pvanheus

#!/bin/sh

COMBATTB_DATA=https://zenodo.org/record/51638/files/combat_tb_neo4j.tar.bz2
if [ ! -d /srv -o ! -w /srv ] ; then
  echo "A directory called /srv must exist and be writeable by your user before using this script." >&2
fi

( if [ ! -d /srv/neo4j ] ; then mkdir -p /srv/neo4j ; fi ; cd /srv/neo4j ; wget -c -O combattb_data.tar.bz2 https://zenodo.org/record/51638/files/combat_tb_neo4j.tar.bz2 ; tar xf combattb_data.tar.bz2 )

docker-compose up --build

pvanheus

rewritten text:

We report here the ~670 Mb genome get together of the Asian seabass (Lates calcarifer), a tropical marine teleost. We utilized long-read sequencing increased by transcriptomics, optical and hereditary mapping alongside shared synteny from firmly related fish species to infer a chromosome-level get together with a contig N50 size more than 1 Mb and framework N50 size more than 25 Mb that traverse ~90% of the genome. The populace structure of L. calcarifer species complex was investigated by re-sequencing 61 people speaking to different areas over the species' local reach. SNP investigations distinguished elevated amounts of hereditary differing qualities and affirmed before signs of a populace stratification including three clades with indications of admixture evident in the South-East Asian populace. The nature of the Asian seabass genome get together far surpasses that of whatever other fish species, and will serve as another standard for fish genomics.

original:

We report here the ~670 Mb

pvanheus

127.0.0.1 - - [09/Jun/2016:20:01:00 +0200] "GET /admin_toolshed/manage_repository?sort=name&id=f2db41e1fa331b3e&f-deleted=False HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.79 Safari/537.36"
.....
Error: No packages found in current linux-64 channels matching: ncbi_blast_plus

You can search for this package on anaconda.org with

    anaconda search -t conda ncbi_blast_plus

You may need to install the anaconda-client command line client with

pvanheus

<dependency_resolvers>
<!-- the default configuration, first look for dependencies installed from the toolshed -->
  <tool_shed_packages />
<!-- then look for env.sh files in directories according to the "galaxy packages" schema.
     These resolvers can take a base_path attribute to specify where to look for
     package definitions, but by default look in the directory specified by tool_dependency_dir
     in Galaxy's config/galaxy.ini -->
  <galaxy_packages />
  <galaxy_packages versionless="true" />
  <conda auto_install="true" auto_init="true" />

pvanheus

TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACC
CTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAGCAAAGGGCTTG
GCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTTGCTCTGTTATCCGTGCCGAGCAGCTTTGTC
CAAAACGAAATCGAGCGCCATCTGCGGGCCCCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGA
TCCAACTCGGGGTCCGCATCGCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGA
AAATCCTGCTACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG
GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCACAATACCGATTCCGCTACCGCTG
GCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGCGCCTCCAACCGGTTCGCGCA
CGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCTTACAACCCCCTGTTCATCTGGGGCGAGTCC
GGTCTCGGCAAGACACACCTGCTACACGCGGCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGG

pvanheus

EBUG:conda.config:Could not import binstar
DEBUG:conda.fetch:channel_urls=()
INFO:stdoutlog:Fetching package metadata: 
DEBUG:requests.packages.urllib3.util.retry:Converted retries value: 3 -> Retry(total=3, connect=None, read=None, redirect=None)
INFO:stdoutlog:

DEBUG:conda.fetch:adding cached pkg to index: python-2.7.11-0.tar.bz2
DEBUG:conda.fetch:adding cached pkg to index: sqlite-3.13.0-0.tar.bz2
DEBUG:conda.fetch:adding cached pkg to index: pandas-0.18.1-np111py27_0.tar.bz2
DEBUG:conda.fetch:adding cached pkg to index: pip-8.1.1-py27_1.tar.bz2

pvanheus

Fatal error: Matched on Error:
discarding /home/galaxy/galaxydemo/shed_tools/_conda/bin from PATH
prepending /home/galaxy/galaxydemo/galaxy/database/jobs/000/36/conda-env/bin to PATH
Error: no such directory: /home/galaxy/galaxydemo/galaxy/database/jobs/000/36/conda-metadata-env/bin

then in logs:

galaxy.tools.deps.conda_util DEBUG 2016-06-15 08:40:42,272 XXX: path is: /home/galaxy/galaxydemo/galaxy/database/jobs/000/36/conda-metadata-env False
galaxy.tools.deps.conda_util DEBUG 2016-06-15 08:40:42,273 XXX: create_args ['--unknown', '--offline', '--prefix', '/home/galaxy/galaxydemo/galaxy/database/jobs/000/36/conda-metadata-env', '--file', '/home/galaxy/galaxydemo/galaxy/database/tmp/jobdepsx31qdza70136bd6dae458367ccc8b3f4d5afbba0945abf8821362f9e05e4ff593adbcf/__package__samtools@__unversioned__', '>', '/dev/null']
Error: too few arguments, must supply command line package specs or --file

pvanheus

<!DOCTYPE html>
<html>
<head>
    <meta charset="utf-8">
    <title>COMBAT-TB</title>
    <!-- meta -->
    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
    <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1.0"/>
    <!-- styles -->
    <link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">

pvanheus

var TestBox = React.createClass({
    getInitialState: function () {
        return {enabled: false, othervalue: ''}
    },

    componentDidMount: function() {
        $(document).ready(function() {
            $('select').material_select();
        });
        $('#staticselect').material_select(this._handleSelectChange.bind(this));

pvanheus

var TestBox = React.createClass({
    getInitialState: function () {
        return {enabled: false, othervalue: ''}
    },

    componentDidMount: function() {
        $(document).ready(function() {
            $('select').material_select();
        });
        // $('#staticselect').material_select(this._handleSelectChange.bind(this));