trooble to find GSL library

[El-Castor]

Hi ,

Thanks for this usefull tool, I'm trying to test it on my hiC data but I have some trooble to install it.

When It do python setup.py I have this error message :

/usr/bin/ld: /tmp/ccRW8Yq1.o: in functionTrainLINEThread(void*)':
line.cpp:(.text+0x159e): undefined reference to gsl_rng_uniform' /usr/bin/ld: line.cpp:(.text+0x15b5): undefined reference to gsl_rng_uniform'
/usr/bin/ld: /tmp/ccRW8Yq1.o: in function TrainLINE()': line.cpp:(.text+0x1aca): undefined reference to gsl_rng_env_setup'
/usr/bin/ld: line.cpp:(.text+0x1ad1): undefined reference to gsl_rng_rand48' /usr/bin/ld: line.cpp:(.text+0x1ae7): undefined reference to gsl_rng_alloc'
/usr/bin/ld: line.cpp:(.text+0x1b02): undefined reference to gsl_rng_set' collect2: error: ld returned 1 exit status LINE compilation has failed.Please make sure to install GSL library

I understand that the tool doesn't fin my gsl library. but the fact is taht I have install it on My conda environment, see below :

`

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 0_gnu conda-forge
blas 1.1 openblas conda-forge
ca-certificates 2020.4.5.1 hecc5488_0 conda-forge
certifi 2016.9.26 py27_0 conda-forge
gsl 2.6 h294904e_0 conda-forge
ld_impl_linux-64 2.34 h53a641e_0 conda-forge
libblas 3.8.0 11_openblas conda-forge
libcblas 3.8.0 11_openblas conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgfortran-ng 7.3.0 hdf63c60_0 anaconda
libgomp 9.2.0 h24d8f2e_2 conda-forge
liblapack 3.8.0 11_openblas conda-forge
libopenblas 0.3.6 h5a2b251_2
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
numpy 1.16.5 py27h95a1406_0 conda-forge
openblas 0.3.3 h9ac9557_1001 conda-forge
openssl 1.1.1f h516909a_0 conda-forge
pip 20.0.2 py_2 conda-forge
python 2.7.15 h5a48372_1011_cpython conda-forge
python_abi 2.7 1_cp27mu conda-forge
readline 8.0 hf8c457e_0 conda-forge
scikit-learn 0.20.4 py27_blas_openblashebff5e3_0 [blas_openblas] conda-forge
scipy 1.2.1 py27_blas_openblash1522bff_0 [blas_openblas] conda-forge
setuptools 44.0.0 py27_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
tqdm 4.45.0 pyh9f0ad1d_0 conda-forge
wheel 0.34.2 py_1 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge
`

More over My library are in the lib folder of my environment :
Running this command : ls <PATH_TO_MY_LIB> | grep "gsl" | head
`
libgsl.a
libgslcblas.a
libgslcblas.so
libgslcblas.so.0
libgslcblas.so.0.0.0
libgsl.so
libgsl.so.25
libgsl.so.25.0.0

`
So I don't understand why It doesn't find th gsl lib, have you got an Idea please ?

thanks in advance

[AshoorH]

Hi,

It seems there is an issue in your environment setup. The C++ linker does not recognize where your GSL library is installed.
In the setup.py you can add -L <path/to/GSL> to the compilation function.

I hope this helps.

[jos4uke]

Hi
I made some fixes to the install doc in this pull request #2
to help
Best

[El-Castor]

Thanks !
@ AshoorH I have an another, after sci installation I don't find the folder called Input_sample in the directory, where I can find it?
I've try your soft on my data in differents resolutions to understand how It works. But I don't know if I have really understand how to used it. I'm wondering, which hic map resolution do used in input for the compartment founding ?More over, to underlie sub-domains I used the hirarchical constrain clustering using the CONISS method. With It I can find the differents compartment type. But with SCI I have not sub-compartement that are related to inactive global compartment and active local compartment. Do you have any idea on it ?
Thanks in advance

[AshoorH]

@El-Castor
SCI uses inter-chromosomes interactions to predict sub-compartments, it requires data to have relatively high read coverage in order to predict sub-compartments. If your inter-chromosomes interaction data quality is low then SCI will not be able to predict such sub-compartments.

[El-Castor]

I don't find the folder called Input_sample in the directory, where I can find it?
which Hi-C map resolution do used in input for the compartment founding, you didn't specified it on your paper ?