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| -rw-r--r-- | README.org | 54 |
1 files changed, 50 insertions, 4 deletions
@@ -100,9 +100,29 @@ To check for correct type usage in the application, run: mypy --show-error-codes . #+END_SRC -** Running QC +** Deploying/Installing QC + +*** CLI: Docker + +Generate the docker image file with +#+BEGIN_SRC shell +guix pack -f docker -S /bin=bin genenetwork-qc +#+END_SRC + +That creates the image file with a path such as: +#+BEGIN_EXAMPLE +/gnu/store/ibz5qlwzv0lyply2by7422z0c6jfaa6s-genenetwork-qc-docker-pack.tar.gz +#+END_EXAMPLE + +You can now load this file into docker withe +#+BEGIN_SRC shell +docker load < /gnu/store/ibz5qlwzv0lyply2by7422z0c6jfaa6s-genenetwork-qc-docker-pack.tar.gz +#+END_SRC + +and from there, you can run the application as detailed in the +[[#run-cli-version][Running QC: CLI-Version]] section below -*** Installing QC +*** CLI: Guix The application can be installed using guix by pointing to the [[./guix.scm][guix.scm]] file as follows: @@ -110,9 +130,16 @@ follows: 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 +*** Web-Version + +**** TODO Document deployment details for the web version of GeneNetwork QC better + +** Running QC *** Command-Line Version +:PROPERTIES: +:CUSTOM_ID: run-cli-version +:END: Install the application as shown in the [[Installing QC]] section above. @@ -136,4 +163,23 @@ qc --help *** Web Version -Coming soon... +**** TODO Document usage of the web-UI version of the application + +*** Docker + +Download the docker image file from [[https://git.genenetwork.org/fredmanglis/gnqc_py/releases][the releases page]] of the application and +load it to docker with something like: +#+BEGIN_SRC shell + docker load < genenetwork-qc-0.0.1-1-oxu472i-docker.tar.gz +#+END_SRC +replacing ~genenetwork-qc-0.0.1-1-oxu472i.tar.gz~ with the actual name of the +release you downloaded + +Run the application with something like: +#+BEGIN_SRC shell +docker run -v /path/to/qnqc_py/tests/test_data:/data -ti \ + genenetwork-qc:latest /bin/qc average /data/average_error_at_end_200MB.tsv +#+END_SRC +replacing ~/path/to/qnqc_py/tests/test_data~ with the path to the folder where +the file you want to check is in, and ~average_error_at_end_200MB.tsv~ with the +name of the file you want to check for errors. |