[med-svn] [falcon] branch master updated (be234b7 -> a22c8da)
Afif Elghraoui
afif at moszumanska.debian.org
Sun Oct 23 12:18:46 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 be234b7 releasing package falconkit version 0.7-1
new b68fa2e Rename source package
new 2a3dcd3 Track FALCON-Integrate for releases, and bundle supporting code
new ffe1a23 Prepare new revision
new 8bf7774 Imported Upstream version 1.7.5
new b828c5c Merge tag 'upstream/1.7.5'
new 8253fbf Revamp packaging for bundled subcomponents
new 6c42754 Update VCS URL to match source package name
new a22c8da releasing package falcon version 1.7.5-1
The 8 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:
.gitignore | 10 -
.travis.yml | 24 +-
DALIGNER/DB2Falcon.c | 133 +
DALIGNER/GNUmakefile | 33 +
DALIGNER/HPC.daligner.c | 1585 ++
DALIGNER/LA4Falcon.c | 802 +
DALIGNER/LA4Ice.c | 568 +
DALIGNER/LAcat.c | 192 +
DALIGNER/LAcheck.c | 361 +
DALIGNER/LAdump.c | 487 +
DALIGNER/LAindex.c | 201 +
DALIGNER/LAmerge.c | 397 +
DALIGNER/LAshow.c | 618 +
DALIGNER/LAsort.c | 285 +
DALIGNER/LAsplit.c | 242 +
DALIGNER/LICENSE | 34 +
DALIGNER/Makefile | 53 +
DALIGNER/README | 521 +
DALIGNER/README_PB.md | 8 +
DALIGNER/align.c | 5157 +++++
DALIGNER/align.h | 354 +
DALIGNER/daligner.c | 731 +
DALIGNER/daligner_p.c | 1 +
DALIGNER/filter.c | 2306 +++
DALIGNER/filter.h | 35 +
DALIGNER/filter_p.c | 2 +
DALIGNER/py_utils/DAPI.py | 72 +
DALIGNER/py_utils/DAPipe.py | 93 +
DALIGNER/py_utils/DBLA_to_falcon.py | 42 +
DALIGNER/py_utils/FALCON_ASM_NOTE | 27 +
DALIGNER/py_utils/LAPI.py | 110 +
DALIGNER/py_utils/LAPipe.py | 177 +
DAMASKER/DB.c | 1736 ++
DAMASKER/DB.h | 420 +
DAMASKER/GNUmakefile | 25 +
DAMASKER/HPC.REPmask.c | 877 +
DAMASKER/HPC.TANmask.c | 530 +
DAMASKER/Makefile | 34 +
DAMASKER/QV.c | 1387 ++
DAMASKER/QV.h | 96 +
DAMASKER/README | 172 +
DAMASKER/REPmask.c | 636 +
DAMASKER/TANmask.c | 462 +
DAMASKER/align.c | 5157 +++++
DAMASKER/align.h | 354 +
DAMASKER/datander.c | 182 +
DAMASKER/tandem.c | 1364 ++
DAMASKER/tandem.h | 24 +
DAZZ_DB/Catrack.c | 259 +
DAZZ_DB/DAM2fasta.c | 213 +
DAZZ_DB/DB.c | 1742 ++
DAZZ_DB/DB.h | 420 +
DAZZ_DB/DB2fasta.c | 180 +
DAZZ_DB/DB2quiva.c | 189 +
DAZZ_DB/DBdump.c | 784 +
DAZZ_DB/DBdust.c | 471 +
DAZZ_DB/DBrm.c | 40 +
DAZZ_DB/DBshow.c | 579 +
DAZZ_DB/DBsplit.c | 216 +
DAZZ_DB/DBstats.c | 346 +
DAZZ_DB/DBupgrade.Dec.31.2014.c | 86 +
DAZZ_DB/DBupgrade.Sep.25.2014.c | 96 +
DAZZ_DB/DUSTupgrade.Jan.1.2015.c | 80 +
DAZZ_DB/GNUmakefile | 41 +
DAZZ_DB/LICENSE | 34 +
DAZZ_DB/Makefile | 75 +
DAZZ_DB/QV.c | 1387 ++
DAZZ_DB/QV.h | 96 +
DAZZ_DB/README | 502 +
DAZZ_DB/fasta2DAM.c | 687 +
DAZZ_DB/fasta2DB.c | 728 +
DAZZ_DB/quiva2DB.c | 510 +
DAZZ_DB/rangen.c | 182 +
DAZZ_DB/simulator.c | 573 +
FALCON-examples/LICENSE | 23 +
FALCON-examples/README.md | 24 +
FALCON-examples/data/git-sym.makefile | 30 +
FALCON-examples/data/makefile | 16 +
FALCON-examples/git-sym.makefile | 31 +
FALCON-examples/logging.ini | 46 +
FALCON-examples/makefile | 20 +
.../run/arab/fc_run.cfg | 9 +-
FALCON-examples/run/arab/input.fofn | 1 +
.../run/ecoli/fc_run.cfg | 8 +-
FALCON-examples/run/ecoli/input.fofn | 3 +
.../run/ecoli2/fc_run.cfg | 6 +-
FALCON-examples/run/ecoli2/input.fofn | 3 +
.../run/lambda-hgap/fc_run.cfg | 24 +-
FALCON-examples/run/lambda-hgap/input.fofn | 1 +
FALCON-examples/run/lambda-smb14/fc_run.cfg | 37 +
FALCON-examples/run/lambda-smb14/input.fofn | 1 +
FALCON-examples/run/lambda-smb14/logging.ini | 46 +
