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adamewing / tldr

Identify and annotate TE-mediated insertions in long-read sequence data
MIT License
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Installing tldr #3

Closed Coracollar closed 3 years ago

Coracollar commented 3 years ago

Hi Adam,

I am interested in using your tldr however following the intallation in the readme is not working for me. I have no software background so I guess there is an "obvious" step I am missing. I tried cloning both tldr and te-nanopore-tools and then running python setup.py intall, and copying setup.py and then do python setup.py install. None of the options work. Could you clarify the installation process?

Thanks

adamewing commented 3 years ago

Were you able to get the steps in the readme prior to the 'python setup.py install' step to work? (minimap2, mafft, samtools, etc). Could you tell me what command(s) you are trying and specifically what is the error message(s) you are getting?

You don't need the te-nanopore-tools repository if you're just looking to detect insertions.

Coracollar commented 3 years ago

Hi, Yeah I conda installed the rest of dependencies. And then copy the setup.py file and did:

$ python setup.py install running install running bdist_egg running egg_info creating tldr.egg-info writing tldr.egg-info/PKG-INFO writing dependency_links to tldr.egg-info/dependency_links.txt writing requirements to tldr.egg-info/requires.txt writing top-level names to tldr.egg-info/top_level.txt writing manifest file 'tldr.egg-info/SOURCES.txt' reading manifest file 'tldr.egg-info/SOURCES.txt' writing manifest file 'tldr.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib warning: install_lib: 'build/lib' does not exist -- no Python modules to install

creating build creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/EGG-INFO installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts running install_scripts running build_scripts creating build/scripts-3.9 error: file '/data/gpfs/projects/punim1048/te-nanopore-tools/tldr/tldr' does not exist

Because of this I tried cloning tldr and obtain:

$ git clone https://github.com/adamewing/tldr Cloning into 'tldr'... remote: Enumerating objects: 291, done. remote: Counting objects: 100% (291/291), done. remote: Compressing objects: 100% (185/185), done. remote: Total 291 (delta 131), reused 220 (delta 69), pack-reused 0 Receiving objects: 100% (291/291), 17.43 MiB | 3.16 MiB/s, done. Resolving deltas: 100% (131/131), done.

(tldr) [coracollar@spartan-login3 te-nanopore-tools]$ python setup.py install running install running bdist_egg running egg_info writing tldr.egg-info/PKG-INFO writing dependency_links to tldr.egg-info/dependency_links.txt writing requirements to tldr.egg-info/requires.txt writing top-level names to tldr.egg-info/top_level.txt reading manifest file 'tldr.egg-info/SOURCES.txt' writing manifest file 'tldr.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib warning: install_lib: 'build/lib' does not exist -- no Python modules to install

installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts running install_scripts running build_scripts error: [Errno 21] Is a directory: 'tldr/tldr'

adamewing commented 3 years ago

OK, could you try starting over clean (i.e. remove the te-nanopore-tools and tldr directories), just clone tldr (don't touch te-nanopore-tools for now - it doesn't have a setup script yet), and try again. You shouldn't need to copy a setup.py anywhere.

Coracollar commented 3 years ago

I tried, apparently there is a prblem with Cython

(tldr) [coracollar@spartan-login3 TEs]$ git clone https://github.com/adamewing/tldr Cloning into 'tldr'... remote: Enumerating objects: 291, done. remote: Counting objects: 100% (291/291), done. remote: Compressing objects: 100% (185/185), done. remote: Total 291 (delta 131), reused 220 (delta 69), pack-reused 0 Receiving objects: 100% (291/291), 17.43 MiB | 6.73 MiB/s, done. Resolving deltas: 100% (131/131), done. (tldr) [coracollar@spartan-login3 TEs]$ python setup.py install python: can't open file '/data/gpfs/projects/punim1048/TEs/setup.py': [Errno 2] No such file or directory (tldr) [coracollar@spartan-login3 TEs]$ ls tldr (tldr) [coracollar@spartan-login3 TEs]$ cd tldr/ (tldr) [coracollar@spartan-login3 tldr]$ python setup.py install running install running bdist_egg running egg_info creating tldr.egg-info writing tldr.egg-info/PKG-INFO writing dependency_links to tldr.egg-info/dependency_links.txt writing requirements to tldr.egg-info/requires.txt writing top-level names to tldr.egg-info/top_level.txt writing manifest file 'tldr.egg-info/SOURCES.txt' reading manifest file 'tldr.egg-info/SOURCES.txt' writing manifest file 'tldr.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib warning: install_lib: 'build/lib' does not exist -- no Python modules to install

