[med-svn] [falcon] branch master updated (a22c8da -> 334246f)

Afif Elghraoui afif at moszumanska.debian.org
Mon Nov 14 07:31:26 UTC 2016


This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch master
in repository falcon.

      from  a22c8da   releasing package falcon version 1.7.5-1
       new  b4e69f8   debian/get-orig-source: handle symlinks pointing to directories
       new  2a04b8e   Imported Upstream version 1.8.2
       new  3ca0355   Merge tag 'upstream/1.8.2'
       new  8accac7   Update and refresh patches
       new  2f3ddc9   Update d/copyright
       new  334246f   releasing package falcon version 1.8.2-1

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:
 DALIGNER/LA4Falcon.c                               |  168 +-
 DAMASKER/tandem.c                                  |    2 +-
 DAZZ_DB/README                                     |   15 +-
 DAZZ_DB/fasta2DB.c                                 |    2 +
 {DAMASKER => DEXTRACTOR}/DB.c                      |    0
 {DAMASKER => DEXTRACTOR}/DB.h                      |    0
 {DAMASKER => DEXTRACTOR}/GNUmakefile               |   15 +-
 {DALIGNER => DEXTRACTOR}/LICENSE                   |    0
 DEXTRACTOR/Makefile                                |   37 +
 {DAMASKER => DEXTRACTOR}/QV.c                      |    0
 {DAMASKER => DEXTRACTOR}/QV.h                      |    0
 DEXTRACTOR/README                                  |  141 ++
 DEXTRACTOR/dexqv.c                                 |  164 ++
 DEXTRACTOR/dexta.c                                 |  219 +++
 DEXTRACTOR/dextract.c                              |  594 +++++++
 DEXTRACTOR/undexqv.c                               |  230 +++
 DEXTRACTOR/undexta.c                               |  285 ++++
 FALCON-examples/git-sym.makefile                   |   10 +-
 FALCON-examples/makefile                           |    4 +-
 FALCON-examples/run/ecoli/input.fofn               |    6 +-
 FALCON-examples/run/ecoli/makefile                 |    4 +
 FALCON-examples/run/ecoli2/input.fofn              |    6 +-
 FALCON-examples/run/synth0/check.py                |    2 +-
 FALCON-examples/run/synth0/data/synth0.fasta       | 1750 --------------------
 FALCON-examples/run/synth0/data/synth5k/README     |    8 +
 .../run/synth0/data/{ => synth5k}/ref.fasta        |    0
 .../run/synth0/data/synth5k/subreads.dexta         |  Bin 0 -> 25665 bytes
 .../run/synth0/data/synth5k/synth5k.bam            |  Bin 0 -> 35341 bytes
 .../run/synth0/data/synth5k/synth5k.bam.bai        |  Bin 0 -> 16 bytes
 .../run/synth0/data/synth5k/synth5k.bam.pbi        |  Bin 0 -> 346 bytes
 .../run/synth0/data/synth5k/synth5k.xml            |   15 +
 FALCON-examples/run/synth0/fc_run.cfg              |   14 +-
 FALCON-examples/run/synth0/input.fofn              |    2 +-
 FALCON-make/makefile                               |    5 +-
 FALCON/falcon_kit/bash.py                          |   37 +-
 FALCON/falcon_kit/functional.py                    |   85 +-
 FALCON/falcon_kit/mains/ovlp_to_graph.py           |   35 +-
 FALCON/falcon_kit/mains/run0.py                    |  683 --------
 FALCON/falcon_kit/mains/run1.py                    |  738 ++++-----
 FALCON/falcon_kit/pype_tasks.py                    |  398 +++++
 FALCON/falcon_kit/run_support.py                   |   69 +-
 FALCON/falcon_kit/stats_preassembly.py             |    5 +-
 FALCON/setup.py                                    |    1 -
