[med-svn] [Git][med-team/circlator][master] 7 commits: Add myself to Uploaders
Andreas Tille
gitlab at salsa.debian.org
Wed Jul 31 13:47:23 BST 2019
Andreas Tille pushed to branch master at Debian Med / circlator
Commits:
cb126e20 by Andreas Tille at 2019-07-31T12:33:39Z
Add myself to Uploaders
- - - - -
49f7eae0 by Andreas Tille at 2019-07-31T12:34:08Z
New upstream version 1.5.6
- - - - -
e2286d56 by Andreas Tille at 2019-07-31T12:34:37Z
Update upstream source from tag 'upstream/1.5.6'
Update to upstream version '1.5.6'
with Debian dir 72e4e3ef900fa8f00e80e4af6b9b10453f3cc17b
- - - - -
681b02ab by Andreas Tille at 2019-07-31T12:34:37Z
New upstream version
- - - - -
bd4479f6 by Andreas Tille at 2019-07-31T12:34:38Z
debhelper-compat 12
- - - - -
1260ee98 by Andreas Tille at 2019-07-31T12:34:43Z
Standards-Version: 4.4.0
- - - - -
bc4403e1 by Andreas Tille at 2019-07-31T12:40:35Z
Upload to unstable
- - - - -
8 changed files:
- .travis.yml
- + CHANGELOG.md
- + Dockerfile
- README.md
- debian/changelog
- − debian/compat
- debian/control
- install_dependencies.sh
Changes:
=====================================
.travis.yml
=====================================
@@ -5,9 +5,13 @@ addons:
- zlib1g-dev
- libncurses5-dev
python:
- - "3.4"
+ - 3.4
sudo: false
install:
- - "source ./install_dependencies.sh"
+ - source ./install_dependencies.sh
+before_script:
+ - pip install codecov
script:
- - "python setup.py test"
+ - coverage run setup.py test
+after_success:
+ - codecov
=====================================
CHANGELOG.md
=====================================
@@ -0,0 +1,365 @@
+# Change Log
+
+## [Unreleased](https://github.com/sanger-pathogens/circlator/tree/HEAD)
+
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.5.5...HEAD)
+
+**Fixed bugs:**
+
+- Infinite recursion in clean.py ? [\#123](https://github.com/sanger-pathogens/circlator/issues/123)
+
+**Closed issues:**
+
+- how to use circlator on computer without internet access [\#108](https://github.com/sanger-pathogens/circlator/issues/108)
+
+**Merged pull requests:**
+
+- fix readme and add to codecov [\#141](https://github.com/sanger-pathogens/circlator/pull/141) ([ssjunnebo](https://github.com/ssjunnebo))
+- Include Docker [\#137](https://github.com/sanger-pathogens/circlator/pull/137) ([ssjunnebo](https://github.com/ssjunnebo))
+- edit Dockerfile [\#136](https://github.com/sanger-pathogens/circlator/pull/136) ([ssjunnebo](https://github.com/ssjunnebo))
+- add Dockerfile [\#135](https://github.com/sanger-pathogens/circlator/pull/135) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [v1.5.5](https://github.com/sanger-pathogens/circlator/tree/v1.5.5) (2018-01-31)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.5.4...v1.5.5)
+
+**Closed issues:**
+
+- nucmer version detected by "circlator progcheck" but not "circlator all" [\#122](https://github.com/sanger-pathogens/circlator/issues/122)
+- Canu version is not being detected properly [\#113](https://github.com/sanger-pathogens/circlator/issues/113)
+
+**Merged pull requests:**
+
+- failsafe to prevent infinite recursion [\#126](https://github.com/sanger-pathogens/circlator/pull/126) ([pathdevg](https://github.com/pathdevg))
+
+## [v1.5.4](https://github.com/sanger-pathogens/circlator/tree/v1.5.4) (2018-01-31)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.5.3...v1.5.4)
+
+**Closed issues:**
+
+- Problems running progcheck, error with installation? [\#124](https://github.com/sanger-pathogens/circlator/issues/124)
+
+**Merged pull requests:**
+
+- Add tests for external version string checking [\#125](https://github.com/sanger-pathogens/circlator/pull/125) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.5.3](https://github.com/sanger-pathogens/circlator/tree/v1.5.3) (2017-11-09)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.5.1...v1.5.3)
