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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.

Home Page:https://dieterichlab.org/software/

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Install asking for python3 while using python 2

Psy-Fer opened this issue · comments

commented

Hello,

I am following on from this issue over at circtools ( dieterich-lab/circtools#82 )

So I made a python2 venv, and while trying to install, it's now telling me I need python 3?

I've dropped the stacktrace below.

Any help would be appreciated.

Cheers,

Processing dependencies for DCC==0.4.7
Searching for pandas<0.24.0
Reading https://pypi.org/simple/pandas/
Downloading https://files.pythonhosted.org/packages/e9/ad/5e92ba493eff96055a23b0a1323a9a803af71ec859ae3243ced86fcbd0a4/pandas-0.23.4.tar.gz#sha256=5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4
Best match: pandas 0.23.4
Processing pandas-0.23.4.tar.gz
Writing /tmp/easy_install-24Uv/pandas-0.23.4/setup.cfg
Running pandas-0.23.4/setup.py -q bdist_egg --dist-dir /tmp/easy_install-24Uv/pandas-0.23.4/egg-dist-tmp-znTUbd
Traceback (most recent call last):
File "setup.py", line 122, in
'scripts/DCC',
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/init.py", line 145, in setup
return distutils.core.setup(**attrs)
File "/home/jamfer/work/python-2714/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/home/jamfer/work/python-2714/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/home/jamfer/work/python-2714/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/install.py", line 67, in run
self.do_egg_install()
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/install.py", line 117, in do_egg_install
cmd.run()
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 418, in run
self.easy_install(spec, not self.no_deps)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 660, in easy_install
return self.install_item(None, spec, tmpdir, deps, True)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 707, in install_item
self.process_distribution(spec, dist, deps)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 752, in process_distribution
[requirement], self.local_index, self.easy_install
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/pkg_resources/init.py", line 782, in resolve
replace_conflicting=replace_conflicting
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/pkg_resources/init.py", line 1065, in best_match
return self.obtain(req, installer)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/pkg_resources/init.py", line 1077, in obtain
return installer(requirement)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 679, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 705, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 890, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1158, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1144, in run_setup
run_setup(setup_script, args)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 253, in run_setup
raise
File "/home/jamfer/work/python-2714/lib/python2.7/contextlib.py", line 35, in exit
self.gen.throw(type, value, traceback)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/home/jamfer/work/python-2714/lib/python2.7/contextlib.py", line 35, in exit
self.gen.throw(type, value, traceback)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 166, in save_modules
saved_exc.resume()
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 141, in resume
six.reraise(type, exc, self._tb)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 154, in save_modules
yield saved
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 250, in run_setup
_execfile(setup_script, ns)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 45, in _execfile
exec(code, globals, locals)
File "/tmp/easy_install-24Uv/pandas-0.23.4/setup.py", line 749, in

File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/init.py", line 144, in setup
_install_setup_requires(attrs)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/init.py", line 139, in _install_setup_requires
dist.fetch_build_eggs(dist.setup_requires)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/dist.py", line 719, in fetch_build_eggs
replace_conflicting=True,
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/pkg_resources/init.py", line 782, in resolve
replace_conflicting=replace_conflicting
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/pkg_resources/init.py", line 1065, in best_match
return self.obtain(req, installer)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/pkg_resources/init.py", line 1077, in obtain
return installer(requirement)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/dist.py", line 786, in fetch_build_egg
return cmd.easy_install(req)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 679, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 705, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 890, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1158, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1144, in run_setup
run_setup(setup_script, args)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 253, in run_setup
raise
File "/home/jamfer/work/python-2714/lib/python2.7/contextlib.py", line 35, in exit
self.gen.throw(type, value, traceback)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/home/jamfer/work/python-2714/lib/python2.7/contextlib.py", line 35, in exit
self.gen.throw(type, value, traceback)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 166, in save_modules
saved_exc.resume()
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 141, in resume
six.reraise(type, exc, self._tb)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 154, in save_modules
yield saved
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 250, in run_setup
_execfile(setup_script, ns)
File "/home/jamfer/work/sandy2714/lib/python2.7/site-packages/setuptools/sandbox.py", line 45, in _execfile
exec(code, globals, locals)
File "/tmp/easy_install-24Uv/pandas-0.23.4/temp/easy_install-eSXFWu/numpy-1.17.0/setup.py", line 31, in
url='https://github.com/dieterich-lab/DCC',
RuntimeError: Python version >= 3.5 required.

commented

Hmm, it seems installing FUCHS on the same environment first, solves the issue. Though I imagine this isn't the intended method.

commented

Also, while trying to use python scripts/DCC

I get the following error

python scripts/DCC -h
Traceback (most recent call last):
File "DCC", line 5, in
DCC.main.main()
AttributeError: 'function' object has no attribute 'main'

I changed DCC to the following, and it works fine

#!/usr/bin/env python2

import DCC.main

DCC.main()

commented

same goes for FUCHS, the script tries to open main, but there is no main in the FUCHS directory, only FUCHS.py, which has a main() function.

changed it to

#!/usr/bin/env python

import FUCHS.FUCHS as fu

fu.main()

as no FUCHS given

commented

Hi @Psy-Fer,

I am wondering why DCC tries to install numpy 1.17.0. The setup files specifically lists < 1.17.0 as requirement. It is in the master branch, therefore git you do a git clone, that change should already be in there. Seems to be pulled in by pandas?

Could you start with a clean venv and install 1) only DCC and then 2) in another new venv just FUCHS to be able to see where these issues arise?

Cheers,
Tobias