 FALCON/test/se161.sh                               |  836 ++++++++++
 FALCON/test/test_functional.py                     |   18 +-
 debian/changelog                                   |    9 +
 debian/copyright                                   |   32 +-
 debian/get-orig-source                             |    2 +-
 debian/patches/build-system.patch                  |   12 +-
 debian/patches/rdflib.patch                        |    2 +-
 debian/patches/versioned-deps.patch                |    4 +-
 pypeFLOW/LICENSE                                   |   32 +
 pypeFLOW/License.txt                               |   20 -
 pypeFLOW/pwatcher/blocking.py                      |  464 ++++++
 pypeFLOW/pwatcher/fs_based.py                      |   60 +-
 pypeFLOW/pwatcher/mains/job_start.sh               |   36 +
 pypeFLOW/pwatcher/mains/network_heartbeat.py       |  176 ++
 pypeFLOW/pwatcher/mains/query_server.py            |  125 ++
 pypeFLOW/pwatcher/network_based.py                 | 1031 ++++++++++++
 pypeFLOW/pypeflow/do_support.py                    |   51 +
 pypeFLOW/pypeflow/do_task.py                       |  149 ++
 pypeFLOW/pypeflow/pwatcher_bridge.py               |   59 +-
 pypeFLOW/pypeflow/simple_pwatcher_bridge.py        |  566 +++++++
 pypeFLOW/pypeflow/util.py                          |   31 +
 pypeFLOW/setup.py                                  |    2 +
 pypeFLOW/travis.sh                                 |    2 +-
 66 files changed, 6412 insertions(+), 3056 deletions(-)
 copy {DAMASKER => DEXTRACTOR}/DB.c (100%)
 copy {DAMASKER => DEXTRACTOR}/DB.h (100%)
 copy {DAMASKER => DEXTRACTOR}/GNUmakefile (62%)
 copy {DALIGNER => DEXTRACTOR}/LICENSE (100%)
 create mode 100644 DEXTRACTOR/Makefile
 copy {DAMASKER => DEXTRACTOR}/QV.c (100%)
 copy {DAMASKER => DEXTRACTOR}/QV.h (100%)
 create mode 100644 DEXTRACTOR/README
 create mode 100644 DEXTRACTOR/dexqv.c
 create mode 100644 DEXTRACTOR/dexta.c
 create mode 100644 DEXTRACTOR/dextract.c
 create mode 100644 DEXTRACTOR/undexqv.c
 create mode 100644 DEXTRACTOR/undexta.c
 create mode 100644 FALCON-examples/run/ecoli/makefile
 delete mode 100644 FALCON-examples/run/synth0/data/synth0.fasta
 create mode 100644 FALCON-examples/run/synth0/data/synth5k/README
 rename FALCON-examples/run/synth0/data/{ => synth5k}/ref.fasta (100%)
 create mode 100644 FALCON-examples/run/synth0/data/synth5k/subreads.dexta
 create mode 100644 FALCON-examples/run/synth0/data/synth5k/synth5k.bam
 create mode 100644 FALCON-examples/run/synth0/data/synth5k/synth5k.bam.bai
 create mode 100644 FALCON-examples/run/synth0/data/synth5k/synth5k.bam.pbi
 create mode 100644 FALCON-examples/run/synth0/data/synth5k/synth5k.xml
 delete mode 100644 FALCON/falcon_kit/mains/run0.py
 create mode 100644 FALCON/falcon_kit/pype_tasks.py
 create mode 100644 FALCON/test/se161.sh
 create mode 100644 pypeFLOW/LICENSE
 delete mode 100644 pypeFLOW/License.txt
 create mode 100755 pypeFLOW/pwatcher/blocking.py
 create mode 100755 pypeFLOW/pwatcher/mains/job_start.sh
 create mode 100644 pypeFLOW/pwatcher/mains/network_heartbeat.py
 create mode 100755 pypeFLOW/pwatcher/mains/query_server.py
 create mode 100755 pypeFLOW/pwatcher/network_based.py
 create mode 100644 pypeFLOW/pypeflow/do_support.py
 create mode 100644 pypeFLOW/pypeflow/do_task.py
 create mode 100644 pypeFLOW/pypeflow/simple_pwatcher_bridge.py
 create mode 100644 pypeFLOW/pypeflow/util.py

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