+
+**Closed issues:**
+
+- Clarification regarding nanopore data [\#119](https://github.com/sanger-pathogens/circlator/issues/119)
+- nucmer version isn't detected correctly [\#117](https://github.com/sanger-pathogens/circlator/issues/117)
+- Error when running circlator: can't find canu version [\#111](https://github.com/sanger-pathogens/circlator/issues/111)
+- progcheck: found nucmer but couldn't get version [\#110](https://github.com/sanger-pathogens/circlator/issues/110)
+- Installation problem: command not found after pip3 install circlator [\#109](https://github.com/sanger-pathogens/circlator/issues/109)
+- memory usage [\#106](https://github.com/sanger-pathogens/circlator/issues/106)
+- Recompile with -fPIC error git / pip3 installs [\#103](https://github.com/sanger-pathogens/circlator/issues/103)
+- fixstart with user supplied gene sequences does not work [\#93](https://github.com/sanger-pathogens/circlator/issues/93)
+
+**Merged pull requests:**
+
+- version bump [\#120](https://github.com/sanger-pathogens/circlator/pull/120) ([ssjunnebo](https://github.com/ssjunnebo))
+- fixes \#110, \#117 [\#118](https://github.com/sanger-pathogens/circlator/pull/118) ([spock](https://github.com/spock))
+- circlator version [\#112](https://github.com/sanger-pathogens/circlator/pull/112) ([ssjunnebo](https://github.com/ssjunnebo))
+- update AUTHORS and LICENSE [\#94](https://github.com/sanger-pathogens/circlator/pull/94) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [v1.5.1](https://github.com/sanger-pathogens/circlator/tree/v1.5.1) (2017-04-21)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.5.0...v1.5.1)
+
+**Closed issues:**
+
+- Circlator with short reads? [\#88](https://github.com/sanger-pathogens/circlator/issues/88)
+
+**Merged pull requests:**
+
+- Canu1.5 [\#89](https://github.com/sanger-pathogens/circlator/pull/89) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.5.0](https://github.com/sanger-pathogens/circlator/tree/v1.5.0) (2017-04-03)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.4.1...v1.5.0)
+
+**Closed issues:**
+
+- version of SPAdes ? [\#85](https://github.com/sanger-pathogens/circlator/issues/85)
+- It looks like circlator keeps a common k-mer at the ends of a contig after changing start position. What for? [\#82](https://github.com/sanger-pathogens/circlator/issues/82)
+- Error running circlator with option --assemble\_not\_only\_assembler [\#80](https://github.com/sanger-pathogens/circlator/issues/80)
+
+**Merged pull requests:**
+
+- Add canu [\#87](https://github.com/sanger-pathogens/circlator/pull/87) ([martinghunt](https://github.com/martinghunt))
+- Included option --CanuCorrectedErrorRate to allow user to modify opti… [\#86](https://github.com/sanger-pathogens/circlator/pull/86) ([NicolaDM](https://github.com/NicolaDM))
+- Splitting reads for small contigs when using Canu [\#84](https://github.com/sanger-pathogens/circlator/pull/84) ([NicolaDM](https://github.com/NicolaDM))
+- Adding the option to use Canu instead of SPAdes [\#83](https://github.com/sanger-pathogens/circlator/pull/83) ([NicolaDM](https://github.com/NicolaDM))
+
+## [v1.4.1](https://github.com/sanger-pathogens/circlator/tree/v1.4.1) (2017-01-24)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.4.0...v1.4.1)
+
+**Closed issues:**
+
+- Circularization of BAC contigs [\#79](https://github.com/sanger-pathogens/circlator/issues/79)
+- failure to circularise: cannot use this pair because longer match was found [\#75](https://github.com/sanger-pathogens/circlator/issues/75)
+- samtools command error [\#66](https://github.com/sanger-pathogens/circlator/issues/66)
+
+**Merged pull requests:**
+
+- Fix assemble not only assembler [\#81](https://github.com/sanger-pathogens/circlator/pull/81) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.4.0](https://github.com/sanger-pathogens/circlator/tree/v1.4.0) (2016-10-17)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.3.1...v1.4.0)
