Do not manage to install Hic-Pro
Deniz
Hi,
I tried two ways of installing/using HiC-Pro on our local cluster.
1. Singularity:
Singularity including posted dependencies were installed using conda.
singularity exec hicpro_latest_ubuntu.img HiC-Pro -h
ERROR : Failed invoking the NEWUSER namespace runtime: Invalid argument
ABORT : Retval = 255
2. From source:
Here is my config-install.txt:
PREFIX = /home/gd8/software/HiC-Pro
BOWTIE2_PATH =
SAMTOOLS_PATH =
R_PATH =
PYTHON_PATH =
CLUSTER_SYS = SGE
make config results in the following exit status:
./scripts/install/install_dependencies.sh -c ./config-install.txt -o /home/gd8/software/HiC-Pro/HiC-Pro_2.11.4 -q
Make sure internet connection works for your shell prompt under current user's privilege ...
Starting HiC-Pro installation ...
Checking dependencies ...
Checking Python libraries ...
The required Python libraries appear to be already installed.
Checking R installation ...
The required R packages appear to be already installed.
Bowtie2 Aligner appears to be already installed.
Samtools appears to be already installed.
Dependencies checked !
Check HiC-Pro configuration ...
Configuration for SGE system.
make[1]: Leaving directory '/home/gd8/software/HiC-Pro'
trying to make install results in:
(g++ -Wall -O2 -std=c++0x -o build_matrix /home/gd8/software/HiC-Pro/scripts/src/build_matrix.cpp; mv build_matrix /home/gd8/software/HiC-Pro/scripts)
(g++ -Wall -O2 -std=c++0x -o cutsite_trimming /home/gd8/software/HiC-Pro/scripts/src/cutsite_trimming.cpp; mv cutsite_trimming /home/gd8/software/HiC-Pro/scripts)
Installing the iced package in --user repository [runner=gd8]
(cd /home/gd8/software/HiC-Pro/scripts/src/ice_mod/; /home/gd8/software/miniconda3/envs/hic/bin/python setup.py install --user;)
/home/gd8/software/miniconda3/envs/hic/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'include_package_data'
warnings.warn(msg)
/home/gd8/software/miniconda3/envs/hic/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'zip_safe'
warnings.warn(msg)
Warning: Assuming default configuration (iced/utils/{setup_utils,setup}.py was not found)Appending iced.utils configuration to iced
Ignoring attempt to set 'name' (from 'iced' to 'iced.utils')
Appending iced.datasets configuration to iced
Ignoring attempt to set 'name' (from 'iced' to 'iced.datasets')
non-existing path in 'iced/io': '../src/cblas'
non-existing path in 'iced/io': '../src/cblas'
Appending iced.io configuration to iced
Ignoring attempt to set 'name' (from 'iced' to 'iced.io')
non-existing path in 'iced': '../src/cblas'
non-existing path in 'iced': '../src/cblas'
Appending iced configuration to
Ignoring attempt to set 'name' (from '' to 'iced')
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "iced.io.fastio_" sources
building extension "iced.io.read" sources
building extension "iced._normalization_" sources
building extension "iced._filter_" sources
building data_files sources
build_src: building npy-pkg config files
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/iced
copying iced/setup.py -> build/lib.linux-x86_64-2.7/iced
copying iced/filter.py -> build/lib.linux-x86_64-2.7/iced
copying iced/normalization.py -> build/lib.linux-x86_64-2.7/iced
copying iced/__init__.py -> build/lib.linux-x86_64-2.7/iced
creating build/lib.linux-x86_64-2.7/iced/utils
copying iced/utils/validation.py -> build/lib.linux-x86_64-2.7/iced/utils
copying iced/utils/_genome.py -> build/lib.linux-x86_64-2.7/iced/utils
copying iced/utils/_validation.py -> build/lib.linux-x86_64-2.7/iced/utils
copying iced/utils/__init__.py -> build/lib.linux-x86_64-2.7/iced/utils
creating build/lib.linux-x86_64-2.7/iced/datasets
copying iced/datasets/setup.py -> build/lib.linux-x86_64-2.7/iced/datasets
copying iced/datasets/base.py -> build/lib.linux-x86_64-2.7/iced/datasets
copying iced/datasets/__init__.py -> build/lib.linux-x86_64-2.7/iced/datasets
creating build/lib.linux-x86_64-2.7/iced/io
copying iced/io/setup.py -> build/lib.linux-x86_64-2.7/iced/io
copying iced/io/_io_else.py -> build/lib.linux-x86_64-2.7/iced/io
copying iced/io/_io_pandas.py -> build/lib.linux-x86_64-2.7/iced/io
copying iced/io/__init__.py -> build/lib.linux-x86_64-2.7/iced/io
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'iced.io.fastio_' extension
compiling C sources
C compiler: gcc -pthread -B /home/gd8/software/miniconda3/envs/hic/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
creating build/temp.linux-x86_64-2.7/iced
creating build/temp.linux-x86_64-2.7/iced/io
compile options: '-I../src/cblas -I/home/gd8/software/miniconda3/envs/hic/lib/python2.7/site-packages/numpy/core/include -I/home/gd8/software/miniconda3/envs/hic/lib/python2.7/site-packages/numpy/core/include -I/home/gd8/software/miniconda3/envs/hic/include/python2.7 -c'
gcc: iced/io/fastio_.c
In file included from /home/gd8/software/miniconda3/envs/hic/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:0,
from /home/gd8/software/miniconda3/envs/hic/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/gd8/software/miniconda3/envs/hic/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from iced/io/fastio_.c:435:
/home/gd8/software/miniconda3/envs/hic/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with " \
^~~~~~~
gcc -pthread -shared -B /home/gd8/software/miniconda3/envs/hic/compiler_compat -L/home/gd8/software/miniconda3/envs/hic/lib -Wl,-rpath=/home/gd8/software/miniconda3/envs/hic/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/iced/io/fastio_.o -L/home/gd8/software/miniconda3/envs/hic/lib -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/iced/io/fastio_.so
/home/gd8/software/miniconda3/envs/hic/compiler_compat/ld: skipping incompatible /lib/libpthread.so.0 when searching for /lib/libpthread.so.0
/home/gd8/software/miniconda/envs/hic/compiler_compat/ld: skipping incompatible /lib/libpthread.so.0 when searching for /lib/libpthread.so.0
/home/gd8/software/miniconda3/envs/hic/compiler_compat/ld: cannot find /lib/libpthread.so.0
/home/gd8/software/miniconda3/envs/hic/compiler_compat/ld: cannot find /usr/lib/libpthread_nonshared.a
collect2: error: ld returned 1 exit status
error: Command "gcc -pthread -shared -B /home/gd8/software/miniconda3/envs/hic/compiler_compat -L/home/gd8/software/miniconda3/envs/hic/lib -Wl,-rpath=/home/gd8/software/miniconda3/envs/hic/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/iced/io/fastio_.o -L/home/gd8/software/miniconda3/envs/hic/lib -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/iced/io/fastio_.so" failed with exit status 1
make: *** [Makefile:60: iced] Error 1
What could I do to get it to work?
Thanks in advance for your support.