.../run/lambda/fc_run.cfg | 25 +-
FALCON-examples/run/lambda/input.fofn | 1 +
FALCON-examples/run/synth0/check.py | 38 +
FALCON-examples/run/synth0/data/ref.fasta | 2 +
FALCON-examples/run/synth0/data/synth0.fasta | 1750 ++
FALCON-examples/run/synth0/fc_run.cfg | 47 +
FALCON-examples/run/synth0/input.fofn | 1 +
FALCON-examples/run/synth0/logging.ini | 30 +
FALCON-examples/run/synth0/logging.json | 31 +
FALCON-examples/run/synth0/logging.many.ini | 66 +
FALCON-examples/run/synth0/makefile | 19 +
FALCON-examples/scripts/check.py | 44 +
FALCON-examples/scripts/circ-sim.py | 92 +
FALCON-examples/scripts/relabel_fasta.py | 30 +
FALCON-examples/scripts/synther.py | 140 +
LICENSE => FALCON-make/LICENSE | 0
FALCON-make/README.md | 84 +
FALCON-make/config-edit-user.sh | 18 +
FALCON-make/config-edit.sh | 17 +
FALCON-make/config-standard.sh | 19 +
FALCON-make/get-pip.py | 19177 +++++++++++++++++++
FALCON-make/makefile | 68 +
.travis.yml => FALCON/.travis.yml | 0
LICENSE => FALCON/LICENSE | 0
MANIFEST.in => FALCON/MANIFEST.in | 0
README.md => FALCON/README.md | 0
{doc => FALCON/doc}/README | 0
{doc => FALCON/doc}/falcon_icon.svg | 0
{doc => FALCON/doc}/falcon_icon2.png | Bin
{examples => FALCON/examples}/build_env.sh | 0
{examples => FALCON/examples}/build_env2.sh | 0
.../examples}/ecoli_asm_graph_exploration.ipynb | 0
{examples => FALCON/examples}/fc_run_LG.cfg | 0
{examples => FALCON/examples}/fc_run_arab.cfg | 0
{examples => FALCON/examples}/fc_run_dmel.cfg | 0
{examples => FALCON/examples}/fc_run_ecoli.cfg | 0
{examples => FALCON/examples}/fc_run_ecoli_2.cfg | 0
{examples => FALCON/examples}/logging.json | 0
{examples => FALCON/examples}/run_ecoli_test.sh | 0
{falcon_kit => FALCON/falcon_kit}/FastaReader.py | 0
{falcon_kit => FALCON/falcon_kit}/__init__.py | 0
{falcon_kit => FALCON/falcon_kit}/bash.py | 46 +-
{falcon_kit => FALCON/falcon_kit}/falcon_kit.py | 0
{falcon_kit => FALCON/falcon_kit}/fc_asm_graph.py | 0
{falcon_kit => FALCON/falcon_kit}/functional.py | 129 +-
.../falcon_kit}/mains/__init__.py | 0
.../falcon_kit}/mains/actg_coordinate.py | 0
.../falcon_kit}/mains/calc_cutoff.py | 0
.../falcon_kit}/mains/consensus.py | 0
.../falcon_kit}/mains/contig_annotate.py | 0
.../falcon_kit}/mains/ctg_link_analysis.py | 0
.../falcon_kit}/mains/dedup_a_tigs.py | 0
.../falcon_kit}/mains/fasta2fasta.py | 0
FALCON/falcon_kit/mains/fetch_reads.py | 133 +
FALCON/falcon_kit/mains/get_read_ctg_map.py | 129 +
.../falcon_kit}/mains/graph_to_contig.py | 0
.../falcon_kit}/mains/graph_to_utgs.py | 0
.../falcon_kit}/mains/ovlp_filter.py | 3 +-
.../falcon_kit}/mains/ovlp_stats.py | 0
.../falcon_kit}/mains/ovlp_to_graph.py | 0
FALCON/falcon_kit/mains/pr_ctg_track.py | 159 +
FALCON/falcon_kit/mains/report_pre_assembly.py | 46 +
FALCON/falcon_kit/mains/rr_ctg_track.py | 169 +
{falcon_kit => FALCON/falcon_kit}/mains/run0.py | 12 +-
{falcon_kit => FALCON/falcon_kit}/mains/run1.py | 136 +-
{falcon_kit => FALCON/falcon_kit}/mains/tasks.py | 0
{falcon_kit => FALCON/falcon_kit}/multiproc.py | 0
{falcon_kit => FALCON/falcon_kit}/run_support.py | 29 +-
.../falcon_kit}/stats_preassembly.py | 65 +-
{falcon_kit => FALCON/falcon_kit}/util/__init__.py | 0
{falcon_kit => FALCON/falcon_kit}/util/io.py | 12 +
{falcon_kit => FALCON/falcon_kit}/util/system.py | 0
setup.py => FALCON/setup.py | 6 +-
{src => FALCON/src}/c/DW_banded.c | 0
{src => FALCON/src}/c/Makefile | 0
{src => FALCON/src}/c/Makefile.osx | 0
