tsibley

import inspect
import json
import os
import sys
from snakemake.resources import parse_resources

# Required for this file to be loaded by snakemake.main() as a --log-handler-script.
def log_handler(msg):
    pass

tsibley

import os
from contextlib import contextmanager
from time import sleep, time

@contextmanager
def Lockfile(path, timeout = 5 * 60):
    started = time()

    while (time() - started) < timeout:
        try:

tsibley

Run as

snakemake all_c

and you'll get this:

$ tree
.
├── a

│   ├── orange

tsibley

Last two "remind to promote" runs, reverse chronological.

Note that because the state includes a relative duration, `releasedAgo`, we
fail to produce a reproducible hash.  Whoops!

<https://github.com/nextstrain/nextstrain.org/actions/runs/3941437674/jobs/6743841749>
Cache restored from key: remind-to-promote-state-hash-3940925583
{
  "config": {
    "pipeline": "38f67fc7-d93c-40c6-a182-501da2f89d9d",

tsibley

# Symlink the raw HID device (not the baked HID device) of a Thing blink(1),
# aka USB vendor:product id 27b8:01ed (cute product id!), using its reported
# serial number as /dev/blink/$serial.  Also set the mode and group to allow
# access.
#
# This rule matches properties of two udev devices in the device tree:
#
#   1. the raw HID device with the SUBSYSTEM condition, and
#   2. the USB parent device (but *not* the baked HID device in between) with
#      all the other conditions.

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# vim: set ft=sh :
__BASHDB_SOURCE="$BASH_SOURCE"

__bashdb:trap() {
    local file="$1" line="$2" fn="$3" cmd="$4"

    echo "→ $file:$line:$fn: $cmd" >&2

    # From here we can return:
    #   0 to continue

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rule tree:
    message: "Building tree"
    input:
        alignment = rules.align.output.alignment
    output:
        tree = "results/tree_raw.nwk"
    shell:
        """
        # Remove any prior RAxML outputs which didn't get cleaned up
        rm -v RAxML_*.* 2>/dev/null || true

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    # XXX TODO: Since Singularity normally supports local paths to image files
    # or directories, it's possible someone might try to pass that.  We're
    # treating those as Docker image names unqualified by docker://, which may
    # cause confusion.  Doing:
    #
    #   assert url.scheme or not Path(url.path).exists()
    #
    # might help… or it might cause false positives and different confusion.
    # Let's not for now and wait and see.
    #   -trs, 5 Jan 2023

tsibley

diff --git a/augur/tree.py b/augur/tree.py
index 820e653f..462e6135 100644
--- a/augur/tree.py
+++ b/augur/tree.py
@@ -3,6 +3,7 @@ Build a tree using a variety of methods.
 """
 
 import os
+import re
 import shlex

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"""
Build a tree using a variety of methods.
"""

import os
import re
import shlex
import shutil
import sys
import time