+
+**Closed issues:**
+
+- Error running SPAdes. [\#76](https://github.com/sanger-pathogens/circlator/issues/76)
+- Circlator using a gene evicted from Uniprot 1 year ago [\#73](https://github.com/sanger-pathogens/circlator/issues/73)
+
+**Merged pull requests:**
+
+- Fixstart expose mincluster opt [\#77](https://github.com/sanger-pathogens/circlator/pull/77) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.3.1](https://github.com/sanger-pathogens/circlator/tree/v1.3.1) (2016-09-27)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.3.0...v1.3.1)
+
+**Closed issues:**
+
+- SPAdes 3.7.1 recommendation [\#72](https://github.com/sanger-pathogens/circlator/issues/72)
+- Spades could not be detected [\#68](https://github.com/sanger-pathogens/circlator/issues/68)
+- fixstart fails if spaces in sequence names [\#64](https://github.com/sanger-pathogens/circlator/issues/64)
+
+**Merged pull requests:**
+
+- Update dnaa [\#74](https://github.com/sanger-pathogens/circlator/pull/74) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.3.0](https://github.com/sanger-pathogens/circlator/tree/v1.3.0) (2016-08-12)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.2.1...v1.3.0)
+
+**Closed issues:**
+
+- Spades version detection error [\#67](https://github.com/sanger-pathogens/circlator/issues/67)
+- minimus2 using hard-coded /usr/local/bin/show-coords [\#65](https://github.com/sanger-pathogens/circlator/issues/65)
+- Temporary folders not cleaned up when process killed [\#58](https://github.com/sanger-pathogens/circlator/issues/58)
+- Add --verbose to the other subcommands [\#57](https://github.com/sanger-pathogens/circlator/issues/57)
+- Spades version detection bit wonky? [\#56](https://github.com/sanger-pathogens/circlator/issues/56)
+- circlator fails and still creates the final output file 06.fixstart.fasta [\#55](https://github.com/sanger-pathogens/circlator/issues/55)
+- Error running circlator 0.14.0 to reproduce results from published article [\#54](https://github.com/sanger-pathogens/circlator/issues/54)
+
+**Merged pull requests:**
+
+- Add --debug option to progcheck [\#71](https://github.com/sanger-pathogens/circlator/pull/71) ([martinghunt](https://github.com/martinghunt))
+- Spades python2 issues [\#70](https://github.com/sanger-pathogens/circlator/pull/70) ([martinghunt](https://github.com/martinghunt))
+- Refactor fixstart [\#69](https://github.com/sanger-pathogens/circlator/pull/69) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.2.1](https://github.com/sanger-pathogens/circlator/tree/v1.2.1) (2016-04-19)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.2.0...v1.2.1)
+
+**Closed issues:**
+
+- disabling mismatch correction in SPAdes [\#51](https://github.com/sanger-pathogens/circlator/issues/51)
+- ImportError: No module named 'circlator' [\#48](https://github.com/sanger-pathogens/circlator/issues/48)
+
+**Merged pull requests:**
+
+- Bug fix running version task [\#63](https://github.com/sanger-pathogens/circlator/pull/63) ([martinghunt](https://github.com/martinghunt))
+- Version bump 1.2.1 [\#62](https://github.com/sanger-pathogens/circlator/pull/62) ([martinghunt](https://github.com/martinghunt))
+- Summarise circularizations [\#61](https://github.com/sanger-pathogens/circlator/pull/61) ([martinghunt](https://github.com/martinghunt))
+- Version reporting improvements [\#60](https://github.com/sanger-pathogens/circlator/pull/60) ([martinghunt](https://github.com/martinghunt))
+- add verbose option [\#59](https://github.com/sanger-pathogens/circlator/pull/59) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.2.0](https://github.com/sanger-pathogens/circlator/tree/v1.2.0) (2016-03-09)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.1.5...v1.2.0)