{src => FALCON/src}/c/common.h | 0
{src => FALCON/src}/c/ext_falcon.c | 0
{src => FALCON/src}/c/falcon.c | 0
{src => FALCON/src}/c/kmer_lookup.c | 4 +-
.../src}/py_scripts/fc_actg_coordinate.py | 0
{src => FALCON/src}/py_scripts/fc_consensus.py | 0
.../src}/py_scripts/fc_contig_annotate.py | 0
.../src}/py_scripts/fc_ctg_link_analysis.py | 0
{src => FALCON/src}/py_scripts/fc_dedup_a_tigs.py | 0
.../src}/py_scripts/fc_graph_to_contig.py | 0
{src => FALCON/src}/py_scripts/fc_graph_to_utgs.py | 0
{src => FALCON/src}/py_scripts/fc_ovlp_filter.py | 0
{src => FALCON/src}/py_scripts/fc_ovlp_stats.py | 0
{src => FALCON/src}/py_scripts/fc_ovlp_to_graph.py | 0
{src => FALCON/src}/py_scripts/fc_run.py | 0
{src => FALCON/src}/py_scripts_v0.1/falcon_asm.py | 0
.../src}/py_scripts_v0.1/falcon_asm_s.py | 0
.../src}/py_scripts_v0.1/falcon_dedup.py | 0
.../src}/py_scripts_v0.1/falcon_fixasm.py | 0
.../src}/py_scripts_v0.1/falcon_overlap.py | 0
.../src}/py_scripts_v0.1/falcon_overlap2.py | 0
{src => FALCON/src}/py_scripts_v0.1/falcon_qrm.py | 0
.../src}/py_scripts_v0.1/falcon_qrm_0.py | 0
.../src}/py_scripts_v0.1/falcon_sense.py | 0
.../src}/py_scripts_v0.1/falcon_ucns_data.py | 0
.../src}/py_scripts_v0.1/falcon_utgcns.py | 0
{src => FALCON/src}/py_scripts_v0.1/get_ovl.sh | 0
{src => FALCON/src}/py_scripts_v0.1/get_rdata.py | 0
{src => FALCON/src}/py_scripts_v0.1/overlapper.py | 0
{src => FALCON/src}/py_scripts_v0.1/ovlp_filter.sh | 0
{src => FALCON/src}/py_scripts_v0.1/redis_graph.py | 0
.../src}/py_scripts_v0.1/remove_dup_ctg.py | 0
{src => FALCON/src}/utils/fetch_preads.py | 0
{test => FALCON/test}/HPCdaligner_synth0.sh | 0
FALCON/test/HPCdaligner_synth0_preads.sh | 9 +
{test => FALCON/test}/helpers.py | 0
{test => FALCON/test}/test_actg_coordinate.py | 0
{test => FALCON/test}/test_consensus.py | 0
{test => FALCON/test}/test_contig_annotate.py | 0
{test => FALCON/test}/test_ctg_link_analysis.py | 0
{test => FALCON/test}/test_functional.py | 82 +-
{test => FALCON/test}/test_graph_to_contig.py | 0
{test => FALCON/test}/test_graph_to_utgs.py | 0
{test => FALCON/test}/test_ovlp_filter.py | 0
{test => FALCON/test}/test_ovlp_stats.py | 0
{test => FALCON/test}/test_ovlp_to_graph.py | 0
{test => FALCON/test}/test_run.py | 0
{test => FALCON/test}/test_run_LG.py | 0
{test => FALCON/test}/test_stats_preassembly.py | 23 +-
{test_data => FALCON/test_data}/t1.fa | 0
{test_data => FALCON/test_data}/t1.fofn | 0
{test_data => FALCON/test_data}/t2.fa | 0
{test_data => FALCON/test_data}/t2.fofn | 0
travis.sh => FALCON/travis.sh | 0
README.md | 62 +-
debian/README.source | 17 +-
debian/changelog | 12 +
debian/control | 39 +-
debian/copyright | 92 +-
debian/docs | 2 -
debian/examples | 2 +-
debian/falconkit.1 | 34 -
debian/fc_run | 7 +
debian/fc_run.1 | 12 +
debian/get-orig-source | 52 +
debian/install | 2 +
debian/links | 4 +
debian/lintian-overrides | 4 +
debian/manpages | 2 +-
debian/patches/add-shebang-lines.patch | 116 -
debian/patches/build-system.patch | 78 +
debian/patches/pyscripts.patch | 14 -
debian/patches/rdflib.patch | 32 +
debian/patches/series | 6 +-
...networkx-version.patch => versioned-deps.patch} | 15 +-
debian/rules | 57 +-
debian/tests/control | 20 +-
debian/watch | 8 +-
default-env.sh | 11 +
env.sh | 11 +
makefile | 25 +
.travis.yml => pypeFLOW/.travis.yml | 7 +-
pypeFLOW/License.txt | 20 +
pypeFLOW/README.rst | 71 +
pypeFLOW/doc/Example1.png | Bin 0 -> 19144 bytes
