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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.
https://dieterichlab.org/software/
GNU General Public License v3.0
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Install asking for python3 while using python 2 #67

Open Psy-Fer opened 4 years ago

Psy-Fer commented 4 years ago

Hello,

I am following on from this issue over at circtools ( https://github.com/dieterich-lab/circtools/issues/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.

Psy-Fer commented 4 years ago

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

Psy-Fer commented 4 years ago

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()

Psy-Fer commented 4 years ago

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

tjakobi commented 4 years ago

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