+
+**Merged pull requests:**
+
+- Expose spades careful only assemble [\#53](https://github.com/sanger-pathogens/circlator/pull/53) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.1.5](https://github.com/sanger-pathogens/circlator/tree/v1.1.5) (2016-03-09)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.1.4...v1.1.5)
+
+**Merged pull requests:**
+
+- Mapping tests [\#50](https://github.com/sanger-pathogens/circlator/pull/50) ([martinghunt](https://github.com/martinghunt))
+- support for samtools \> 1.2 [\#49](https://github.com/sanger-pathogens/circlator/pull/49) ([gedankenstuecke](https://github.com/gedankenstuecke))
+
+## [v1.1.4](https://github.com/sanger-pathogens/circlator/tree/v1.1.4) (2016-02-19)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.1.3...v1.1.4)
+
+**Closed issues:**
+
+- too many values to unpack error on merge command [\#44](https://github.com/sanger-pathogens/circlator/issues/44)
+
+**Merged pull requests:**
+
+- Nucmer simplify true [\#47](https://github.com/sanger-pathogens/circlator/pull/47) ([martinghunt](https://github.com/martinghunt))
+- Make usage clearer [\#46](https://github.com/sanger-pathogens/circlator/pull/46) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.1.3](https://github.com/sanger-pathogens/circlator/tree/v1.1.3) (2016-01-25)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.1.2...v1.1.3)
+
+**Closed issues:**
+
+- contig.fastg went missing because of SPAdes 3.6.1 output changes [\#39](https://github.com/sanger-pathogens/circlator/issues/39)
+
+**Merged pull requests:**
+
+- Bug running merge \(issue 44\) [\#45](https://github.com/sanger-pathogens/circlator/pull/45) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.1.2](https://github.com/sanger-pathogens/circlator/tree/v1.1.2) (2015-11-30)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.1.1...v1.1.2)
+
+**Merged pull requests:**
+
+- Spades 3.6.2 [\#43](https://github.com/sanger-pathogens/circlator/pull/43) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.1.1](https://github.com/sanger-pathogens/circlator/tree/v1.1.1) (2015-10-30)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.1.0...v1.1.1)
+
+**Merged pull requests:**
+
+- Spades 3.6.1 [\#42](https://github.com/sanger-pathogens/circlator/pull/42) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.1.0](https://github.com/sanger-pathogens/circlator/tree/v1.1.0) (2015-10-20)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.0.2...v1.1.0)
+
+**Closed issues:**
+
+- Numpy for python3 [\#30](https://github.com/sanger-pathogens/circlator/issues/30)
+
+**Merged pull requests:**
+
+- More logging; better spades assembly; update dependencies [\#41](https://github.com/sanger-pathogens/circlator/pull/41) ([martinghunt](https://github.com/martinghunt))
+- Spades try all kmers [\#40](https://github.com/sanger-pathogens/circlator/pull/40) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.0.2](https://github.com/sanger-pathogens/circlator/tree/v1.0.2) (2015-09-03)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.0.1...v1.0.2)
+
+**Closed issues:**
+
+- circlator progcheck report PATH of binary? [\#36](https://github.com/sanger-pathogens/circlator/issues/36)
+
+**Merged pull requests:**
+
+- Dnaa filtering [\#38](https://github.com/sanger-pathogens/circlator/pull/38) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.0.1](https://github.com/sanger-pathogens/circlator/tree/v1.0.1) (2015-09-01)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v1.0.0...v1.0.1)
+
+**Merged pull requests:**
+
+- Progcheck report full paths [\#37](https://github.com/sanger-pathogens/circlator/pull/37) ([martinghunt](https://github.com/martinghunt))
+
