| ## --- install plack | |
| cpanm Plack | |
| # -- save this file as jbrowse.plack | |
| use Plack::App::Directory; | |
| my $app = Plack::App::Directory->new({ root => '.'})->to_app; | |
| $app; | |
| ## -- drop it at the top level of jbrowse folder |
| import sys, os | |
| if len(sys.argv) != 2: | |
| print 'You seem to have forgotten to provide the input GGF3 file.' | |
| exit() | |
| if __name__ == "__main__": | |
| found = False | |
| END = outofbound = issues = 0 | |
| outfile = open(os.path.basename(sys.argv[1]).replace(".gff", "_corrected.gff"), 'w') |
| require 'formula' | |
| class Vim < Formula | |
| homepage 'http://www.vim.org/' | |
| url 'https://vim.googlecode.com/hg/', :revision => '57e8b75298d6' | |
| version '7.3.712' | |
| def features; %w(tiny small normal big huge) end | |
| def interp; %w(lua mzscheme perl python python3 tcl ruby) end |
| use strict; | |
| use warnings; | |
| use Bio::Chado::Schema; | |
| use Bio::DB::SeqFeature::Store; | |
| use Bio::DB::SeqFeature::Store::GFF3Loader; | |
| use YAML::Tiny; | |
| use lib 'lib'; | |
| use MOD::SGD; |
| #! /bin/sh | |
| INSTANCE_ID='' | |
| ELASTIC_IP='' | |
| if [[ `ec2-describe-instances` =~ 'running' ]]; then | |
| echo "AWS instance is already running !" | |
| exit 2 | |
| else | |
| ec2start $INSTANCE_ID |
| SELECT 'dictyBase' db, /* Column 1 */ | |
| GENE_ID.accession db_id, /* Column 2 */ | |
| GENE.uniquename gene_symbol, /* Column 3 */ | |
| TO_CHAR(q_prop.value) qualifier, /* Column 4 */ | |
| 'GO' || ':' || GO_ID.accession go_id, /* Column 5 */ | |
| 'PMID' || ':' || pub.uniquename db_reference, /* Column 6 */ | |
| evsyn.synonym_ evidence_code, /* Column 7 */ | |
| TO_CHAR(with_prop.value) with_from, /* Column 8 */ | |
| cv.name aspect, /* Column 9 */ | |
| GENE.name object_name, /* Column 10 */ |
I was having issues with upgrading perlbrewon OSX Lion. self-upgrade did not upgrade. This command worked fine on Linux. This issue can be found at: App-perlbrew #226
Following steps helped resolve this issue
| package GAFLoader; | |
| use strict; | |
| use warnings; | |
| use Bio::Chado::Schema; | |
| use IO::String; | |
| use LWP::UserAgent; | |
| use Moose; |
| [Unit] | |
| Description=X Virtual Frame Buffer Service | |
| After=network.target | |
| [Service] | |
| ExecStart=/usr/bin/Xvfb :99 -screen 0 1024x768x24 | |
| [Install] | |
| WantedBy=multi-user.target |