HOME ubale to open X server

I have installed HOME after creating an environment for python2.7 as described in the github installation instructions. Upon downloading the testdata (or trying to use my own), I get this error log while running HOME from the testdata directory:

HOME-pairwise -t CG -i ./sample_file_CG.txt -o ./CG -npp 24 /home/pgontarz/HOME_env/local/bin/HOME-pairwise: line 6: $'\nCreated on Mon Apr 16 12:15:36 2018\n\n@author: akanksha\n': command not found import: unable to open X server ' @ error/import.c/ImportImageCommand/364. import: unable to open X server' @ error/import.c/ImportImageCommand/364. import: unable to open X server ' @ error/import.c/ImportImageCommand/364. from: can't read /var/mail/collections import: unable to open X server' @ error/import.c/ImportImageCommand/364. import: unable to open X server ' @ error/import.c/ImportImageCommand/364. import: unable to open X server' @ error/import.c/ImportImageCommand/364. import: unable to open X server ' @ error/import.c/ImportImageCommand/364. from: can't read /var/mail/collections import: unable to open X server' @ error/import.c/ImportImageCommand/364. import: unable to open X server ' @ error/import.c/ImportImageCommand/364. import: unable to open X server' @ error/import.c/ImportImageCommand/364. import: unable to open X server ' @ error/import.c/ImportImageCommand/364. from: can't read /var/mail/HOME from: can't read /var/mail/os.path /home/pgontarz/HOME_env/local/bin/HOME-pairwise: line 25: syntax error near unexpected token(' /home/pgontarz/HOME_env/local/bin/HOME-pairwise: line 25: `def remEmptyDir(mypath):'

I am wondering if there is some issue with my installation of HOME? Building the virutalenv ran with no errors reported as did source /bin/activate.

pgontarz@regmedhpc2:~$ virtualenv -p /usr/bin/python2.7 HOME_env Running virtualenv with interpreter /usr/bin/python2.7 New python executable in /home/pgontarz/HOME_env/bin/python2.7 Also creating executable in /home/pgontarz/HOME_env/bin/python Installing setuptools, pkg_resources, pip, wheel...done. pgontarz@regmedhpc2:~$ source HOME_env/bin/activate (HOME_env) pgontarz@regmedhpc2:~$ which python /home/pgontarz/HOME_env/bin/python (HOME_env) pgontarz@regmedhpc2:~$ which pip /home/pgontarz/HOME_env/bin/pip (HOME_env) pgontarz@regmedhpc2:~$ pip -V pip 20.2.3 from /home/pgontarz/HOME_env/local/lib/python2.7/site-packages/pip (python 2.7) (HOME_env) pgontarz@regmedhpc2:~$ pip install git+https://github.com/ListerLab/HOME.git DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality. Collecting git+https://github.com/ListerLab/HOME.git Cloning https://github.com/ListerLab/HOME.git to /tmp/pip-req-build-ljgoAz Collecting numpy Using cached numpy-1.16.6-cp27-cp27mu-manylinux1_x86_64.whl (17.0 MB) Processing ./.cache/pip/wheels/e8/2f/e8/dcb43af3774d04ee19d01758335fc91a72c5074f8437a76dad/pandas-0.17.1-cp27-cp27mu-linux_x86_64.whl Collecting scipy==0.16.0 Using cached scipy-0.16.0-cp27-cp27mu-manylinux1_x86_64.whl (38.2 MB) Collecting scikit-learn==0.16.1 Using cached scikit-learn-0.16.1.tar.gz (7.3 MB) Processing ./.cache/pip/wheels/70/29/19/37b211c5de170f745ec0875af6b3e7cf293a4e70b0491aa455/statsmodels-0.6.1-cp27-cp27mu-linux_x86_64.whl Collecting pytz>=2011k Using cached pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting python-dateutil Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) Collecting patsy Using cached patsy-0.5.1-py2.py3-none-any.whl (231 kB) Collecting six>=1.5 Using cached six-1.15.0-py2.py3-none-any.whl (10 kB) Building wheels for collected packages: HOME, scikit-learn Building wheel for HOME (setup.py) ... done Created wheel for HOME: filename=HOME-1.0.0-py2-none-any.whl size=20971 sha256=3766aa49664dfcd6f6ee969c5500e84be7e2d9906188f1828a10a0bf54d7cd06 Stored in directory: /tmp/pip-ephem-wheel-cache-xvBrvW/wheels/33/77/39/0699ff79d381c958b6df0835f85b05d941395fe1bf6da305cd Building wheel for scikit-learn (setup.py) ... error ERROR: Command errored out with exit status 1: command: /home/pgontarz/HOME_env/bin/python2.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-q3xJqc/scikit-learn/setup.py'"'"'; file='"'"'/tmp/pip-install-q3xJqc/scikit-learn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-lpsMHo cwd: /tmp/pip-install-q3xJqc/scikit-learn/ Complete output (8 lines): Partial import of sklearn during the build process. Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-q3xJqc/scikit-learn/setup.py", line 173, in setup_package() File "/tmp/pip-install-q3xJqc/scikit-learn/setup.py", line 165, in setup_package from numpy.distutils.core import setup ImportError: No module named numpy.distutils.core

ERROR: Failed building wheel for scikit-learn Running setup.py clean for scikit-learn Successfully built HOME Failed to build scikit-learn Installing collected packages: numpy, pytz, six, python-dateutil, pandas, scipy, scikit-learn, patsy, statsmodels, HOME Running setup.py install for scikit-learn ... done DEPRECATION: scikit-learn was installed using the legacy 'setup.py install' method, because a wheel could not be built for it. pip 21.0 will remove support for this functionality. A possible replacement is to fix the wheel build issue reported above. You can find discussion regarding this at https://github.com/pypa/pip/issues/8368. Successfully installed HOME-1.0.0 numpy-1.16.6 pandas-0.17.1 patsy-0.5.1 python-dateutil-2.8.1 pytz-2020.1 scikit-learn-0.16.1 scipy-0.16.0 six-1.15.0 statsmodels-0.6.1

ListerLab / HOME

HOME ubale to open X server #32