pypeFLOW/doc/Example2.png | Bin 0 -> 182447 bytes
pypeFLOW/doc/Makefile | 153 +
pypeFLOW/doc/concurrent_execution.rst | 15 +
pypeFLOW/doc/conf.py | 242 +
pypeFLOW/doc/examples.rst | 175 +
pypeFLOW/doc/index.rst | 28 +
pypeFLOW/doc/introduction.rst | 62 +
pypeFLOW/doc/modules.rst | 7 +
pypeFLOW/doc/pypeflow.rst | 35 +
pypeFLOW/doc/rdf_resprentation.rst | 134 +
pypeFLOW/example/PypeTest.py | 268 +
pypeFLOW/example/README.txt | 10 +
pypeFLOW/example/test_shutdown.py | 72 +
.../example/testdata/.placeholder | 0
pypeFLOW/examples-pwatcher/README.md | 60 +
pypeFLOW/examples-pwatcher/ab/delete.json | 1 +
pypeFLOW/examples-pwatcher/ab/jobs/b | 3 +
pypeFLOW/examples-pwatcher/ab/jobs/c | 3 +
.../examples-pwatcher/ab/logging-cfg.json | 28 +-
pypeFLOW/examples-pwatcher/ab/makefile | 10 +
pypeFLOW/examples-pwatcher/ab/query-ab.json | 5 +
pypeFLOW/examples-pwatcher/ab/run.json | 12 +
.../escher--unbelievable-527581_1024_768.jpg | Bin 0 -> 202550 bytes
pypeFLOW/presentation/pipelines.png | Bin 0 -> 617718 bytes
pypeFLOW/presentation/pypeFLOW_tutorial.html | 2412 +++
pypeFLOW/presentation/pypeFLOW_tutorial.rst | 505 +
.../mains => pypeFLOW/pwatcher}/__init__.py | 0
pypeFLOW/pwatcher/fs_based.py | 797 +
.../pwatcher}/mains/__init__.py | 0
pypeFLOW/pwatcher/mains/fs_heartbeat.py | 149 +
pypeFLOW/pwatcher/mains/pwatcher.py | 12 +
pypeFLOW/pwatcher/mains/pypeflow_example.py | 133 +
.../mains => pypeFLOW/pypeflow}/__init__.py | 0
pypeFLOW/pypeflow/common.py | 149 +
pypeFLOW/pypeflow/controller.py | 875 +
pypeFLOW/pypeflow/data.py | 315 +
pypeFLOW/pypeflow/pwatcher_bridge.py | 370 +
pypeFLOW/pypeflow/task.py | 892 +
pypeFLOW/readme.slurm.md | 112 +
pypeFLOW/setup.py | 27 +
{falcon_kit/mains => pypeFLOW/src}/__init__.py | 0
pypeFLOW/src/tests/test_pypeflow_common.py | 23 +
pypeFLOW/src/tests/test_pypeflow_controller.py | 497 +
pypeFLOW/src/tests/test_pypeflow_data.py | 202 +
pypeFLOW/src/tests/test_pypeflow_task.py | 326 +
pypeFLOW/travis.sh | 11 +
travis.sh | 22 +-
300 files changed, 72378 insertions(+), 461 deletions(-)
delete mode 100644 .gitignore
create mode 100644 DALIGNER/DB2Falcon.c
create mode 100644 DALIGNER/GNUmakefile
create mode 100644 DALIGNER/HPC.daligner.c
create mode 100644 DALIGNER/LA4Falcon.c
create mode 100644 DALIGNER/LA4Ice.c
create mode 100644 DALIGNER/LAcat.c
create mode 100644 DALIGNER/LAcheck.c
create mode 100644 DALIGNER/LAdump.c
create mode 100644 DALIGNER/LAindex.c
create mode 100644 DALIGNER/LAmerge.c
create mode 100644 DALIGNER/LAshow.c
create mode 100644 DALIGNER/LAsort.c
create mode 100644 DALIGNER/LAsplit.c
create mode 100644 DALIGNER/LICENSE
create mode 100644 DALIGNER/Makefile
create mode 100644 DALIGNER/README
create mode 100644 DALIGNER/README_PB.md
create mode 100644 DALIGNER/align.c
create mode 100644 DALIGNER/align.h
create mode 100644 DALIGNER/daligner.c
create mode 100644 DALIGNER/daligner_p.c
create mode 100644 DALIGNER/filter.c
create mode 100644 DALIGNER/filter.h
create mode 100644 DALIGNER/filter_p.c
create mode 100644 DALIGNER/py_utils/DAPI.py
create mode 100644 DALIGNER/py_utils/DAPipe.py
create mode 100644 DALIGNER/py_utils/DBLA_to_falcon.py
create mode 100644 DALIGNER/py_utils/FALCON_ASM_NOTE
create mode 100644 DALIGNER/py_utils/LAPI.py
create mode 100644 DALIGNER/py_utils/LAPipe.py
create mode 100644 DAMASKER/DB.c
create mode 100644 DAMASKER/DB.h
create mode 100644 DAMASKER/GNUmakefile
create mode 100755 DAMASKER/HPC.REPmask.c
