nylander
commented
11 months ago Hi, the installation instructions are incomplete.
Try this:
$ git clone https://github.com/Molmed/fastq_demux.git
$ cd fastq_demux
$ pip install -r requirements.txt .
$ pip install .
$ fastq_demux --help
Hi,
I was suggested to use fastqdemux for demultiplexing paired-end reads with combinatorial dual indexes.
I installed fastq_demux using pip, and the codes below.
_git clone https://github.com/Molmed/fastq_demux.git pip install -r fastqdemux/requirements.txt
It seems to work. Please see the results below:
_Collecting click Using cached click-8.1.3-py3-none-any.whl (96 kB) Collecting pytest Using cached pytest-7.1.2-py3-none-any.whl (297 kB) Collecting pytest-cov Using cached pytest_cov-3.0.0-py3-none-any.whl (20 kB) Collecting codecov Using cached codecov-2.1.12-py2.py3-none-any.whl (16 kB) Requirement already satisfied: packaging in ./miniconda3/lib/python3.9/site-packages (from pytest->-r fastq_demux/requirements/dev (line 3)) (21.3) Requirement already satisfied: attrs>=19.2.0 in ./miniconda3/lib/python3.9/site-packages (from pytest->-r fastq_demux/requirements/dev (line 3)) (21.4.0) Requirement already satisfied: iniconfig in ./miniconda3/lib/python3.9/site-packages (from pytest->-r fastq_demux/requirements/dev (line 3)) (1.1.1) Requirement already satisfied: tomli>=1.0.0 in ./.local/lib/python3.9/site-packages (from pytest->-r fastq_demux/requirements/dev (line 3)) (2.0.1) Requirement already satisfied: py>=1.8.2 in ./miniconda3/lib/python3.9/site-packages (from pytest->-r fastq_demux/requirements/dev (line 3)) (1.11.0) Requirement already satisfied: pluggy<2.0,>=0.12 in ./miniconda3/lib/python3.9/site-packages (from pytest->-r fastq_demux/requirements/dev (line 3)) (1.0.0) Requirement already satisfied: coverage[toml]>=5.2.1 in ./.local/lib/python3.9/site-packages (from pytest-cov->-r fastq_demux/requirements/dev (line 4)) (6.3.2) Requirement already satisfied: requests>=2.7.9 in ./miniconda3/lib/python3.9/site-packages (from codecov->-r fastq_demux/requirements/dev (line 5)) (2.27.1) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./miniconda3/lib/python3.9/site-packages (from requests>=2.7.9->codecov->-r fastq_demux/requirements/dev (line 5)) (1.26.9) Requirement already satisfied: idna<4,>=2.5 in ./miniconda3/lib/python3.9/site-packages (from requests>=2.7.9->codecov->-r fastq_demux/requirements/dev (line 5)) (3.3) Requirement already satisfied: charset-normalizer~=2.0.0 in ./miniconda3/lib/python3.9/site-packages (from requests>=2.7.9->codecov->-r fastq_demux/requirements/dev (line 5)) (2.0.12) Requirement already satisfied: certifi>=2017.4.17 in ./miniconda3/lib/python3.9/site-packages (from requests>=2.7.9->codecov->-r fastq_demux/requirements/dev (line 5)) (2021.10.8) Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in ./miniconda3/lib/python3.9/site-packages (from packaging->pytest->-r fastqdemux/requirements/dev (line 3)) (3.0.7) Installing collected packages: click, pytest, codecov, pytest-cov Successfully installed click-8.1.3 codecov-2.1.12 pytest-7.1.2 pytest-cov-3.0.0
I don't understand what to do next. I try to run it with the scripts below, and none of them work. What shall I do? Does the package require an environment? If so, how can I do it? I will appreciate your help a lot. Many thanks!
_$ fastq_demux --help -bash: fastq_demux: command not found
$ python -m fastq_demux --help /home/yeserin/miniconda3/bin/python: No module named fastq_demux.main; 'fastq_demux' is a package and cannot be directly executed
$ python -m fastq_demux/fastq_demux --help /home/yeserin/miniconda3/bin/python: No module named fastq_demux/fastq_demux
$ python -m fastq_demux/fastq_demux/demux --help /home/yeserin/miniconda3/bin/python: No module named fastq_demux/fastq_demux/demux
$ python -m fastq_demux/fastq_demux/demux.py --help /home/yeserin/miniconda3/bin/python: Error while finding module specification for 'fastq_demux/fastq_demux/demux.py' (ModuleNotFoundError: No module named 'fastq_demux/fastq_demux/demux'). Try using 'fastq_demux/fastq_demux/demux' instead of 'fastq_demux/fastqdemux/demux.py' as the module name.