creating build creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/EGG-INFO installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts running install_scripts running build_scripts creating build/scripts-3.9 copying and adjusting tldr/tldr -> build/scripts-3.9 changing mode of build/scripts-3.9/tldr from 644 to 755 creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-3.9/tldr -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/tldr to 755 copying tldr.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying tldr.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying tldr.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying tldr.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying tldr.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... creating dist creating 'dist/tldr-0.1-py3.9.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing tldr-0.1-py3.9.egg Copying tldr-0.1-py3.9.egg to /home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages Adding tldr 0.1 to easy-install.pth file Installing tldr script to /home/coracollar/anaconda3/envs/tldr/bin

Installed /home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/tldr-0.1-py3.9.egg Processing dependencies for tldr==0.1 Searching for numpy>=1.9.0 Reading https://pypi.org/simple/numpy/ Downloading https://files.pythonhosted.org/packages/bf/e8/15aea783ea72e2d4e51e3ec365e8dc4a1a32c9e5eb3a6d695b0d58e67cdd/numpy-1.19.2.zip#sha256=0d310730e1e793527065ad7dde736197b705d0e4c9999775f212b03c44a8484c Best match: numpy 1.19.2 Processing numpy-1.19.2.zip Writing /tmp/easy_install-rjlp48mm/numpy-1.19.2/setup.cfg Running numpy-1.19.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-rjlp48mm/numpy-1.19.2/egg-dist-tmp-zj4i4npo Running from numpy source directory. /tmp/easy_install-rjlp48mm/numpy-1.19.2/setup.py:470: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates run_build = parse_setuppy_commands() Cythonizing sources Processing numpy/random/_bounded_integers.pxd.in Processing numpy/random/_mt19937.pyx Traceback (most recent call last): File "/tmp/easy_install-rjlp48mm/numpy-1.19.2/tools/cythonize.py", line 59, in process_pyx from Cython.Compiler.Version import version as cython_version ModuleNotFoundError: No module named 'Cython'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/tmp/easy_install-rjlp48mm/numpy-1.19.2/tools/cythonize.py", line 235, in main() File "/tmp/easy_install-rjlp48mm/numpy-1.19.2/tools/cythonize.py", line 231, in main find_process_files(root_dir) File "/tmp/easy_install-rjlp48mm/numpy-1.19.2/tools/cythonize.py", line 222, in find_process_files process(root_dir, fromfile, tofile, function, hash_db) File "/tmp/easy_install-rjlp48mm/numpy-1.19.2/tools/cythonize.py", line 188, in process processor_function(fromfile, tofile) File "/tmp/easy_install-rjlp48mm/numpy-1.19.2/tools/cythonize.py", line 64, in process_pyx raise OSError('Cython needs to be installed in Python as a module') OSError: Cython needs to be installed in Python as a module Traceback (most recent call last): File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-rjlp48mm/numpy-1.19.2/setup.py", line 499, in File "/tmp/easy_install-rjlp48mm/numpy-1.19.2/setup.py", line 479, in setup_package File "/tmp/easy_install-rjlp48mm/numpy-1.19.2/setup.py", line 274, in generate_cython RuntimeError: Running cythonize failed!

