how to install linux straw

[Shawn Bai]

Hi, all,

I want to install the command line version for Straw. But using ' pip install hic-straw ' seems to have some G++ problem. And I don't have the sudo access, how should I install it?

Thanks,

Shawn

[David Katz]

try typing in the command 'module load gcc/9.2.0' before typing 'pip install hic-straw '

[Shawn Bai]

Hi, David, I am now in an environment with python 3.10.12 and trying to install straw, but:

(st) bai@shawn-enternal:~$ pip install --use-pep517 hic-straw
Collecting hic-straw
  Using cached hic-straw-1.3.1.tar.gz (18 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pybind11>=2.4 (from hic-straw)
  Using cached pybind11-2.11.1-py3-none-any.whl.metadata (9.5 kB)
Using cached pybind11-2.11.1-py3-none-any.whl (227 kB)
Building wheels for collected packages: hic-straw
  Building wheel for hic-straw (pyproject.toml) ... error
  error: subprocess-exited-with-error
 
  × Building wheel for hic-straw (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [16 lines of output]
      running bdist_wheel
      running build
      running build_ext
      creating tmp
      gcc -pthread -B /home/bai/mambaforge/envs/st/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/bai/mambaforge/envs/st/include -fPIC -O2 -isystem /home/bai/mambaforge/envs/st/include -fPIC -I/home/bai/mambaforge/envs/st/include/python3.10 -c /tmp/tmpn0f615q0.cpp -o tmp/tmpn0f615q0.o -std=c++14
      gcc -pthread -B /home/bai/mambaforge/envs/st/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/bai/mambaforge/envs/st/include -fPIC -O2 -isystem /home/bai/mambaforge/envs/st/include -fPIC -I/home/bai/mambaforge/envs/st/include/python3.10 -c /tmp/tmpwer2nvk8.cpp -o tmp/tmpwer2nvk8.o -fvisibility=hidden
      building 'hicstraw' extension
      creating build
      creating build/temp.linux-x86_64-cpython-310
      creating build/temp.linux-x86_64-cpython-310/src
      gcc -pthread -B /home/bai/mambaforge/envs/st/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/bai/mambaforge/envs/st/include -fPIC -O2 -isystem /home/bai/mambaforge/envs/st/include -fPIC -I/tmp/pip-build-env-i6ty5bjz/normal/lib/python3.10/site-packages/pybind11/include -I/tmp/pip-build-env-i6ty5bjz/normal/lib/python3.10/site-packages/pybind11/include -I/home/bai/mambaforge/envs/st/include/python3.10 -c src/straw.cpp -o build/temp.linux-x86_64-cpython-310/src/straw.o -DVERSION_INFO=\"1.3.1\" -std=c++14 -fvisibility=hidden
      src/straw.cpp:37:10: fatal error: zlib.h: No such file or directory
         37 | #include "zlib.h"
            |          ^~~~~~~~
      compilation terminated.
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]
 
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for hic-straw
Failed to build hic-straw
ERROR: Could not build wheels for hic-straw, which is required to install pyproject.toml-based projects

[Shawn Bai]