I hereby claim:
- I am samstudio8 on github.
- I am samstudio8 (https://keybase.io/samstudio8) on keybase.
- I have a public key whose fingerprint is 1CA4 381B D09D 09D9 A250 0BFF 3DCD 66BB A142 ADA9
To claim this, I am signing this object:
# grab an off the shelf container with cuda9 | |
FROM nvidia/cuda:9.0-devel-ubuntu16.04 | |
# update gcc to gcc-6 as the default gcc-5 is too old | |
RUN apt-get update && apt-get install -y software-properties-common wget git | |
RUN add-apt-repository ppa:ubuntu-toolchain-r/test | |
RUN apt-get update && apt-get install -y gcc-6 g++-6 | |
# update cmake as the default is too old | |
RUN wget -qO- "https://cmake.org/files/v3.15/cmake-3.15.1-Linux-x86_64.tar.gz" | tar --strip-components=1 -xz -C /usr/ |
# A little bash script to download our juicy ONT PION data | |
# If this doesn't work for you, express your disappointment to @samstudio8. | |
# Use "EVEN" or "LOG" for $1, eg: `bash get_pion_signal.sh EVEN` | |
MODE=$1 | |
echo "Fetching signal blocks. Don't be afraid to CRTL+C and resume if needed..." | |
for i in {00..25} | |
do | |
echo $i; | |
wget -c https://nanopore.s3.climb.ac.uk/Zymo-PromethION-$MODE-BB-SN_signal.tar.$i; |
import sys | |
THRESHOLD = 0.25 # reads must have 25% of their k-mers assigned | |
for line in sys.stdin: | |
fields = line.strip().split() | |
kmers_fields = fields[4:] | |
total_kmers = sum([int(x.split(":")[1]) for x in kmers_fields]) | |
unassigned_kmers = sum([int(x.split(":")[1]) for x in kmers_fields if x[0] == "0"]) |
PATH=$PATH:/home/ubuntu/ware/blast/ncbi-blast-2.7.1+/bin; | |
kraken2-build --download-taxonomy --threads 24 --db /working/databases/kraken2-test/ | |
kraken2-build --download-library archaea --db /working/databases/kraken2-test/ | |
kraken2-build --download-library bacteria --db /working/databases/kraken2-test/ | |
kraken2-build --download-library fungi --db /working/databases/kraken2-test/ | |
kraken2-build --download-library protozoa --db /working/databases/kraken2-test/ | |
kraken2-build --download-library viral --db /working/databases/kraken2-test/ | |
kraken2-build --download-library UniVec_Core --db /working/databases/kraken2-test/ | |
kraken2-build --threads 24 --build --db /working/databases/kraken2-test/ |
import fitbit | |
import gather_keys_oauth2 as Oauth2 | |
import datetime | |
CLIENT_ID = 'YOUR CLIENT' | |
CLIENT_SECRET = 'YOUR SECRET' | |
server = Oauth2.OAuth2Server(CLIENT_ID, CLIENT_SECRET) | |
server.browser_authorize() | |
ACCESS_TOKEN = str(server.fitbit.client.session.token['access_token']) |
""" | |
A scrappy esoteric glue program for Ben because he only really likes databases. | |
Given a tab delimited file where: | |
fields[0] ORF id | |
fields[1] 1-pos Start | |
fields[2] 1-pos End | |
fields[-1] Structural Prediction Code | |
Output a cast dataframe with a line per ORF, describing all structural predictions | |
for that ORF as a single string. Additionally enumerating each viable code's proportion | |
of that string as a percentage. You may alter CODES to add/remove prediction codes |
# Fail2Ban configuration file | |
# | |
# NOTE | |
# You should set up in the jail.conf file, the maxretry and findtime carefully in order to avoid false positives. | |
# | |
# Author: http://www.go2linux.org | |
# Modified by: samnicholls.net | |
# * Mon 6 Jun 2016 - Updated failregex to capture HOST group correctly | |
[Definition] |
Program received signal SIGSEGV, Segmentation fault. | |
_int_malloc (av=av@entry=0x7ffff7dd6b40 <main_arena>, bytes=bytes@entry=24) at malloc.c:3803 | |
3803 set_head (remainder, remainder_size | PREV_INUSE); | |
(gdb) bt | |
#0 _int_malloc (av=av@entry=0x7ffff7dd6b40 <main_arena>, bytes=bytes@entry=24) at malloc.c:3803 | |
#1 0x00007ffff7a9e950 in __GI___libc_malloc (bytes=24) at malloc.c:2914 | |
#2 0x0000000000400812 in main () |
(gdb) bt | |
#0 0x000000318f632625 in raise () from /lib64/libc.so.6 | |
#1 0x000000318f633e05 in abort () from /lib64/libc.so.6 | |
#2 0x00000031926bea7d in __gnu_cxx::__verbose_terminate_handler() () from /usr/lib64/libstdc++.so.6 | |
#3 0x00000031926bcbd6 in std::__exception_ptr::exception_ptr::operator=(std::__exception_ptr::exception_ptr const&) () from /usr/lib64/libstdc++.so.6 | |
#4 0x0000000023b8dbf0 in ?? () | |
#5 0x00007ffffffbb500 in ?? () | |
#6 0x00000000004452e2 in boost::archive::basic_binary_iarchive<boost::archive::binary_iarchive>::init() () | |
#7 0x000000000043d5d4 in CMergeUnit::Update(int, std::vector<CHitUnit, std::allocator<CHitUnit> >&) () | |
#8 0x0000000000409a57 in CHashSearch::MergeRes(int, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&) () |
I hereby claim:
To claim this, I am signing this object: