[med-svn] [augustus] branch master updated (afc8458 -> 040dd3e)
Sascha Steinbiss
sascha at steinbiss.name
Sat Apr 2 15:36:14 UTC 2016
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sascha-guest pushed a change to branch master
in repository augustus.
from afc8458 add augustus doc package
new 6746895 Imported Upstream version 3.2.2+dfsg
new 942f979 Merge tag 'upstream/3.2.2+dfsg'
new 4164f63 use correct docs as suggested by upstream
new 15a80d0 d/copyright cosmetics
new d9e461a fix syntax of doc-base file
new 040dd3e add override for timestamped tarball
The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
debian/augustus-doc.doc-base | 7 +-
...an-overrides => augustus-doc.lintian-overrides} | 2 +-
debian/copyright | 22 +-
debian/rules | 38 +-
docs/CDS.sp.README | 10 +
docs/pipeline2gbrowser.txt | 41 +
docs/tutorial/augustus.css | 15 +
docs/tutorial/data/PF00171_full.txt | 611536 ++++++++++++++++++
docs/tutorial/data/PF00171_seed.txt | 1440 +
docs/tutorial/data/PF00225_full.blocks.txt | 22846 +
docs/tutorial/data/PF00225_full.txt | 7572 +
docs/tutorial/data/PF00225_seed.txt | 1044 +
docs/tutorial/data/PRINTS-example.txt | 722 +
docs/tutorial/data/allest.7M-8M.lst | 8458 +
docs/tutorial/data/allest.7M-8M.psl | 9073 +
docs/tutorial/data/augustus.abinitio.aa | 471 +
docs/tutorial/data/chr2R.2M-7M.aa | 8977 +
docs/tutorial/data/chr2R.2M-7M.fa | 100001 +++
docs/tutorial/data/chr2R.7M-8M.wig | 385677 +++++++++++
docs/tutorial/data/chr2R.fa | 422936 ++++++++++++
docs/tutorial/data/chr3.42M.fa | 25003 +
docs/tutorial/data/chr4.103M.fa | 25003 +
docs/tutorial/data/chr5.124M.fa | 25003 +
docs/tutorial/data/est.chr2R.7M-8M.fa | 61009 ++
docs/tutorial/data/est.psl | 10487 +
.../tutorial/data/extrinsic.bug.cfg | 58 +-
docs/tutorial/data/gff2browser.pl | 51 +
docs/tutorial/data/hints.rnaseq.intron.gff | 791 +
docs/tutorial/data/ppx.cfg | 13 +
docs/tutorial/data/sequence.fasta | 69467 ++
docs/tutorial/index.html | 115 +
docs/tutorial/ppx.html | 390 +
docs/tutorial/prediction.html | 422 +
docs/tutorial/results/PF00171.fbs.txt | 25 +
docs/tutorial/results/PF00171.prfl | 391 +
docs/tutorial/results/PF00171_seed.blocks.txt | 2160 +
docs/tutorial/results/PF00225.fbs.txt | 21 +
docs/tutorial/results/PF00225.prfl | 330 +
docs/tutorial/results/PF00225_seed.blocks.txt | 1305 +
docs/tutorial/results/PF00225_seed.prfl | 330 +
docs/tutorial/results/PR00249.fbs.txt | 16 +
docs/tutorial/results/PR00249.prfl | 259 +
docs/tutorial/results/abinitio-browser.gff | 26 +
docs/tutorial/results/abinitio.browser | 306 +
docs/tutorial/results/augustus-ppx.browser | 46 +
docs/tutorial/results/augustus-ppx.gff | 124 +
docs/tutorial/results/augustus.abinitio.gff | 1990 +
docs/tutorial/results/augustus.hints.gff | 18343 +
docs/tutorial/results/badgenes.lst | 8 +
docs/tutorial/results/est.f.psl | 8606 +
docs/tutorial/results/ests.browser.gz | Bin 0 -> 227184 bytes
docs/tutorial/results/genes.gb | 59961 ++
docs/tutorial/results/genes.gb.test | 11318 +
docs/tutorial/results/genes.gb.train | 48643 ++
docs/tutorial/results/hints.est.gff | 19002 +
docs/tutorial/results/hints.gff | 42264 ++
docs/tutorial/results/hints.rnaseq.ep.gff | 22471 +
docs/tutorial/results/output-abinitio.gff | 58 +
docs/tutorial/results/output-browser.gff | 46 +
docs/tutorial/results/output.gff | 124 +
docs/tutorial/results/prot.vs.genome.psl | 7291 +
docs/tutorial/results/scipio.browser | 6826 +
docs/tutorial/results/scipio.gff | 6823 +
docs/tutorial/results/scipio.yaml | 138401 ++++
docs/tutorial/results/withhints.browser | 685 +
docs/tutorial/scipio.html | 228 +
docs/tutorial/training.html | 434 +
docs/tutorial/tutorial.js | 37 +
68 files changed, 2197541 insertions(+), 57 deletions(-)
