Question: Error in installation of RandFold 2.0
0
gravatar for akshay_ware
13 days ago by
akshay_ware10
Manipal School of Life Science
akshay_ware10 wrote:

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

ADD COMMENTlink modified 11 days ago by h.mon27k • written 13 days ago by akshay_ware10
1

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.

ADD REPLYlink written 12 days ago by h.mon27k

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

ADD REPLYlink modified 12 days ago • written 12 days ago by akshay_ware10
2
gravatar for h.mon
11 days ago by
h.mon27k
Brazil
h.mon27k wrote:

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
ADD COMMENTlink written 11 days ago by h.mon27k
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