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/data/gpfs/projects/punim1048/TEs/tldr/setup.py", line 62, in setup( File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/init.py", line 163, in setup return distutils.core.setup(*attrs) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/distutils/core.py", line 148, in setup dist.run_commands() File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/install.py", line 67, in run self.do_egg_install() File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/install.py", line 117, in do_egg_install cmd.run(show_deprecation=False) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 425, in run self.easy_install(spec, not self.no_deps) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 667, in easy_install return self.install_item(None, spec, tmpdir, deps, True) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 714, in install_item self.process_distribution(spec, dist, deps) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 758, in process_distribution distros = WorkingSet([]).resolve( File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/pkg_resources/init.py", line 779, in resolve dist = best[req.key] = env.best_match( File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/pkg_resources/init.py", line 1064, in best_match return self.obtain(req, installer) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/pkg_resources/init.py", line 1076, in obtain return installer(requirement) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 686, in easy_install return self.install_item(spec, dist.location, tmpdir, deps) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 712, in install_item dists = self.install_eggs(spec, download, tmpdir) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 897, in install_eggs return self.build_and_install(setup_script, setup_base) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1167, in build_and_install self.run_setup(setup_script, setup_base, args) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1151, in run_setup run_setup(setup_script, args) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 266, in run_setup raise File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 166, in save_modules saved_exc.resume() File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 141, in resume six.reraise(type, exc, self._tb) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/_vendor/six.py", line 685, in reraise raise value.with_traceback(tb) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-rjlp48mm/numpy-1.19.2/setup.py", line 499, in File "/tmp/easy_install-rjlp48mm/numpy-1.19.2/setup.py", line 479, in setup_package File "/tmp/easy_install-rjlp48mm/numpy-1.19.2/setup.py", line 274, in generate_cython RuntimeError: Running cythonize failed! (tldr) [coracollar@spartan-login3 tldr]$ tldr Traceback (most recent call last): File "/home/coracollar/anaconda3/envs/tldr/bin/tldr", line 4, in import('pkg_resources').run_script('tldr==0.1', 'tldr') File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/pkg_resources/init.py", line 3268, in def _initialize_master_working_set(): File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/pkg_resources/init.py", line 3251, in _call_aside f(args, **kwargs) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/pkg_resources/init.py", line 3280, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/pkg_resources/init.py", line 582, in _build_master ws.require(requires) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/pkg_resources/init.py", line 899, in require needed = self.resolve(parse_requirements(requirements)) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/pkg_resources/init.py", line 785, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'numpy>=1.9.0' distribution was not found and is required by tldr (tldr) [coracollar@spartan-login3 tldr]$

adamewing commented 3 years ago

Ah, ok thanks. I've added cython to the dependencies installed by setup.py - could you do a git pull and re-try python setup.py install and let me know how you go?

Coracollar commented 3 years ago

(tldr) [coracollar@spartan-login3 tldr]$ git pull remote: Enumerating objects: 8, done. remote: Counting objects: 100% (8/8), done. remote: Compressing objects: 100% (4/4), done. remote: Total 6 (delta 4), reused 4 (delta 2), pack-reused 0 Unpacking objects: 100% (6/6), done. From https://github.com/adamewing/tldr 19bedd1..c43c9ad master -> origin/master Updating 19bedd1..c43c9ad Fast-forward setup.py | 1 + 1 file changed, 1 insertion(+) (tldr) [coracollar@spartan-login3 tldr]$ python setup.py install running install running bdist_egg running egg_info writing tldr.egg-info/PKG-INFO writing dependency_links to tldr.egg-info/dependency_links.txt writing requirements to tldr.egg-info/requires.txt writing top-level names to tldr.egg-info/top_level.txt reading manifest file 'tldr.egg-info/SOURCES.txt' writing manifest file 'tldr.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib warning: install_lib: 'build/lib' does not exist -- no Python modules to install

creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/EGG-INFO installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts running install_scripts running build_scripts creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-3.9/tldr -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/tldr to 755 copying tldr.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying tldr.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying tldr.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying tldr.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying tldr.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... creating 'dist/tldr-0.1-py3.9.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing tldr-0.1-py3.9.egg Removing /home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/tldr-0.1-py3.9.egg Copying tldr-0.1-py3.9.egg to /home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages tldr 0.1 is already the active version in easy-install.pth Installing tldr script to /home/coracollar/anaconda3/envs/tldr/bin