copy debian/{augustus-data.lintian-overrides => augustus-doc.lintian-overrides} (52%)
create mode 100644 docs/CDS.sp.README
create mode 100644 docs/pipeline2gbrowser.txt
create mode 100644 docs/tutorial/augustus.css
create mode 100644 docs/tutorial/data/PF00171_full.txt
create mode 100644 docs/tutorial/data/PF00171_seed.txt
create mode 100644 docs/tutorial/data/PF00225_full.blocks.txt
create mode 100644 docs/tutorial/data/PF00225_full.txt
create mode 100644 docs/tutorial/data/PF00225_seed.txt
create mode 100644 docs/tutorial/data/PRINTS-example.txt
create mode 100644 docs/tutorial/data/allest.7M-8M.lst
create mode 100644 docs/tutorial/data/allest.7M-8M.psl
create mode 100644 docs/tutorial/data/augustus.abinitio.aa
create mode 100644 docs/tutorial/data/chr2R.2M-7M.aa
create mode 100644 docs/tutorial/data/chr2R.2M-7M.fa
create mode 100644 docs/tutorial/data/chr2R.7M-8M.wig
create mode 100644 docs/tutorial/data/chr2R.fa
create mode 100644 docs/tutorial/data/chr3.42M.fa
create mode 100644 docs/tutorial/data/chr4.103M.fa
create mode 100644 docs/tutorial/data/chr5.124M.fa
create mode 100644 docs/tutorial/data/est.chr2R.7M-8M.fa
create mode 100644 docs/tutorial/data/est.psl
copy config/extrinsic/extrinsic.cfg => docs/tutorial/data/extrinsic.bug.cfg (80%)
create mode 100644 docs/tutorial/data/gff2browser.pl
create mode 100644 docs/tutorial/data/hints.rnaseq.intron.gff
create mode 100644 docs/tutorial/data/ppx.cfg
create mode 100644 docs/tutorial/data/sequence.fasta
create mode 100644 docs/tutorial/index.html
create mode 100644 docs/tutorial/ppx.html
create mode 100644 docs/tutorial/prediction.html
create mode 100644 docs/tutorial/results/PF00171.fbs.txt
create mode 100644 docs/tutorial/results/PF00171.prfl
create mode 100644 docs/tutorial/results/PF00171_seed.blocks.txt
create mode 100644 docs/tutorial/results/PF00225.fbs.txt
create mode 100644 docs/tutorial/results/PF00225.prfl
create mode 100644 docs/tutorial/results/PF00225_seed.blocks.txt
create mode 100644 docs/tutorial/results/PF00225_seed.prfl
create mode 100644 docs/tutorial/results/PR00249.fbs.txt
create mode 100644 docs/tutorial/results/PR00249.prfl
create mode 100644 docs/tutorial/results/abinitio-browser.gff
create mode 100644 docs/tutorial/results/abinitio.browser
create mode 100644 docs/tutorial/results/augustus-ppx.browser
create mode 100644 docs/tutorial/results/augustus-ppx.gff
create mode 100644 docs/tutorial/results/augustus.abinitio.gff
create mode 100644 docs/tutorial/results/augustus.hints.gff
create mode 100644 docs/tutorial/results/badgenes.lst
create mode 100644 docs/tutorial/results/est.f.psl
create mode 100644 docs/tutorial/results/ests.browser.gz
create mode 100644 docs/tutorial/results/genes.gb
create mode 100644 docs/tutorial/results/genes.gb.test
create mode 100644 docs/tutorial/results/genes.gb.train
create mode 100644 docs/tutorial/results/hints.est.gff
create mode 100644 docs/tutorial/results/hints.gff
create mode 100644 docs/tutorial/results/hints.rnaseq.ep.gff
create mode 100644 docs/tutorial/results/output-abinitio.gff
create mode 100644 docs/tutorial/results/output-browser.gff
create mode 100644 docs/tutorial/results/output.gff
create mode 100644 docs/tutorial/results/prot.vs.genome.psl
create mode 100644 docs/tutorial/results/scipio.browser
create mode 100644 docs/tutorial/results/scipio.gff
create mode 100644 docs/tutorial/results/scipio.yaml
create mode 100644 docs/tutorial/results/withhints.browser
create mode 100644 docs/tutorial/scipio.html
create mode 100644 docs/tutorial/training.html
create mode 100644 docs/tutorial/tutorial.js
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