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pvanheus / ERR176616.kraken2.report.txt
Created January 24, 2019 10:06
1.12 33870 33870 U 0 unclassified
98.88 2978494 12 R 1 root
98.87 2978389 28 R1 131567 cellular organisms
98.83 2977151 146 D 2 Bacteria
98.81 2976546 136 D1 1783272 Terrabacteria group
98.80 2976359 30 P 201174 Actinobacteria
98.80 2976326 852 C 1760 Actinobacteria
98.76 2974981 496 O 85007 Corynebacteriales
98.74 2974346 1298 F 1762 Mycobacteriaceae
98.69 2972883 2670134 G 1763 Mycobacterium
@pvanheus
pvanheus / demo.rs
Created January 7, 2019 12:32
let output_file = match matches.value_of("OUTPUT_FILE") {
Some(name) => fasta::Writer::new(File::create(name).expect(format!("Failed to open output file ({})", name).as_str())),
None => fasta::Writer::new(io::stdout())
};
//
// error[E0308]: match arms have incompatible types
// --> src/main.rs:42:23
// |
@pvanheus
pvanheus / patric_genomes.cli
Created December 9, 2018 21:22
download genomes from Genbank, using Python aiohttp
#!/usr/bin/env python
import argparse
import asyncio
from pathlib import Path
import socket
import re
import pandas
from aiohttp import ClientSession, TCPConnector
@pvanheus
pvanheus / d2p2.scala
Last active December 2, 2018 21:36
import scala.annotation.tailrec
@tailrec
def diff1(s1: String, s2: String, differences: Int): Boolean =
if (differences > 1) false
else if (s1.length == 0) {
if (differences == 1) true else false
} else
diff1(s1.substring(1),
s2.substring(1),
@pvanheus
pvanheus / gist:3448222de234d35e86e5a0e2c6397b2f
Created November 6, 2018 14:41
cd client && yarn run build-production-maps
yarn run v1.12.1
$ NODE_ENV=production gulp staging && concurrently "yarn run style" "yarn run webpack-production-maps" "yarn run gulp clean && yarn run gulp-production-maps" && yarn run save-build-hash
[14:26:48] Using gulpfile /tools/software/galaxy/galaxy1/client/gulpfile.js
[14:26:48] Starting 'stage-libs'...
[14:26:48] Starting 'fonts'...
[14:26:48] Finished 'fonts' after 179 ms
$ GXY_BUILD_SOURCEMAPS=1 webpack -p
$ gulp clean
$ grunt && gulp style
@pvanheus
pvanheus / client build fail
Created November 6, 2018 13:54
yarn@1.12.1
added 1 package in 2.397s
╭─────────────────────────────────────╮
│ │
│ Update available 5.6.0 → 6.4.1 │
│ Run npm i npm to update │
│ │
╰─────────────────────────────────────╯
@pvanheus
pvanheus / gist:4f39571509aa5e5881f9bfc4121ff527
Created September 13, 2018 20:14
<tool id="shapeit_phase" name="shapeit_phase" version="0.1.0">
<description>genomic data with or without reference panel</description>
<requirements>
<requirement type="package" version="v2.r790">shapeit</requirement>
</requirements>
<stdio>
<exit_code range="1:" />
</stdio>
@pvanheus
pvanheus / gist:4269f262dfb5ccc99082cd0bcca42a88
Created September 7, 2018 20:41
$ planemo test
git --git-dir /home/pvh/.planemo/gx_repo fetch >/dev/null 2>&1
cd /tmp/tmp292k01; git clone --branch 'master' '/home/pvh/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/pvh/.planemo/gx_venv_None; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/pvh/.virtualenvs/planemo/bin/virtualenv -p /home/pvh/.virtualenvs/planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}
Cloning into 'galaxy-dev'...
done.
Set COMMON_STARTUP_ARGS to --dev-wheels
Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample
Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.samp
@pvanheus
pvanheus / gist:24615ececac112937b706d87dfb5b846
Created August 17, 2018 13:39
[galaxy]
192.168.10.7 ansible_ssh_user="ubuntu" ansible_ssh_private_key_file="~/.ssh/id_rsa" # galaxy1
[galaxy:vars]
ansible_python_interpreter=/usr/bin/python3
galaxy_user_name=galaxyuser
galaxy_admin=pvh@sanbi.ac.za
galaxy_server_dir=/tools/software/galaxy/galaxy1
galaxy_data=/usr/people/galaxyuser/galaxy1
galaxy_changeset_id=release_18.05
@pvanheus
pvanheus / tool_test_output.html
Created July 5, 2018 11:58
<html>
<head>
<style>
body
{
font: 12px verdana, "Bitstream Vera Sans", geneva, arial, helvetica, helve, sans-serif;
line-height: 160%;
}