Installed /home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/tldr-0.1-py3.9.egg Processing dependencies for tldr==0.1 Searching for numpy>=1.9.0 Reading https://pypi.org/simple/numpy/ Downloading https://files.pythonhosted.org/packages/bf/e8/15aea783ea72e2d4e51e3ec365e8dc4a1a32c9e5eb3a6d695b0d58e67cdd/numpy-1.19.2.zip#sha256=0d310730e1e793527065ad7dde736197b705d0e4c9999775f212b03c44a8484c Best match: numpy 1.19.2 Processing numpy-1.19.2.zip Writing /tmp/easy_install-w2io2381/numpy-1.19.2/setup.cfg Running numpy-1.19.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-w2io2381/numpy-1.19.2/egg-dist-tmp-qo3hproq Running from numpy source directory. /tmp/easy_install-w2io2381/numpy-1.19.2/setup.py:470: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates run_build = parse_setuppy_commands() Cythonizing sources Processing numpy/random/_bounded_integers.pxd.in Processing numpy/random/_mt19937.pyx Traceback (most recent call last): File "/tmp/easy_install-w2io2381/numpy-1.19.2/tools/cythonize.py", line 59, in process_pyx from Cython.Compiler.Version import version as cython_version ModuleNotFoundError: No module named 'Cython'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/tmp/easy_install-w2io2381/numpy-1.19.2/tools/cythonize.py", line 235, in main() File "/tmp/easy_install-w2io2381/numpy-1.19.2/tools/cythonize.py", line 231, in main find_process_files(root_dir) File "/tmp/easy_install-w2io2381/numpy-1.19.2/tools/cythonize.py", line 222, in find_process_files process(root_dir, fromfile, tofile, function, hash_db) File "/tmp/easy_install-w2io2381/numpy-1.19.2/tools/cythonize.py", line 188, in process processor_function(fromfile, tofile) File "/tmp/easy_install-w2io2381/numpy-1.19.2/tools/cythonize.py", line 64, in process_pyx raise OSError('Cython needs to be installed in Python as a module') OSError: Cython needs to be installed in Python as a module Traceback (most recent call last): File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-w2io2381/numpy-1.19.2/setup.py", line 499, in File "/tmp/easy_install-w2io2381/numpy-1.19.2/setup.py", line 479, in setup_package File "/tmp/easy_install-w2io2381/numpy-1.19.2/setup.py", line 274, in generate_cython RuntimeError: Running cythonize failed!

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/data/gpfs/projects/punim1048/TEs/tldr/setup.py", line 62, in setup( File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/init.py", line 163, in setup return distutils.core.setup(**attrs) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/distutils/core.py", line 148, in setup dist.run_commands() File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/distutils/dist.py", line 966, in run_commands self.run_command(cmd) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/distutils/dist.py", line 985, in run_command cmd_obj.run() File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/install.py", line 67, in run self.do_egg_install() File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/install.py", line 117, in do_egg_install cmd.run(show_deprecation=False) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 425, in run self.easy_install(spec, not self.no_deps) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 667, in easy_install return self.install_item(None, spec, tmpdir, deps, True) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 714, in install_item self.process_distribution(spec, dist, deps) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 758, in process_distribution distros = WorkingSet([]).resolve( File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/pkg_resources/init.py", line 779, in resolve dist = best[req.key] = env.best_match( File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/pkg_resources/init.py", line 1064, in best_match return self.obtain(req, installer) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/pkg_resources/init.py", line 1076, in obtain return installer(requirement) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 686, in easy_install return self.install_item(spec, dist.location, tmpdir, deps) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 712, in install_item dists = self.install_eggs(spec, download, tmpdir) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 897, in install_eggs return self.build_and_install(setup_script, setup_base) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1167, in build_and_install self.run_setup(setup_script, setup_base, args) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/command/easy_install.py", line 1151, in run_setup run_setup(setup_script, args) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 266, in run_setup raise File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 166, in save_modules saved_exc.resume() File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 141, in resume six.reraise(type, exc, self._tb) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/_vendor/six.py", line 685, in reraise raise value.with_traceback(tb) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 154, in save_modules yield saved File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 195, in setup_context yield File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 263, in run_setup _execfile(setup_script, ns) File "/home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/setuptools/sandbox.py", line 45, in _execfile exec(code, globals, locals) File "/tmp/easy_install-w2io2381/numpy-1.19.2/setup.py", line 499, in File "/tmp/easy_install-w2io2381/numpy-1.19.2/setup.py", line 479, in setup_package File "/tmp/easy_install-w2io2381/numpy-1.19.2/setup.py", line 274, in generate_cython RuntimeError: Running cythonize failed!

