blob: e31b7d7d8193b2ef1622563ff01a5d43b60ffdfd (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
|
#+OPTIONS: ^:nil
# INSTALLATION
Other options for running this tool.
## GNU Guix
### Running the CLI uploader
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
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
guix environment guix --ad-hoc git python openssl python-pycurl python-magic nss-certs python-pyshex -- python3 bh20sequploader/main.py example/sequence.fasta example/maximum_metadata_example.yaml
```
Note that python-pyshex is packaged in
http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics
so you'll need it to the GUIX_PACKAGE_PATH - see the README in that
repository.
### Using the Web Uploader
To run the web uploader in a GNU Guix environment/container run it with something like
```
guix environment guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs --network openssl -- env FLASK_ENV=development PYTHONPATH=$PYTHONPATH:./bh20sequploader FLASK_APP=bh20simplewebuploader/main.py flask run
* Serving Flask app "bh20simplewebuploader/main.py"
* Environment: production
WARNING: This is a development server. Do not use it in a production deployment.
Use a production WSGI server instead.
* Debug mode: off
* Running on http://127.0.0.1:5000/ (Press CTRL+C to quit)
```
WIP: add gunicorn container
Currently the full webserver container deploy command looks like
```
penguin2:~/iwrk/opensource/code/vg/bh20-seq-resource$ env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-oinformatics/ ~/iwrk/opensource/guix/guix/pre-inst-env guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc minimap2 python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp FLASK_ENV=development FLASK_APP=bh20simplewebuploader/main.py flask run
```
Note: see above on GUIX_PACKAGE_PATH.
|
