Question: Error in installation of RandFold 2.0
0
gravatar for akshay_ware
11 months 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 months ago by h.mon31k • written 11 months 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 11 months ago by h.mon31k

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 11 months ago • written 11 months ago by akshay_ware10
2
gravatar for h.mon
11 months ago by
h.mon31k
Brazil
h.mon31k 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 months ago by h.mon31k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 853 users visited in the last hour