On 20 Oct 2020, at 2:11 pm, adamewing notifications@github.com wrote:

python setup.py install

adamewing commented 3 years ago

Could you try installing cython through conda or pip?

Coracollar commented 3 years ago

I did it. It got more crazy. But might hav etc do with the HPC instead of the program. I copy paste just in case.

(tldr) [coracollar@spartan-login3 tldr]$ python setup.py install running install running bdist_egg running egg_info writing tldr.egg-info/PKG-INFO writing dependency_links to tldr.egg-info/dependency_links.txt writing requirements to tldr.egg-info/requires.txt writing top-level names to tldr.egg-info/top_level.txt reading manifest file 'tldr.egg-info/SOURCES.txt' writing manifest file 'tldr.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib warning: install_lib: 'build/lib' does not exist -- no Python modules to install

creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/EGG-INFO installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts running install_scripts running build_scripts creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-3.9/tldr -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/tldr to 755 copying tldr.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying tldr.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying tldr.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying tldr.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying tldr.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... creating 'dist/tldr-0.1-py3.9.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing tldr-0.1-py3.9.egg Removing /home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/tldr-0.1-py3.9.egg Copying tldr-0.1-py3.9.egg to /home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages tldr 0.1 is already the active version in easy-install.pth Installing tldr script to /home/coracollar/anaconda3/envs/tldr/bin

Installed /home/coracollar/anaconda3/envs/tldr/lib/python3.9/site-packages/tldr-0.1-py3.9.egg Processing dependencies for tldr==0.1 Searching for numpy>=1.9.0 Reading https://pypi.org/simple/numpy/ Downloading https://files.pythonhosted.org/packages/bf/e8/15aea783ea72e2d4e51e3ec365e8dc4a1a32c9e5eb3a6d695b0d58e67cdd/numpy-1.19.2.zip#sha256=0d310730e1e793527065ad7dde736197b705d0e4c9999775f212b03c44a8484c Best match: numpy 1.19.2 Processing numpy-1.19.2.zip Writing /tmp/easy_install-wntr2ooa/numpy-1.19.2/setup.cfg Running numpy-1.19.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-wntr2ooa/numpy-1.19.2/egg-dist-tmp-cht8436j Running from numpy source directory. /tmp/easy_install-wntr2ooa/numpy-1.19.2/setup.py:470: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates run_build = parse_setuppy_commands() Cythonizing sources Processing numpy/random/_bounded_integers.pxd.in Processing numpy/random/_mt19937.pyx Processing numpy/random/_generator.pyx Processing numpy/random/_philox.pyx Processing numpy/random/_bounded_integers.pyx.in Processing numpy/random/_common.pyx Processing numpy/random/_sfc64.pyx Processing numpy/random/bit_generator.pyx Processing numpy/random/_pcg64.pyx Processing numpy/random/mtrand.pyx /tmp/easy_install-wntr2ooa/numpy-1.19.2/numpy/distutils/system_info.py:1914: UserWarning: Optimized (vendor) Blas libraries are not found. Falls back to netlib Blas library which has worse performance. A better performance should be easily gained by switching Blas library. if self._calc_info(blas): /tmp/easy_install-wntr2ooa/numpy-1.19.2/numpy/distutils/system_info.py:1914: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. if self._calc_info(blas): /tmp/easy_install-wntr2ooa/numpy-1.19.2/numpy/distutils/system_info.py:1914: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. if self._calc_info(blas): non-existing path in 'numpy/distutils': 'site.cfg' /tmp/easy_install-wntr2ooa/numpy-1.19.2/numpy/distutils/system_info.py:1748: UserWarning: Lapack (http://www.netlib.org/lapack/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [lapack]) or by setting the LAPACK environment variable. return getattr(self, '_calcinfo{}'.format(name))() /tmp/easy_install-wntr2ooa/numpy-1.19.2/numpy/distutils/system_info.py:1748: UserWarning: Lapack (http://www.netlib.org/lapack/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [lapack_src]) or by setting the LAPACK_SRC environment variable. return getattr(self, '_calcinfo{}'.format(name))() /home/coracollar/anaconda3/envs/tldr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros' warnings.warn(msg)

