error when installing minus80

[xtLiu2017]

Hello Rob,
We are trying to install minus80 on our ubuntu server. I ran $pip3 install minus80 --prefix /project/chadm/Xiaotong/python_package, and we encounter the following issue.

...
Building wheel for minus80 (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-wky9u_c3/minus80/setup.py'"'"'; file='"'"'/tmp/pip-install-wky9u_c3/minus80/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-dcnrqgi3
cwd: /tmp/pip-install-wky9u_c3/minus80/
Complete output (35 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib
creating build/lib/minus80
copying minus80/RawFile.py -> build/lib/minus80
copying minus80/Accession.py -> build/lib/minus80
copying minus80/GCPCloudData.py -> build/lib/minus80
copying minus80/RelationalDB.py -> build/lib/minus80
copying minus80/FireBaseCloudData.py -> build/lib/minus80
copying minus80/init.py -> build/lib/minus80
copying minus80/Tools.py -> build/lib/minus80
copying minus80/Project.py -> build/lib/minus80
copying minus80/Cohort.py -> build/lib/minus80
copying minus80/ColumnDB.py -> build/lib/minus80
copying minus80/Freezable.py -> build/lib/minus80
copying minus80/CloudData.py -> build/lib/minus80
copying minus80/Config.py -> build/lib/minus80
copying minus80/Exceptions.py -> build/lib/minus80
creating build/lib/minus80/cli
copying minus80/cli/minus80.py -> build/lib/minus80/cli
copying minus80/cli/init.py -> build/lib/minus80/cli
running egg_info
writing minus80.egg-info/PKG-INFO
writing dependency_links to minus80.egg-info/dependency_links.txt
writing entry points to minus80.egg-info/entry_points.txt
writing requirements to minus80.egg-info/requires.txt
writing top-level names to minus80.egg-info/top_level.txt
reading manifest file 'minus80.egg-info/SOURCES.txt'
writing manifest file 'minus80.egg-info/SOURCES.txt'
installing to build/bdist.linux-x86_64/wheel
running install
Installing apsw from GitHub using
error: [Errno 2] No such file or directory: 'pip'

ERROR: Failed building wheel for minus80
...

Can you help look into it? Please let me know if you need more details (liux4215@umn.edu). Thanks.
Xiaotong

[schae234]

Hi @xtLiu2017 , it looks like the installer cannot find pip, which is the python package manager I used. Is pip in your PATH? Also, can you share what command you used to kick off the installation?

[xtLiu2017]

Hi Rob, you are right my computer does not have pip in the PATH but has pip3. That's why I ran:
$pip3 install minus80 --prefix /project/chadm/Xiaotong/python_package

[xtLiu2017]

Hi Rob, I add alias to my ~/.bashrc by doing alias pip=pip3. Now I can run pip on my command line but get the same error when installing minus80 and camoco.
Can you think of any solutions that may work？
Thanks,
Xiaotong

[schae234]

Hi @xtLiu2017 I've pushed some changes to github that should address your issue. What is happening is there is a dependency for minus80 called apsw that is tricky to get installed (using pip). Minus80 tries to autoinstall this package using a shell command but since your call is to pip3 and minus80 is trying to use pip its not working.

Can you pull the most recent changes from the master branch of github, manually install apsw using these instructions and then try to install minus80 using the normal workflow?

[xtLiu2017]

Hi Rob, thanks. I got the same error after installing apsw for python3.
ERROR: Command errored out with exit status 1: command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-j3je5ee3/Minus80/setup.py'"'"'; __file__='"'"'/tmp/pip-install-j3je5ee3/Minus80/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-6cvqbcfz/install-record.txt --single-version-externally-managed --home /tmp/pip-target-2___1xhc --compile --install-headers /tmp/pip-target-2___1xhc/include/python/Minus80 cwd: /tmp/pip-install-j3je5ee3/Minus80/ Complete output (3 lines): running install Installing apsw from GitHub using error: [Errno 2] No such file or directory: 'pip' ---------------------------------------- ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-j3je5ee3/Minus80/setup.py'"'"'; __file__='"'"'/tmp/pip-install-j3je5ee3/Minus80/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-6cvqbcfz/install-record.txt --single-version-externally-managed --home /tmp/pip-target-2___1xhc --compile --install-headers /tmp/pip-target-2___1xhc/include/python/Minus80 Check the logs for full command output.

Not sure if this is related to the issue -- I can import apsw in python3 (3.8) but not in python (2.7).
Thanks,
Xiaotong

[schae234]

Hi @xtLiu2017 I think you are still having conflicting environment issues. Can you double check that you are installing the version of minus80 from github and not from the pip repository? I made that change to the code on github, but it hasn't been integrated into the latest release.

Here is a set of commands I used to get things up and running using python 3.8 using the built-in python virtual environment module:

# ensure python 3.8 
$ python --version
Python 3.8.6

# create and activate a python environment to install all the proper dependencies
$ python -m venv .minus80_venv

# Activate the virtual env to use clean slate and override any system or users installed versions of python
$ source .minus80_venv/bin/activate

# install the latest minus80 from github in your custom python environment using pip
$ .minus80_venv/bin/pip install git+https://github.com/LinkageIO/Minus80.git@e4913f58b9f74b501ac6cc36080d1265bf4feb50

# minus80 should be installed in the python env
$ .minus80_venv/bin/minus80

Note that minus80 will be self contained in the environment (.minus80_venv) you created for it, so all the binaries and libs will be in that directory that is created for you virtual environment.

[xtLiu2017]

Thanks, Rob. I've installed minus80 by downloading from your latest link git+https://github.com/LinkageIO/Minus80.git@e4913f58b9f74b501ac6cc36080d1265bf4feb50.