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pvanheus / nose.patch
Created August 27, 2022 19:26
patch nose 1.3.7 to work with Python 3.10+
diff -ur nose.old/case.py nose/case.py
--- nose.old/case.py 2022-08-27 19:21:19.686914283 +0000
+++ nose/case.py 2022-08-27 19:22:16.688908658 +0000
@@ -9,7 +9,7 @@
from nose.config import Config
from nose.failure import Failure # for backwards compatibility
from nose.util import resolve_name, test_address, try_run
-import collections
+from collections.abc import Callable
@pvanheus
pvanheus / submit_microreact.py
Last active August 16, 2021 08:46
#!/usr/bin/env python
import argparse
import json
from typing import TextIO
import urllib3
def submit_project(project_name: str, csv_file: TextIO, newick_file: TextIO,
access_token: str = None):
@pvanheus
pvanheus / gist:2e8df28121125b18553832284a9558cd
Created July 23, 2020 15:57
run-parts: executing /app/scripts/0_init_container.sh
Apply database migrations from /app/cloudman
/app/venv/lib/python3.6/site-packages/urllib3/connectionpool.py:986: InsecureRequestWarning: Unverified HTTPS request is being made to host '192.168.10.54'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
InsecureRequestWarning,
System check identified some issues:
WARNINGS:
?: (urls.W005) URL namespace 'admin' isn't unique. You may not be able to reverse all URLs in this namespace
?: (urls.W005) URL namespace 'djcloudbridge' isn't unique. You may not be able to reverse all URLs in this namespace
?: (urls.W005) URL namespace 'pubapp' isn't unique. You may not be able to reverse all URLs in this namespace
@pvanheus
pvanheus / starting_with_data.R
Last active May 14, 2020 17:21
download.file(url = "https://ndownloader.figshare.com/files/2292169",
destfile = "data_raw/portal_data_joined.csv")
getwd() # show where I am
surveys <- read.csv("data_raw/portal_data_joined.csv")
head(surveys)
View(surveys)
weight_g <- c(10, 50, 30)
@pvanheus
pvanheus / Thanh-Le-Viet-SARS-CoV-2-Amplicon-Galaxy-Workflow.ga
Created May 5, 2020 08:24
{
"a_galaxy_workflow": "true",
"annotation": "Workflow for generating SARS-Cov2 consensus ",
"format-version": "0.1",
"name": "SARS-Cov2-Amplicon-Artic (imported from uploaded file)",
"steps": {
"0": {
"annotation": "",
"content_id": null,
"errors": null,
@pvanheus
pvanheus / Galaxy-Workflow-SARS-CoV-2-Amplicon-Analysis.ga
Created May 5, 2020 08:22
{
"a_galaxy_workflow": "true",
"annotation": "",
"format-version": "0.1",
"name": "SARS-CoV-2 ARTIC amplicon analysis (v. 2)",
"steps": {
"0": {
"annotation": "",
"content_id": null,
"errors": null,
@pvanheus
pvanheus / Galaxy-Workflow-Copy_of_COVID-19__variation_analysis_(imported_from_uploaded_file).ga
Created May 5, 2020 08:12
{
"a_galaxy_workflow": "true",
"annotation": "",
"format-version": "0.1",
"name": "Copy of COVID-19: variation analysis (imported from uploaded file)",
"steps": {
"0": {
"annotation": "",
"content_id": null,
"errors": null,
@pvanheus
pvanheus / gist:6687f868732b3412d6f177bab4eb720e
Created April 30, 2020 19:25
19:11:27.943318 IP 192.168.66.107.48212 > 129.114.17.223.443: Flags [.], ack 3096, win 487, options [nop,nop,TS val 2519331564 ecr 1801106980,nop,nop,sack 1 {11994:17466}], length 0
19:12:27.947113 IP 192.168.66.107.48212 > 129.114.17.223.443: Flags [.], ack 3096, win 487, options [nop,nop,TS val 2519391566 ecr 1801106980,nop,nop,sack 1 {11994:17466}], length 0
19:12:28.136522 IP 129.114.17.223.443 > 192.168.66.107.48212: Flags [.], ack 779, win 114, options [nop,nop,TS val 1801167234 ecr 2519331564], length 0
19:12:32.946732 IP 129.114.17.223.443 > 192.168.66.107.48212: Flags [FP.], seq 17466:17497, ack 779, win 114, options [nop,nop,TS val 1801172045 ecr 2519331564], length 31
19:12:32.946767 IP 192.168.66.107.48212 > 129.114.17.223.443: Flags [.], ack 3096, win 535, options [nop,nop,TS val 2519396565 ecr 1801106980,nop,nop,sack 1 {11994:17498}], length 0
19:13:33.099106 IP 192.168.66.107.48212 > 129.114.17.223.443: Flags [.], ack 3096, win 535, options [nop,nop,TS val 2519456715 ecr 1801106980,nop,nop,sa
@pvanheus
pvanheus / gist:cf855255414f950272cb0c4811c9f018
Created April 30, 2020 11:06
$ curl -verbose https://testtoolshed.g2.bx.psu.edu/
* Trying 129.114.17.223...
* TCP_NODELAY set
* Connected to testtoolshed.g2.bx.psu.edu (129.114.17.223) port 443 (#0)
* ALPN, offering h2
* ALPN, offering http/1.1
* successfully set certificate verify locations:
* CAfile: /etc/ssl/certs/ca-certificates.crt
CApath: /etc/ssl/certs
* TLSv1.3 (OUT), TLS handshake, Client hello (1):
@pvanheus
pvanheus / gist:02fccc9cc0fa15e71dc18f1da5de13b8
Created April 23, 2020 11:35
13:33:18.790460 IP galaxy-masters2.sanbi.ac.za.44220 > js-129-114-17-223.jetstream-cloud.org.https: Flags [S], seq 711925144, win 28200, options [mss 1410,sackOK,TS val 1513391783 ecr 0,nop,wscale 7], length 0
13:33:18.980677 IP js-129-114-17-223.jetstream-cloud.org.https > galaxy-masters2.sanbi.ac.za.44220: Flags [S.], seq 3622071767, ack 711925145, win 26844, options [mss 8960,sackOK,TS val 1168817789 ecr 1513391783,nop,wscale 8], length 0
13:33:18.980773 IP galaxy-masters2.sanbi.ac.za.44220 > js-129-114-17-223.jetstream-cloud.org.https: Flags [.], ack 1, win 221, options [nop,nop,TS val 1513391973 ecr 1168817789], length 0
13:33:18.981872 IP galaxy-masters2.sanbi.ac.za.44220 > js-129-114-17-223.jetstream-cloud.org.https: Flags [P.], seq 1:518, ack 1, win 221, options [nop,nop,TS val 1513391974 ecr 1168817789], length 517
13:33:19.171876 IP js-129-114-17-223.jetstream-cloud.org.https > galaxy-masters2.sanbi.ac.za.44220: Flags [.], ack 518, win 110, options [nop,nop,TS val 1168817980 ecr 1513391974], length