Warning: Using unoptimized lapack

Warning: Using unoptimized lapack

no previously-included directories found matching 'doc/build' no previously-included directories found matching 'doc/source/generated' no previously-included directories found matching 'benchmarks/env' no previously-included directories found matching 'benchmarks/results' no previously-included directories found matching 'benchmarks/html' no previously-included directories found matching 'benchmarks/numpy' warning: no previously-included files matching '.pyo' found anywhere in distribution warning: no previously-included files matching '.pyd' found anywhere in distribution warning: no previously-included files matching '.swp' found anywhere in distribution warning: no previously-included files matching '.bak' found anywhere in distribution warning: no previously-included files matching '*~' found anywhere in distribution warning: no previously-included files found matching 'LICENSES_bundled.txt' error: Setup script exited with error: Command "gcc -pthread -B /home/coracollar/anaconda3/envs/tldr/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/coracollar/anaconda3/envs/tldr/include -fPIC -O2 -isystem /home/coracollar/anaconda3/envs/tldr/include -fPIC -Ibuild/src.linux-x86_64-3.9/numpy/core/src/common -Inumpy/core/include -Ibuild/src.linux-x86_64-3.9/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/home/coracollar/anaconda3/envs/tldr/include/python3.9 -Ibuild/src.linux-x86_64-3.9/numpy/core/src/common -Ibuild/src.linux-x86_64-3.9/numpy/core/src/npymath -c build/src.linux-x86_64-3.9/numpy/core/src/npysort/radixsort.c -o build/temp.linux-x86_64-3.9/build/src.linux-x86_64-3.9/numpy/core/src/npysort/radixsort.o -MMD -MF build/temp.linux-x86_64-3.9/build/src.linux-x86_64-3.9/numpy/core/src/npysort/radixsort.o.d" failed with exit status 1

On 20 Oct 2020, at 4:00 pm, adamewing notifications@github.com wrote:

Could you try installing cython through conda or pip?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/adamewing/tldr/issues/3#issuecomment-712589283, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANZ7PMCUMLUGWNNEBYNA763SLUKPHANCNFSM4SXF64MQ.

adamewing commented 3 years ago

It looks like it's having trouble building numpy... you you maybe try installing numpy via conda or pip and let me know if it's succeessful? Otherwise, could you let me know what your system is e.g. debian/ubuntu/centos/OS X/etc.

Coracollar commented 3 years ago

Hi, I am working in a linux/ubuntu environment (and HPC called Spartan from unimelb). I tried installing those and kept having problems. But I found the actually source of the problem. I was in a python 3.9 environment change to 3.6 and worked.

(tldr) [coracollar@spartan-login1 tldr]$ tldr usage: tldr [-h] -b BAMS -e ELTS -r REF [-p PROCS] [-m MINREADS] [-o OUTBASE] [-c CHROMS] [--max_te_len MAX_TE_LEN] [--min_te_len MIN_TE_LEN] [--min_alt_frac MIN_ALT_FRAC] [--min_alt_depth MIN_ALT_DEPTH] [--min_total_depth_frac MIN_TOTAL_DEPTH_FRAC] [--wiggle WIGGLE] [--flanksize FLANKSIZE] [-n NONREF] [--debug] [--color_consensus] [--detail_output] [--extend_consensus EXTEND_CONSENSUS] [--trdcol] [--keep_pickles] tldr: error: the following arguments are required: -b/--bams, -e/--elts, -r/--ref (tldr) [coracollar@spartan-login1 tldr]$

On 21 Oct 2020, at 2:39 pm, adamewing notifications@github.com wrote:

It looks like it's having trouble building numpy... you you maybe try installing numpy via conda or pip and let me know if it's succeessful? Otherwise, could you let me know what your system is e.g. debian/ubuntu/centos/OS X/etc.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/adamewing/tldr/issues/3#issuecomment-713277237, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANZ7PMGGL7UFZMP4F2VCMRLSLZJWLANCNFSM4SXF64MQ.