create mode 100644 DAMASKER/HPC.TANmask.c
create mode 100644 DAMASKER/Makefile
create mode 100644 DAMASKER/QV.c
create mode 100644 DAMASKER/QV.h
create mode 100644 DAMASKER/README
create mode 100644 DAMASKER/REPmask.c
create mode 100644 DAMASKER/TANmask.c
create mode 100644 DAMASKER/align.c
create mode 100644 DAMASKER/align.h
create mode 100644 DAMASKER/datander.c
create mode 100644 DAMASKER/tandem.c
create mode 100644 DAMASKER/tandem.h
create mode 100644 DAZZ_DB/Catrack.c
create mode 100644 DAZZ_DB/DAM2fasta.c
create mode 100644 DAZZ_DB/DB.c
create mode 100644 DAZZ_DB/DB.h
create mode 100644 DAZZ_DB/DB2fasta.c
create mode 100644 DAZZ_DB/DB2quiva.c
create mode 100644 DAZZ_DB/DBdump.c
create mode 100644 DAZZ_DB/DBdust.c
create mode 100644 DAZZ_DB/DBrm.c
create mode 100644 DAZZ_DB/DBshow.c
create mode 100644 DAZZ_DB/DBsplit.c
create mode 100644 DAZZ_DB/DBstats.c
create mode 100644 DAZZ_DB/DBupgrade.Dec.31.2014.c
create mode 100644 DAZZ_DB/DBupgrade.Sep.25.2014.c
create mode 100644 DAZZ_DB/DUSTupgrade.Jan.1.2015.c
create mode 100644 DAZZ_DB/GNUmakefile
create mode 100644 DAZZ_DB/LICENSE
create mode 100644 DAZZ_DB/Makefile
create mode 100644 DAZZ_DB/QV.c
create mode 100644 DAZZ_DB/QV.h
create mode 100644 DAZZ_DB/README
create mode 100644 DAZZ_DB/fasta2DAM.c
create mode 100644 DAZZ_DB/fasta2DB.c
create mode 100644 DAZZ_DB/quiva2DB.c
create mode 100644 DAZZ_DB/rangen.c
create mode 100644 DAZZ_DB/simulator.c
create mode 100644 FALCON-examples/LICENSE
create mode 100644 FALCON-examples/README.md
create mode 100644 FALCON-examples/data/git-sym.makefile
create mode 100644 FALCON-examples/data/makefile
create mode 100644 FALCON-examples/git-sym.makefile
create mode 100644 FALCON-examples/logging.ini
create mode 100644 FALCON-examples/makefile
copy examples/fc_run_arab.cfg => FALCON-examples/run/arab/fc_run.cfg (81%)
create mode 100644 FALCON-examples/run/arab/input.fofn
copy examples/fc_run_ecoli.cfg => FALCON-examples/run/ecoli/fc_run.cfg (84%)
create mode 100644 FALCON-examples/run/ecoli/input.fofn
copy examples/fc_run_ecoli_2.cfg => FALCON-examples/run/ecoli2/fc_run.cfg (86%)
create mode 100644 FALCON-examples/run/ecoli2/input.fofn
copy examples/fc_run_ecoli_2.cfg => FALCON-examples/run/lambda-hgap/fc_run.cfg (52%)
create mode 100644 FALCON-examples/run/lambda-hgap/input.fofn
create mode 100644 FALCON-examples/run/lambda-smb14/fc_run.cfg
create mode 100644 FALCON-examples/run/lambda-smb14/input.fofn
create mode 100644 FALCON-examples/run/lambda-smb14/logging.ini
copy examples/fc_run_ecoli_2.cfg => FALCON-examples/run/lambda/fc_run.cfg (51%)
create mode 100644 FALCON-examples/run/lambda/input.fofn
create mode 100755 FALCON-examples/run/synth0/check.py
create mode 100644 FALCON-examples/run/synth0/data/ref.fasta
create mode 100644 FALCON-examples/run/synth0/data/synth0.fasta
create mode 100644 FALCON-examples/run/synth0/fc_run.cfg
create mode 100644 FALCON-examples/run/synth0/input.fofn
create mode 100644 FALCON-examples/run/synth0/logging.ini
create mode 100644 FALCON-examples/run/synth0/logging.json
create mode 100644 FALCON-examples/run/synth0/logging.many.ini
create mode 100644 FALCON-examples/run/synth0/makefile
create mode 100755 FALCON-examples/scripts/check.py
create mode 100755 FALCON-examples/scripts/circ-sim.py
create mode 100644 FALCON-examples/scripts/relabel_fasta.py
create mode 100755 FALCON-examples/scripts/synther.py
copy LICENSE => FALCON-make/LICENSE (100%)
