Comments (9)
Hi @seaward901 ,
Can you provide the full output of the installation command? Also, what version of python are you using?
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Are you installing within a virtual environment? E.g.:
#make new python environment and source it
python3 -m venv my-newenv
source my-newenv/bin/activate
#sometimes you have to upgrade pip and install wheel:
pip install --upgrade pip
pip install wheel
#install gff3tool
pip install gff3tool
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I'm not 100% sure what's going on. My first guess is permissions. It looks like you're not using a python virtual environment. Could you try that?
python3 -m venv my-newenv
source my-newenv/bin/activate
Otherwise, it may be an issue with python3.9 (we've only tested up to python3.7). It will take us a while to get around to testing it in 3.9, though.
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Same problem here. Python version: 3.7.6 and my python environment was set up via miniconda3.
(base) [jxyue@gpunode ~]$ ~/miniconda3/bin/pip install gff3tool
Collecting gff3tool
Using cached gff3tool-2.0.1.tar.gz (79 kB)
Building wheels for collected packages: gff3tool
Building wheel for gff3tool (setup.py) ... -
And it will take forever ...
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@yjx1217 Sorry, I'm not sure what's going on. I ran a fresh install of miniconda (Mac) and did the following:
(base) :~ $ ~/miniconda3/bin/pip install gff3tool
Collecting gff3tool
Using cached gff3tool-2.0.1.tar.gz (79 kB)
Building wheels for collected packages: gff3tool
Building wheel for gff3tool (setup.py) ... done
Created wheel for gff3tool: filename=gff3tool-2.0.1-cp38-cp38-macosx_10_9_x86_64.whl size=258503026 sha256=15f261a4ddbaa9823751f68ae51e5a6695f32a901ba7260440908ea07d0c214e
Stored in directory: ~/Library/Caches/pip/wheels/13/3e/9c/540a887846eb72db332510fdef60828b9c5eab651e91e51f13
Successfully built gff3tool
Installing collected packages: gff3tool
Successfully installed gff3tool-2.0.1
(base) : ~$ python -V
Python 3.8.5
(base) :~$ ls ~/miniconda3/bin/
2to3 gff3_sort lzmainfo pythonw wish
2to3-3.8 gff3_to_fasta lzmore reset wish8.6
activate idle3 ncursesw6-config sqlite3 xz
c_rehash idle3.8 openssl sqlite3_analyzer xzcat
captoinfo infocmp pip tabs xzcmp
chardetect infotocap pip3 tclsh xzdec
clear lzcat pydoc tclsh8.6 xzdiff
conda lzcmp pydoc3 tic xzegrep
conda-env lzdiff pydoc3.8 toe xzfgrep
cph lzegrep python tput xzgrep
deactivate lzfgrep python.app tqdm xzless
easy_install lzgrep python3 tset xzmore
gff3_QC lzless python3-config unlzma
gff3_fix lzma python3.8 unxz
gff3_merge lzmadec python3.8-config wheel
It took about 2 minutes for the gff3tool to build.
Can you confirm that wheel is installed and up to date in ~/miniconda3/bin/?
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Hi mpoelchau,
Thanks for checking! Yes, it is a bit weird. But I managed to installed gff3tool via setup.py , so at least I can use it for my work. :-)
Best,
Jia-Xing
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