From bf93a6a2fec690eee4bff4891469cd5947102b3a Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 9 Apr 2020 17:02:38 -0500 Subject: Moved Guix documentation into separate file (as it confused people ;) --- doc/INSTALL.md | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 doc/INSTALL.md (limited to 'doc/INSTALL.md') diff --git a/doc/INSTALL.md b/doc/INSTALL.md new file mode 100644 index 0000000..c5c486c --- /dev/null +++ b/doc/INSTALL.md @@ -0,0 +1,31 @@ +# INSTALLATION + +Other options for running this tool. + +## GNU Guix + +Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you even when you don't have root access on an Ubuntu system. + +1. **Set up and enter a container with the necessary dependencies.** After installing Guix as `~/opt/guix/bin/guix`, run: + +```sh +~/opt/guix/bin/guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs +``` + +2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief: + +```sh +pip3 install --user schema-salad arvados-python-client +``` + +Pip installed the following modules + +``` +arvados-python-client-2.0.1 ciso8601-2.1.3 future-0.18.2 google-api-python-client-1.6.7 httplib2-0.17.1 oauth2client-4.1.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 rsa-4.0 ruamel.yaml-0.15.77 six-1.14.0 uritemplate-3.0.1 ws4py-0.5.1 +``` + +3. Run the tool directly with + +```sh +~/opt/guix/bin/guix environment guix --ad-hoc git python openssl python-pycurl nss-certs -- python3 bh20sequploader/main.py +``` -- cgit v1.2.3 From d53e1e98b800d7dc5720de0b3c14c94452159315 Mon Sep 17 00:00:00 2001 From: Adam Novak Date: Thu, 9 Apr 2020 16:11:03 -0700 Subject: Move the web uploader GUIX instructions to the GUIX file --- README.md | 18 ------------------ doc/INSTALL.md | 20 ++++++++++++++++++++ 2 files changed, 20 insertions(+), 18 deletions(-) (limited to 'doc/INSTALL.md') diff --git a/README.md b/README.md index 960472e..d83eaac 100644 --- a/README.md +++ b/README.md @@ -176,23 +176,5 @@ gunicorn bh20simplewebuploader.main:app This runs on [http://127.0.0.1:8000/](http://127.0.0.1:8000/) by default, but can be adjusted with various [gunicorn options](http://docs.gunicorn.org/en/latest/run.html#commonly-used-arguments) -## GNU Guix -To run the web uploader in a GNU Guix environment - -``` -guix environment guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl -- env FLASK_APP=bh20simplewebuploader/main.py flask run -``` - -The containerized version looks like - -``` -guix environment -C guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl -``` - -and - -``` -env FLASK_APP=bh20simplewebuploader/main.py flask run -``` diff --git a/doc/INSTALL.md b/doc/INSTALL.md index c5c486c..f7fd811 100644 --- a/doc/INSTALL.md +++ b/doc/INSTALL.md @@ -29,3 +29,23 @@ arvados-python-client-2.0.1 ciso8601-2.1.3 future-0.18.2 google-api-python-clien ```sh ~/opt/guix/bin/guix environment guix --ad-hoc git python openssl python-pycurl nss-certs -- python3 bh20sequploader/main.py ``` + +### Using the Web Uploader + +To run the web uploader in a GNU Guix environment + +``` +guix environment guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl -- env FLASK_APP=bh20simplewebuploader/main.py flask run +``` + +The containerized version looks like + +``` +guix environment -C guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl +``` + +and + +``` +env FLASK_APP=bh20simplewebuploader/main.py flask run +``` -- cgit v1.2.3 From 42bef034915c84d3e3ee71d018a37f4292da5504 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 10 Apr 2020 11:48:24 -0500 Subject: Cleaned up Guix install instructions --- doc/INSTALL.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) (limited to 'doc/INSTALL.md') diff --git a/doc/INSTALL.md b/doc/INSTALL.md index f7fd811..5e9e7e9 100644 --- a/doc/INSTALL.md +++ b/doc/INSTALL.md @@ -4,12 +4,14 @@ Other options for running this tool. ## GNU Guix -Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you even when you don't have root access on an Ubuntu system. +### Running the CLI uploader -1. **Set up and enter a container with the necessary dependencies.