ar0ch

################################
# GitLab email server settings #
################################
# see https://gitlab.com/gitlab-org/omnibus-gitlab/blob/629def0a7a26e7c2326566f0758d4a27857b52a3/doc/settings/smtp.md#smtp-settings
# Use smtp instead of sendmail/postfix.
gitlab_rails['smtp_enable'] = true
gitlab_rails['smtp_address'] = "smtp.mailgun.org"
gitlab_rails['smtp_port'] = 587
gitlab_rails['smtp_authentication'] = "plain"
gitlab_rails['smtp_enable_starttls_auto'] = true

ar0ch

#!/bin/bash
for a in *;do;
  echo $a;cd $a;
  for i in *.faa;do;
    j=`echo $i | cut -d. -f1`;
    for k in *.faa;do;
      l=`echo $k | cut -d. -f1`;
      water -asequence $i -bsequence $k -datafile EBLOSUM60 -gapopen 10 -gapextend 0.5 -outfile  $j.$l -nobrief > /dev/null 2>&1;
      sed -i s/\#//g $j.$l;
      awk 'FNR == 19{printf $2" "}; FNR==26{print $2" "}; FNR==20{printf $2" "}' $j.$l | tr -d '()' | sed s'|/| |'g > $j.$l.tmp;

ar0ch

>abcZ_abcZ_254
TTTGATACCGTTGCCGAAGGTTTGGGTGAAATTCGCGATTTATTGCGCCGTTATCATCATGTCAGCCATGAGTTGGAAAA
CGGTTCGGGTGAGGCTTTGTTGAAAGAACTCAACGAATTACAACTTGAAATCGAAGCGAAGGACGGCTGGAAGCTGGATG
CGGCAGTCAAGCAGACTTTGGGGGAACTCGGTTTGCCGGAAAACGAAAAAATCGGCAACCTTTCCGGCGGTCAGAAAAAG
CGTGTCGCCTTGGCGCAGGCTTGGGTGCAGAAGCCCGACGTATTGCTGCTGGACGAACCGACCAACCATTTGGATATCGA
CGCGATTATTTGGCTGGAAAATCTGCTCAAAGCGTTTGAAGGCAGCTTGGTTGTGATTACCCACGACCGCCGTTTTTTGG
ACAATATCGCCACGCGGATTGTCGAACTCGATC
>adk_adk_92
GAAGCGAAAAAAATCATTGACGAAGGCGGCTTGGTGCGCGACGACATCATTATCGGCATGGTCAAAGAACGCATCGCGCA
AGACGACTGCAAAAACGGTTTCCTGTTTGACGGTTTCCCGCGCACATTGGCACAAGCCGAAGCGATGGTTGAAGCAGGCG

ar0ch

staticperl mkperl -MConfig::Simple -MPod::Usage -MGetopt::Long -MFile::Path -Mwarnings --use Config_heavy.pl -v --add "abil/nasp.pm" -v

ar0ch

From 96c2f53e77c6898132fb0e6c89ce4433a35c31bc Mon Sep 17 00:00:00 2001
From: Aroon Chande <git@atc.io>
Date: Tue, 24 Oct 2017 09:52:30 -0400
Subject: [PATCH] Update Unicycler
 - Add racon and miniasm run dependencies
 - Set py27 incompatible

---
 recipes/unicycler/meta.yaml |    8 +++++---
 1 files changed, 5 insertions(+), 3 deletions(-)

ar0ch

>Illumina_DpnII_expression_PCR_Primer_2
AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
>Illumina_Single_End_Sequencing_Primer
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>custom3
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>Illumina_DpnII_expression_Sequencing_Primer
CGACAGGTTCAGAGTTCTACAGTCCGACGATC
>Illumina_Multiplexing_PCR_Primer_2.01
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT

ar0ch

>NC_011283.1:1770808-1774323
atgtccggaaacatgaaaacaatggatggcaacacggcggcggcctggatctcctacgcc
tttaccgacgtggcggccatctaccccatcaccccctccacgccgatggcggaaaatgtc
gatgaatgggccgctaaggggaaaaagaatctgtttggccagccggtgcgcctgatggag
atgcaatccgaagccggtgccgccggggcggtgcacggcgcgctgcaggcgggagcgctc
accaccacctacaccgcgtcgcaggggctgctgctgatgatccccaatttgtacaaaatt
gccggtgaactgctgccgggtgtttttcacgtcagcgcgcgggcgctggcgaccaattcg
ctgaatatttttggcgaccaccaggacgtgatggcggtacggcagaccggctgcgccatg
ctggtggagaataacgttcagcaggtgatggacctgtcggcggtggcgcacctggcggcg
atcgccgggcggatcccgtttatcaactttttcgacggctttcgcacctcgcacgaaata

ar0ch

>NC_011283.1
gttcgagtggagtccgccgtgtcactttcgctttggcagcagtgtcttgc
ccgattgcaggatgagttaccagccacagaattcagcatgtggatccgcc
cattgcaggcggaactgagcgataacacgctggcactgtatgcgccaaac
cgttttgtgctcgactgggtaagggacaaatacctcaataatatcaatgg
actcctcaatgacttttgcggtgctgatgccccgcagctgcgttttgagg
tgggtgctaagccagccagctcgctgcagaaaggagcggtaagcccggct
gcggcggccattccggcggcgcaggtgcagaccgcgcgcgtggcgccgac
gatcgtgcgcccaggctgggataatgtcccggcgccagcggagccgacct
accgctctaacgttaacgtgaaacacacgtttgataacttcgtcgaaggt

ar0ch

library(shiny)
# Also uses parallel, shinyjs, tools

# Create a long-running task, executed in a forked process. (Doesn't work on Windows)
# 
# The return value is a promise-like object with three
# methods:
# - completed(): FALSE initially, then TRUE if the task succeeds,
#   fails, or is cancelled. Reactive, so when the state changes
#   any reactive readers will invalidate.

ar0ch

#!/usr/bin/env python
import sys
import os
import re
import shutil
import xml.etree.ElementTree as ET
try:
    from urllib.request import urlopen, urlretrieve
except ImportError:
    from urllib import urlopen, urlretrieve