create mode 100644 FALCON-make/README.md
create mode 100644 FALCON-make/config-edit-user.sh
create mode 100644 FALCON-make/config-edit.sh
create mode 100644 FALCON-make/config-standard.sh
create mode 100644 FALCON-make/get-pip.py
create mode 100644 FALCON-make/makefile
copy .travis.yml => FALCON/.travis.yml (100%)
rename LICENSE => FALCON/LICENSE (100%)
rename MANIFEST.in => FALCON/MANIFEST.in (100%)
copy README.md => FALCON/README.md (100%)
rename {doc => FALCON/doc}/README (100%)
rename {doc => FALCON/doc}/falcon_icon.svg (100%)
rename {doc => FALCON/doc}/falcon_icon2.png (100%)
rename {examples => FALCON/examples}/build_env.sh (100%)
rename {examples => FALCON/examples}/build_env2.sh (100%)
rename {examples => FALCON/examples}/ecoli_asm_graph_exploration.ipynb (100%)
rename {examples => FALCON/examples}/fc_run_LG.cfg (100%)
rename {examples => FALCON/examples}/fc_run_arab.cfg (100%)
rename {examples => FALCON/examples}/fc_run_dmel.cfg (100%)
rename {examples => FALCON/examples}/fc_run_ecoli.cfg (100%)
rename {examples => FALCON/examples}/fc_run_ecoli_2.cfg (100%)
copy {examples => FALCON/examples}/logging.json (100%)
rename {examples => FALCON/examples}/run_ecoli_test.sh (100%)
rename {falcon_kit => FALCON/falcon_kit}/FastaReader.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/__init__.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/bash.py (84%)
rename {falcon_kit => FALCON/falcon_kit}/falcon_kit.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/fc_asm_graph.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/functional.py (59%)
copy {falcon_kit => FALCON/falcon_kit}/mains/__init__.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/mains/actg_coordinate.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/mains/calc_cutoff.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/mains/consensus.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/mains/contig_annotate.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/mains/ctg_link_analysis.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/mains/dedup_a_tigs.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/mains/fasta2fasta.py (100%)
create mode 100644 FALCON/falcon_kit/mains/fetch_reads.py
create mode 100644 FALCON/falcon_kit/mains/get_read_ctg_map.py
rename {falcon_kit => FALCON/falcon_kit}/mains/graph_to_contig.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/mains/graph_to_utgs.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/mains/ovlp_filter.py (99%)
rename {falcon_kit => FALCON/falcon_kit}/mains/ovlp_stats.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/mains/ovlp_to_graph.py (100%)
create mode 100644 FALCON/falcon_kit/mains/pr_ctg_track.py
create mode 100644 FALCON/falcon_kit/mains/report_pre_assembly.py
create mode 100644 FALCON/falcon_kit/mains/rr_ctg_track.py
rename {falcon_kit => FALCON/falcon_kit}/mains/run0.py (98%)
rename {falcon_kit => FALCON/falcon_kit}/mains/run1.py (83%)
rename {falcon_kit => FALCON/falcon_kit}/mains/tasks.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/multiproc.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/run_support.py (94%)
rename {falcon_kit => FALCON/falcon_kit}/stats_preassembly.py (75%)
rename {falcon_kit => FALCON/falcon_kit}/util/__init__.py (100%)
rename {falcon_kit => FALCON/falcon_kit}/util/io.py (94%)
rename {falcon_kit => FALCON/falcon_kit}/util/system.py (100%)
rename setup.py => FALCON/setup.py (90%)
