Installation issues

[LeebanY]

Hi,

First of all, thanks for taking the time to answer these questions and for providing this software.

I'm having several issues trying to install SibeliaZ on the cluster. Using the installation method in the README, the make files can't seem to find libraries necessary for building the programs. I fixed most of these by adding full paths, but I can't fix this error that I get:

file INSTALL cannot copy file "/storage/home/users/x/FISH_WGA/SibeliaZ/build/spoa/lib/libspoa.a" to "/usr/local/lib64/libspoa.a".

I don't have admin access to be able to copy files to the /usr/ directory.

When I tried binary executables that you provided access to in another comment, the executables seem to be looking for libraries elsewhere and I'm not sure how to alter this:

./graphdump: /lib64/libc.so.6: version GLIBC_2.14' not found (required by ./graphdump) ./graphdump: /usr/local/Modules/modulefiles/tools/gcc/4.9.3/lib64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by ./graphdump)

Is there anyway to easily download and install the program without having to provide full paths or adjust library paths in binary files? I feel like I may be doing something wrong.

Thanks, Leeban

[iminkin]

Hi @LeebanY,

If you don't have admin rights at your cluster, you can still locally install SibeliaZ. It works best to make an installation to a directory that is in your PATH, e.g. ~/bin folder (a folder for binaries in your home directory). To make a local installation, run the following commands (while in a freshly cloned repository of SibeliaZ):

git submodule update --init --recursive

mkdir build

cd build

cmake .. -DCMAKE_INSTALL_PREFIX=<path to install the binaries>

make install

Where <path to install the binaries> is a local path you can write to. It is best to try to set this path to ~/bin if you have such a folder on your system. With regard to the precompiled binaries, it seems that the version I compiled is not compatible with your particular system, so please try to make a local installation. Please let me know if you were able to install the software or you need extra help.

[LeebanY]

Hi,

Thanks for the reply.

So, I tried installing to ~/bin and got this error:

[ 58%] Building CXX object TwoPaCo/src/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o /storage/home/users/x/bin/SibeliaZ/TwoPaCo/src/graphdump/graphdump.cpp:14:31: fatal error: tbb/parallel_sort.h: No such file or directory #include <tbb/parallel_sort.h>

I also tried to install in the bin directory of a couple of different conda environments and this doesn't work either.

No matter where I install, this error seems to be keep cropping up.

Thanks, Leeban

[iminkin]

@LeebanY,

You have to install the TBB library on your machine. Unfortunately, it can be quite tricky to do so without admin access. But it is a quite common one, so you can try to ask your system administrator to install it. If you are running on a Debian-like system (e.g. Ubuntu), then you need to install the package libtbb-dev.

[LeebanY]

@iminkin

So, I've downloaded tbb via conda but I guess graphdump is expecting the tbb directory to be in a particular location. Is there anyway to provide the path for my tbb directory beforehand?

I've tried -DTBB_DIR= with this command: cmake .. -DCMAKE_INSTALL_PREFIX=

I've also tried moving my tbb directory to various different places in my filesystem and that doesn't seem to have an effect.

Can I manually edit the Cmake files to point the installation towards my tbb directory?

Thanks, Leeban

[iminkin]

@LeebanY ,

Which package did you install, tbb or tbb-devel? I think you need tbb-devel.

[LeebanY]

@iminkin

I tried both. Neither seemed to work.

[iminkin]

@LeebanY

I plan to make SibeliaZ not depend on TBB. I will release a new version probably this month.

[iminkin]

Sorry for getting to it late, but sibeliaz is now available at bioconda: https://bioconda.github.io/recipes/sibeliaz/README.html?highlight=sibeliaz#package-Recipe%20'sibeliaz'