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tille pushed a commit to tag debian/3.9.1-1
in repository snakemake.
commit 4b3f40158a954678daeb273b173f84e698efa9ad
Merge: 48f7e7d 8111782
Author: Andreas Tille <ti...@debian.org>
Date: Mon Jan 9 14:12:51 2017 +0100
Merge tag 'upstream/3.9.1'
Upstream version 3.9.1
.dockerignore | 8 +
.gitignore | 1 +
AUTHORS.rst | 0
CHANGELOG.md | 10 +
Dockerfile | 7 +
LICENSE.md | 18 +-
bin/snakemake | 20 -
bitbucket-pipelines.yml | 8 -
docs/{api.rst => api_reference/snakemake.rst} | 2 +
.../snakemake_utils.rst} | 2 +
docs/conf.py | 9 +-
docs/executable.rst | 176 +
docs/getting_started/examples.rst | 301 +
docs/getting_started/img/c-dag.png | Bin 0 -> 8155 bytes
docs/getting_started/img/cufflinks-dag.png | Bin 0 -> 26777 bytes
docs/getting_started/img/latex-dag.png | Bin 0 -> 9527 bytes
docs/getting_started/installation.rst | 70 +
docs/index.rst | 211 +-
docs/project_info/authors.rst | 58 +
docs/project_info/citations.rst | 51 +
docs/project_info/contributing.rst | 205 +
docs/project_info/faq.rst | 413 +
docs/project_info/history.rst | 8 +
docs/project_info/img/idea.png | Bin 0 -> 43456 bytes
docs/project_info/license.rst | 10 +
docs/project_info/more_resources.rst | 34 +
docs/requirements.txt | 4 +-
docs/snakefiles/configuration.rst | 111 +
docs/snakefiles/deployment.rst | 81 +
docs/snakefiles/modularization.rst | 99 +
docs/snakefiles/remote_files.rst | 409 +
docs/snakefiles/rules.rst | 695 +
docs/snakefiles/utils.rst | 81 +
docs/snakefiles/writing_snakefiles.rst | 55 +
docs/tutorial/additional_features.rst | 249 +
docs/tutorial/advanced.rst | 365 +
docs/tutorial/basics.rst | 476 +
docs/tutorial/welcome.rst | 178 +
docs/tutorial/workflow/.gitignore | 1 +
docs/tutorial/workflow/Snakefile | 70 +
docs/tutorial/workflow/dag_call.png | Bin 0 -> 23038 bytes
docs/tutorial/workflow/dag_index.png | Bin 0 -> 13781 bytes
docs/tutorial/workflow/data/genome.fa | 3838 +
docs/tutorial/workflow/data/genome.fa.amb | 228 +
docs/tutorial/workflow/data/genome.fa.ann | 3 +
docs/tutorial/workflow/data/genome.fa.bwt | Bin 0 -> 230320 bytes
docs/tutorial/workflow/data/genome.fa.pac | Bin 0 -> 57556 bytes
docs/tutorial/workflow/data/genome.fa.sa | Bin 0 -> 115160 bytes
docs/tutorial/workflow/data/samples/A.fastq | 100000 ++++++++++++++++++
docs/tutorial/workflow/data/samples/B.fastq | 100000 ++++++++++++++++++
docs/tutorial/workflow/data/samples/C.fastq | 100000 ++++++++++++++++++
docs/tutorial/workflow/package.sh | 1 +
docs/tutorial/workflow/requirements.txt | 9 +
environment.yml | 7 +-
biglogo.pdf => images/biglogo.pdf | Bin
biglogo.png => images/biglogo.png | Bin
biglogo.svg => images/biglogo.svg | 0
logo.png => images/logo.png | Bin
logo.svg => images/logo.svg | 0
setup.py | 1 -
snakemake/__init__.py | 35 +-
snakemake/__main__.py | 3 +
snakemake/conda.py | 19 +-
snakemake/dag.py | 127 +-
snakemake/executors.py | 73 +-
snakemake/jobs.py | 15 +-
snakemake/output_index.py | 8 +
snakemake/parser.py | 6 +-
snakemake/remote/FTP.py | 10 +-
snakemake/remote/S3.py | 15 +-
snakemake/rules.py | 31 +-
snakemake/scheduler.py | 31 +-
snakemake/script.py | 21 +-
snakemake/utils.py | 7 +-
snakemake/version.py | 2 +-
snakemake/workflow.py | 28 +-
snakemake/wrapper.py | 4 +-
tests/test (with parentheses)/Snakefile | 10 +
.../expected-results/test.out | 2 +
tests/test (with parentheses)/test.in | 2 +
tests/test_conda/Snakefile | 13 +-
tests/test_dup_out_patterns/Snakefile | 12 +
.../expected-results/.gitkeep | 0
tests/test_format_wildcards/Snakefile | 9 +
.../test_format_wildcards/expected-results/foo.txt | 1 +
tests/test_restartable_job_cmd_exit_1/Snakefile | 19 +
.../expected-results/.done | 0
tests/test_restartable_job_cmd_exit_1/qsub | 7 +
tests/test_restartable_job_cmd_exit_1/qsub.py | 14 +
tests/test_restartable_job_qsub_exit_1/Snakefile | 14 +
.../expected-results/.done | 0
tests/test_restartable_job_qsub_exit_1/qsub | 11 +
tests/test_restartable_job_qsub_exit_1/qsub.log | 1 +
tests/test_restartable_job_qsub_exit_1/qsub.py | 14 +
tests/test_threads/Snakefile | 7 +
tests/test_threads/expected-results/test.out | 1 +
tests/testapi.py | 16 +
tests/tests.py | 66 +-
wercker.yml | 14 +
99 files changed, 309045 insertions(+), 206 deletions(-)
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