rename {src => FALCON/src}/c/DW_banded.c (100%)
rename {src => FALCON/src}/c/Makefile (100%)
rename {src => FALCON/src}/c/Makefile.osx (100%)
rename {src => FALCON/src}/c/common.h (100%)
rename {src => FALCON/src}/c/ext_falcon.c (100%)
rename {src => FALCON/src}/c/falcon.c (100%)
rename {src => FALCON/src}/c/kmer_lookup.c (99%)
rename {src => FALCON/src}/py_scripts/fc_actg_coordinate.py (100%)
rename {src => FALCON/src}/py_scripts/fc_consensus.py (100%)
rename {src => FALCON/src}/py_scripts/fc_contig_annotate.py (100%)
rename {src => FALCON/src}/py_scripts/fc_ctg_link_analysis.py (100%)
rename {src => FALCON/src}/py_scripts/fc_dedup_a_tigs.py (100%)
rename {src => FALCON/src}/py_scripts/fc_graph_to_contig.py (100%)
rename {src => FALCON/src}/py_scripts/fc_graph_to_utgs.py (100%)
rename {src => FALCON/src}/py_scripts/fc_ovlp_filter.py (100%)
rename {src => FALCON/src}/py_scripts/fc_ovlp_stats.py (100%)
rename {src => FALCON/src}/py_scripts/fc_ovlp_to_graph.py (100%)
rename {src => FALCON/src}/py_scripts/fc_run.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/falcon_asm.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/falcon_asm_s.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/falcon_dedup.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/falcon_fixasm.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/falcon_overlap.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/falcon_overlap2.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/falcon_qrm.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/falcon_qrm_0.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/falcon_sense.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/falcon_ucns_data.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/falcon_utgcns.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/get_ovl.sh (100%)
rename {src => FALCON/src}/py_scripts_v0.1/get_rdata.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/overlapper.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/ovlp_filter.sh (100%)
rename {src => FALCON/src}/py_scripts_v0.1/redis_graph.py (100%)
rename {src => FALCON/src}/py_scripts_v0.1/remove_dup_ctg.py (100%)
rename {src => FALCON/src}/utils/fetch_preads.py (100%)
rename {test => FALCON/test}/HPCdaligner_synth0.sh (100%)
create mode 100644 FALCON/test/HPCdaligner_synth0_preads.sh
rename {test => FALCON/test}/helpers.py (100%)
rename {test => FALCON/test}/test_actg_coordinate.py (100%)
rename {test => FALCON/test}/test_consensus.py (100%)
rename {test => FALCON/test}/test_contig_annotate.py (100%)
rename {test => FALCON/test}/test_ctg_link_analysis.py (100%)
rename {test => FALCON/test}/test_functional.py (51%)
rename {test => FALCON/test}/test_graph_to_contig.py (100%)
rename {test => FALCON/test}/test_graph_to_utgs.py (100%)
rename {test => FALCON/test}/test_ovlp_filter.py (100%)
rename {test => FALCON/test}/test_ovlp_stats.py (100%)
rename {test => FALCON/test}/test_ovlp_to_graph.py (100%)
rename {test => FALCON/test}/test_run.py (100%)
rename {test => FALCON/test}/test_run_LG.py (100%)
rename {test => FALCON/test}/test_stats_preassembly.py (70%)
rename {test_data => FALCON/test_data}/t1.fa (100%)
rename {test_data => FALCON/test_data}/t1.fofn (100%)
rename {test_data => FALCON/test_data}/t2.fa (100%)
rename {test_data => FALCON/test_data}/t2.fofn (100%)
copy travis.sh => FALCON/travis.sh (100%)
delete mode 100644 debian/falconkit.1