** After installing Guix as `~/opt/guix/bin/guix`, run: +Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you + +1. **Set up and enter a Guix environment with the necessary dependencies.** After installing Guix run: ```sh -~/opt/guix/bin/guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs +guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs ``` 2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief: @@ -27,7 +29,7 @@ arvados-python-client-2.0.1 ciso8601-2.1.3 future-0.18.2 google-api-python-clien 3. Run the tool directly with ```sh -~/opt/guix/bin/guix environment guix --ad-hoc git python openssl python-pycurl nss-certs -- python3 bh20sequploader/main.py +guix environment guix --ad-hoc git python openssl python-pycurl nss-certs -- python3 bh20sequploader/main.py ``` ### Using the Web Uploader @@ -49,3 +51,5 @@ and ``` env FLASK_APP=bh20simplewebuploader/main.py flask run ``` + +WIP: add gunicorn container -- cgit v1.2.3 From f27a6a3e3be2446660e2f59c1106dcaba32971cf Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 10 Apr 2020 12:13:00 -0500 Subject: Note on running container with Guix --- doc/INSTALL.md | 22 ++++++++-------------- 1 file changed, 8 insertions(+), 14 deletions(-) (limited to 'doc/INSTALL.md') diff --git a/doc/INSTALL.md b/doc/INSTALL.md index 5e9e7e9..bde9dd2 100644 --- a/doc/INSTALL.md +++ b/doc/INSTALL.md @@ -34,22 +34,16 @@ guix environment guix --ad-hoc git python openssl python-pycurl nss-certs -- pyt ### Using the Web Uploader -To run the web uploader in a GNU Guix environment +To run the web uploader in a GNU Guix environment/container ``` -guix environment guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl -- env FLASK_APP=bh20simplewebuploader/main.py flask run -``` - -The containerized version looks like - -``` -guix environment -C guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl -``` - -and - -``` -env FLASK_APP=bh20simplewebuploader/main.py flask run +guix environment -C guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl -- env FLASK_APP=bh20simplewebuploader/main.py flask run + * Serving Flask app "bh20simplewebuploader/main.py" + * Environment: production + WARNING: This is a development server. Do not use it in a production deployment. + Use a production WSGI server instead. + * Debug mode: off + * Running on http://127.0.0.1:5000/ (Press CTRL+C to quit) ``` WIP: add gunicorn container -- cgit v1.2.3 From 9e44ae814862ea91456d95b31981c16ecae6d317 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 10 Apr 2020 12:34:42 -0500 Subject: Magic dependency --- doc/INSTALL.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'doc/INSTALL.md') diff --git a/doc/INSTALL.md b/doc/INSTALL.md index bde9dd2..d8d7f3e 100644 --- a/doc/INSTALL.md +++ b/doc/INSTALL.md @@ -29,7 +29,7 @@ arvados-python-client-2.0.1 ciso8601-2.1.3 future-0.18.2 google-api-python-clien 3. Run the tool directly with ```sh -guix environment guix --ad-hoc git python openssl python-pycurl nss-certs -- python3 bh20sequploader/main.py +guix environment guix --ad-hoc git python openssl python-pycurl python-magic nss-certs -- python3 bh20sequploader/main.py example/sequence.fasta example/metadata.yaml ``` ### Using the Web Uploader @@ -37,7 +37,7 @@ guix environment guix --ad-hoc git python openssl python-pycurl nss-certs -- pyt To run the web uploader in a GNU Guix environment/container ``` -guix environment -C guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl -- env FLASK_APP=bh20simplewebuploader/main.py flask run +guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-magic nss-certs --network openssl -- env FLASK_APP=bh20simplewebuploader/main.py flask run * Serving Flask app "bh20simplewebuploader/main.py" * Environment: production WARNING: This is a development server. Do not use it in a production deployment. -- cgit v1.2.3