diff options
| -rw-r--r-- | README.org | 79 | ||||
| -rw-r--r-- | guix.scm | 2 |
2 files changed, 62 insertions, 19 deletions
@@ -1,5 +1,5 @@ #+STARTUP: inlineimages -#+TITLE: Quality Control Application +#+TITLE: GeneNetwork Quality Control Application ** Project Goals @@ -29,13 +29,59 @@ following criteria: For reproducibility, this project is developed using guix. -To launch a guix shell for development, do: +To launch a guix shell for development, do +#+BEGIN_SRC shell + guix shell --container --network --pure --manifest=manifest.scm --share=/some/host/directory=/the/upload/directory +#+END_SRC +which environment that is isolated from the rest of your system. + +We share a host directory with the container (that is writeable by the user that +started the web application) to serve as the upload directory for the +application. +*** Run the CLI version + +To run the CLI version of the application, we need to set up the correct ~PYTHONPATH~ +#+BEGIN_SRC shell +export PYTHONPATH="${PYTHONPATH:+$PYTHONPATH:}$(pwd)" +#+END_SRC +which enables us to run the script with #+BEGIN_SRC shell - guix shell --container --network --manifest=manifest.scm +python3 scripts/qc.py --help #+END_SRC -to get an environment that is isolated from the rest of your system. +Without setting up the ~PYTHONPATH~ environment variable, you might get an error +like the following +#+BEGIN_EXAMPLE shell +$ python3 scripts/qc.py --help +Traceback (most recent call last): + File "/home/frederick/genenetwork/gnqc_py/scripts/qc.py", line 8, in <module> + from quality_control.errors import ParseError +ModuleNotFoundError: No module named 'quality_control' +#+END_EXAMPLE + +*NOTE*: Setting up the ~PYTHONPATH~ environment variable is only necessary for +the development environment. It *MUST NOT* require that the end-user set this up +at all! + +*** Run the web version + +To run the web-version of the qc app in development mode, you need to set up a +few environment variables +#+BEGIN_SRC shell +export FLASK_APP=wsgi.py +export FLASK_ENV=development +export QCAPP_INSTANCE_PATH=/path/to/directory/with/config.py +#+END_SRC +then you can run the application with +#+BEGIN_SRC shell +flask run +#+END_SRC + +You then need to manually start the *rq* worker(s) +#+BEGIN_SRC shell +rq worker qcapp_queue +#+END_SRC *** Checks @@ -56,23 +102,23 @@ To check for correct type usage in the application, run: ** Running QC -*** Command-Line Version +*** Installing QC -Clone this repository +The application can be installed using guix by pointing to the [[./guix.scm][guix.scm]] file as +follows: #+BEGIN_SRC shell - git clone http://git.genenetwork.org/fredmanglis/gnqc_py.git -#+END_SRC -then install the application -#+BEGIN_SRC shell - $ python3 -m venv .venv - $ source .venv/bin/activate - (.venv) $ pip install . +guix package [-p /path/to/qc/profile] -f guix.scm #+END_SRC +Once installed, the sections that follow show how to use the *qc* application + +*** Command-Line Version + +Install the application as shown in the [[Installing QC]] section above. To run qc against a file, the syntax is: #+BEGIN_SRC shell - python3 -m qc [--strainsfile <strainsfile-path>] [--verbose] <filetype> <filepath> + qc [--strainsfile <strainsfile-path>] [--verbose] <filetype> <filepath> #+END_SRC where - ~<filetype>~ is one of "*average*" or "*standard-error*" @@ -85,12 +131,9 @@ where To view the usage information for the application, run #+BEGIN_SRC shell - python3 -m qc --help +qc --help #+END_SRC -**** TODO Figure out how to put qc.py in a /bin or /scripts directory and still be able to import the modules in the repo -**** TODO Reduce the command to simply ~qc [--strainsfile <strainsfile-path>] [--verbose] <filetype> <filepath>~ - *** Web Version Coming soon... @@ -42,4 +42,4 @@ "GeneNetwork qc is a quality control application for the data files that eventually are used to add to the data in the GeneNetwork project.") (home-page "https://git.genenetwork.org/fredmanglis/gnqc_py") - (license license:gpl3)) + (license license:agpl3+)) |