create mode 100644 debian/fc_run
create mode 100644 debian/fc_run.1
create mode 100755 debian/get-orig-source
create mode 100644 debian/install
create mode 100644 debian/links
create mode 100644 debian/lintian-overrides
delete mode 100644 debian/patches/add-shebang-lines.patch
create mode 100644 debian/patches/build-system.patch
delete mode 100644 debian/patches/pyscripts.patch
create mode 100644 debian/patches/rdflib.patch
rename debian/patches/{networkx-version.patch => versioned-deps.patch} (54%)
create mode 100644 default-env.sh
create mode 100644 env.sh
create mode 100644 makefile
copy .travis.yml => pypeFLOW/.travis.yml (88%)
create mode 100644 pypeFLOW/License.txt
create mode 100644 pypeFLOW/README.rst
create mode 100644 pypeFLOW/doc/Example1.png
create mode 100644 pypeFLOW/doc/Example2.png
create mode 100644 pypeFLOW/doc/Makefile
create mode 100644 pypeFLOW/doc/concurrent_execution.rst
create mode 100644 pypeFLOW/doc/conf.py
create mode 100644 pypeFLOW/doc/examples.rst
create mode 100644 pypeFLOW/doc/index.rst
create mode 100644 pypeFLOW/doc/introduction.rst
create mode 100644 pypeFLOW/doc/modules.rst
create mode 100644 pypeFLOW/doc/pypeflow.rst
create mode 100644 pypeFLOW/doc/rdf_resprentation.rst
create mode 100644 pypeFLOW/example/PypeTest.py
create mode 100644 pypeFLOW/example/README.txt
create mode 100644 pypeFLOW/example/test_shutdown.py
rename .gitmodules => pypeFLOW/example/testdata/.placeholder (100%)
create mode 100644 pypeFLOW/examples-pwatcher/README.md
create mode 100644 pypeFLOW/examples-pwatcher/ab/delete.json
create mode 100644 pypeFLOW/examples-pwatcher/ab/jobs/b
create mode 100644 pypeFLOW/examples-pwatcher/ab/jobs/c
rename examples/logging.json => pypeFLOW/examples-pwatcher/ab/logging-cfg.json (70%)
create mode 100644 pypeFLOW/examples-pwatcher/ab/makefile
create mode 100644 pypeFLOW/examples-pwatcher/ab/query-ab.json
create mode 100644 pypeFLOW/examples-pwatcher/ab/run.json
create mode 100644 pypeFLOW/presentation/escher--unbelievable-527581_1024_768.jpg
create mode 100644 pypeFLOW/presentation/pipelines.png
create mode 100644 pypeFLOW/presentation/pypeFLOW_tutorial.html
create mode 100644 pypeFLOW/presentation/pypeFLOW_tutorial.rst
copy {falcon_kit/mains => pypeFLOW/pwatcher}/__init__.py (100%)
create mode 100755 pypeFLOW/pwatcher/fs_based.py
copy {falcon_kit => pypeFLOW/pwatcher}/mains/__init__.py (100%)
create mode 100644 pypeFLOW/pwatcher/mains/fs_heartbeat.py
create mode 100644 pypeFLOW/pwatcher/mains/pwatcher.py
create mode 100644 pypeFLOW/pwatcher/mains/pypeflow_example.py
copy {falcon_kit/mains => pypeFLOW/pypeflow}/__init__.py (100%)
create mode 100644 pypeFLOW/pypeflow/common.py
create mode 100644 pypeFLOW/pypeflow/controller.py
create mode 100644 pypeFLOW/pypeflow/data.py
create mode 100644 pypeFLOW/pypeflow/pwatcher_bridge.py
create mode 100644 pypeFLOW/pypeflow/task.py
create mode 100644 pypeFLOW/readme.slurm.md
create mode 100644 pypeFLOW/setup.py
rename {falcon_kit/mains => pypeFLOW/src}/__init__.py (100%)
create mode 100644 pypeFLOW/src/tests/test_pypeflow_common.py
create mode 100644 pypeFLOW/src/tests/test_pypeflow_controller.py
create mode 100644 pypeFLOW/src/tests/test_pypeflow_data.py
create mode 100644 pypeFLOW/src/tests/test_pypeflow_task.py
create mode 100755 pypeFLOW/travis.sh
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/falcon.git
More information about the debian-med-commit
mailing list