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yeban / SequenceServer CLA
Created Oct 14, 2020
sequenceserver_cla
View SequenceServer CLA
SequenceServer Individual Contributor License Agreement
Thank you for your interest in contributing to SequenceServer.
This contributor agreement ("Agreement") documents the rights granted by contributors to Us. To make this document effective, please sign it and send it to Us, following the instructions at . This is a legally binding document, so please read it carefully before agreeing to it. The Agreement may cover more than one software project managed by Us.
1. Definitions
"We" or "Us" means the maintaners of SequenceServer: Anurag Priyam and Dr. Yannick Wurm.
"You" means the individual who Submits a Contribution to Us.
"Contribution" means any work of authorship that is Submitted by You to Us in which You own or assert ownership of the Copyright. If You do not own the Copyright in the entire work of authorship, please follow the instructions in .
"Copyright" means all rights protecting works of authorship owned or controlled by You, including copyright, moral and neighboring rights, as appropriate, fo
View features.xml
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<!DOCTYPE DASFEATURES SYSTEM "http://www.biodas.org/dtd/dasgff.dtd">
<DASGFF>
<GFF version="1.0" href="http://localhost:4567/das/rubydas/features?segment=Si_gnF.scaffold02797:5943908,6066389;type=mRNA;type=exon;type=CDS;maxbins=3232">
<SEGMENT id="Si_gnF.scaffold02797" version="1.0" start="5939256" stop="6066389">
<FEATURE id="9216" label="maker-Si_gnF.scaffold02797-snap-gene-60.39-mRNA-1">
<TYPE id="mRNA"/>
<METHOD id="maker"/>
<START>6003626</START>
<END>6008125</END>
View ox_invalid_format_elements_overlap.rb
require 'ox'
Ox.parse(DATA.read)
__END__
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
<BlastOutput_program>tblastn</BlastOutput_program>
<BlastOutput_version>TBLASTN 2.2.30+</BlastOutput_version>
View jb_pl_test_output
# Failed test 'bin/draw-basepair-track.pl compiled ok'
# at tests/perl_tests/00.compile.t line 45.
# stdout:
# stderr: Can't locate GD/Image.pm in @INC (you may need to install the GD::Image module) (@INC contains: /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/5.18.2/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/5.18.2 /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/bin/../src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/bin/../src/perl5 /Users/priyam/jbrowse/src/perl5/../../extlib/lib/perl5/darwin-thread-multi-2level /Users/priyam/jbrowse/src/perl5/../../extlib/lib/perl5 /Users/priyam/jbrowse/lib /Users/priyam/jbrowse/src/perl5 /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thr
View ruby-setup.sh
#!/usr/bin/env sh
set -x
cd
# Download chruby to ~/.chruby.
wget -O /tmp/chruby-0.3.9.tar.gz https://github.com/postmodern/chruby/archive/v0.3.9.tar.gz
tar xvf /tmp/chruby-0.3.9.tar.gz -C /tmp
rm /tmp/chruby-0.3.9.tar.gz
View gff3_to_json.lua
function usage()
io.stderr:write(string.format("Usage: %s <GFF file>\n" , arg[0]))
os.exit(1)
end
if #arg < 1 then
usage()
os.exit(1)
end
View gt_segfault.gff
This file has been truncated, but you can view the full file.
##gff-version 3
scaffold00002 . contig 1 5659355 . . . ID=scaffold00002;Name=scaffold00002
scaffold00002 maker gene 5418413 5434733 . + . ID=maker-scaffold00002-augustus-gene-54.23;Name=maker-scaffold00002-augustus-gene-54.23
scaffold00002 maker mRNA 5418413 5434733 . + . ID=maker-scaffold00002-augustus-gene-54.23-mRNA-1;Parent=maker-scaffold00002-augustus-gene-54.23;Name=maker-scaffold00002-augustus-gene-54.23-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|0.2|0.33|0.83|0.4|0.33|6|2271|1028
scaffold00002 maker exon 5418413 5418704 . + . ID=maker-scaffold00002-augustus-gene-54.23-mRNA-1:exon:1799;Parent=maker-scaffold00002-augustus-gene-54.23-mRNA-1
scaffold00002 maker exon 5419004 5419181 . + . ID=maker-scaffold00002-augustus-gene-54.23-mRNA-1:exon:1800;Parent=maker-scaffold00002-augustus-gene-54.23-mRNA-1
scaffold00002 maker exon 5426189 5426463 . + . ID=maker-scaffold00002-augustus-gene-54.23-mRNA-1:exon:1801;Parent=maker-scaffold00002-augustus-gene-54.23-mRNA-1
View subpart.gff
scaffold00002 repeatmasker match 1244186 1244228 274 + . ID=scaffold00002:hit:1026:1.3.0.12;Name=species:R1_DPs|genus:LINE%2FR1;Target=species:R1_DPs|genus:LINE%2FR1 650 780 +
scaffold00002 repeatmasker match_part 1244186 1244228 274 + . ID=scaffold00002:hsp:1026:1.3.0.12;Parent=scaffold00002:hit:1026:1.3.0.12;Target=species:R1_DPs|genus:LINE%2FR1 650 780 +
scaffold00002 repeatmasker match 1261641 1261712 273 + . ID=scaffold00002:hit:1027:1.3.0.12;Name=species:GRANDE1_ZD-int|genus:LTR%2FGypsy;Target=species:GRANDE1_ZD-int|genus:LTR%2FGypsy 11010 11080 +
scaffold00002 repeatmasker match_part 1261641 1261712 273 + . ID=scaffold00002:hsp:1027:1.3.0.12;Parent=scaffold00002:hit:1027:1.3.0.12;Target=species:GRANDE1_ZD-int|genus:LTR%2FGypsy 11010 11080 +
# [...]
scaffold00002 repeatrunner protein_match 1241335 1241652 296 - . ID=scaffold00002:hit:1026:1.3.0.12;Name=gi|538540|pir||A40831;Target=gi|538540|pir||A40831 662 763 +
scaffold00002 repeatrunner match_part 1241335 1241652 296 - . ID=scaffold00002:hsp:1026:1.3.
@yeban
yeban / rooter.sh
Created Apr 26, 2012
cd to the project root (identified by the presence of a SCM directory, like .git, or .bzr)
View rooter.sh
# Copyright (C) 2011 Anurag Priyam - MIT License
#
# cd to the project root (identified by the presence of a SCM directory, like
# .git, or .bzr)
#
# Install
# -------
#
# Put something like this in your .zshrc:
#
@yeban
yeban / jekyll.tag-cloud.rb
Created Apr 3, 2012
Flexible, logarithmic distribution, tag cloud for Jekyll.
View jekyll.tag-cloud.rb
# Copyright (C) 2011 Anurag Priyam - MIT License
module Jekyll
# Jekyll plugin to generate tag clouds.
#
# The plugin defines a `tag_cloud` tag that is rendered by Liquid into a tag
# cloud:
#
# <div class='cloud'>