergy'
fold.o: In function `backtrack':
fold.c:(.text+0x3d48): undefined reference to `HairpinE'
fold.c:(.text+0x3f36): undefined reference to `LoopEnergy'
fold.o: In function `stack_energy':
fold.c:(.text+0x5241): undefined reference to `LoopEnergy'
fold.c:(.text+0x53b5): undefined reference to `HairpinE'
collect2: error: ld returned 1 exit status
Makefile:7: recipe for target 'randfold' failed
make: *** [randfold] Error 1

Please help

Thanks in Advance

[h.mon]

Did you consider installing from conda?

If, for some reason, you can't or don't want to use conda, please provide more details, as where did you download randfold from, your OS (and its version), and the version of GCC.

[akshay_ware]

Hello, I am using Ubuntu 18.4 I am not using conda. I am trying to install Cap-MirSeq pipeline in that i am facing error. as posted earlier. when I tried RandFold 2.0 alone, it was installed properly but not with pipeline.

Thanks

Answer 1

[h.mon]

Cap-MirSeq pipelina is also found on conda, so you should give serious consideration about using conda to install it.

In case you want to follow through with manual install, I was able to install randfold with:

mkdir ~/src/RANDFOLD
mkdir -p ~/bin/RANDFOLD/2.0.1
cd ~/src/RANDFOLD/
wget http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.1.tar.gz
tar -x -z -f randfold-2.0.1.tar.gz 
cd randfold-2.0.1-a7feeeaeba2afe567dbd061b9f4965646386bc98/
chmod -x randfold.c Readme.txt

tar -x -z -f squid.tar.gz
cd squid-1.9g/
env CFLAGS="-O3" ./configure --prefix=$HOME/bin/RANDFOLD/2.0.1
make
make install
cd ../

sed -i "s|INCLUDE=-I\.|INCLUDE=-I. -I$HOME/bin/RANDFOLD/2.0.1/include|" Makefile
sed -i "s|LIBS=-lm -lsquid|LIBS=-lm -lsquid -L$HOME/bin/RANDFOLD/2.0.1/lib|" Makefile
make
cp randfold ~/bin/RANDFOLD/2.0.1/

export PATH=~/bin/RANDFOLD/2.0.1/bin:$PATH