+## [v1.0.0](https://github.com/sanger-pathogens/circlator/tree/v1.0.0) (2015-08-24)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v0.16.1...v1.0.0)
+
+**Merged pull requests:**
+
+- Generalise get\_dnaa; write versions etc info file [\#35](https://github.com/sanger-pathogens/circlator/pull/35) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.16.1](https://github.com/sanger-pathogens/circlator/tree/v0.16.1) (2015-08-20)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v0.16.0...v0.16.1)
+
+**Merged pull requests:**
+
+- Require fastaq 3.6.1; version bump [\#34](https://github.com/sanger-pathogens/circlator/pull/34) ([martinghunt](https://github.com/martinghunt))
+- Add travis [\#32](https://github.com/sanger-pathogens/circlator/pull/32) ([martinghunt](https://github.com/martinghunt))
+- Added AUTHORS with mh12 as author [\#29](https://github.com/sanger-pathogens/circlator/pull/29) ([aslett1](https://github.com/aslett1))
+
+## [v0.16.0](https://github.com/sanger-pathogens/circlator/tree/v0.16.0) (2015-08-12)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v0.15.1...v0.16.0)
+
+**Merged pull requests:**
+
+- New task progcheck [\#28](https://github.com/sanger-pathogens/circlator/pull/28) ([martinghunt](https://github.com/martinghunt))
+- New task get\_dnaa; update dnaA fasta file [\#27](https://github.com/sanger-pathogens/circlator/pull/27) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.15.1](https://github.com/sanger-pathogens/circlator/tree/v0.15.1) (2015-07-31)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v0.15.0...v0.15.1)
+
+**Merged pull requests:**
+
+- bug fix fixstart --ignore option [\#26](https://github.com/sanger-pathogens/circlator/pull/26) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.15.0](https://github.com/sanger-pathogens/circlator/tree/v0.15.0) (2015-07-29)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v0.14.2...v0.15.0)
+
+**Merged pull requests:**
+
+- sanity check input; contig filtering [\#25](https://github.com/sanger-pathogens/circlator/pull/25) ([martinghunt](https://github.com/martinghunt))
+- Remove mention of bacteria [\#24](https://github.com/sanger-pathogens/circlator/pull/24) ([martinghunt](https://github.com/martinghunt))
+- help exits without error [\#23](https://github.com/sanger-pathogens/circlator/pull/23) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v0.14.2](https://github.com/sanger-pathogens/circlator/tree/v0.14.2) (2015-07-10)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v0.14.1...v0.14.2)
+
+**Merged pull requests:**
+
+- add homebrew command [\#22](https://github.com/sanger-pathogens/circlator/pull/22) ([andrewjpage](https://github.com/andrewjpage))
+- Fix a few typos [\#21](https://github.com/sanger-pathogens/circlator/pull/21) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.14.1](https://github.com/sanger-pathogens/circlator/tree/v0.14.1) (2015-06-24)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v0.14.0...v0.14.1)
+
+**Merged pull requests:**
+
+- do not ignore log files [\#20](https://github.com/sanger-pathogens/circlator/pull/20) ([martinghunt](https://github.com/martinghunt))
+- Clean refactor [\#19](https://github.com/sanger-pathogens/circlator/pull/19) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.14.0](https://github.com/sanger-pathogens/circlator/tree/v0.14.0) (2015-06-04)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v0.13.2...v0.14.0)
+
+**Closed issues:**
+
+- Install failed - bio-assembly-refinement/setup.py", line 6, [\#13](https://github.com/sanger-pathogens/circlator/issues/13)
+
+**Merged pull requests:**
+
+- Expose spades kmer [\#18](https://github.com/sanger-pathogens/circlator/pull/18) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.13.2](https://github.com/sanger-pathogens/circlator/tree/v0.13.2) (2015-06-02)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v0.13.1...v0.13.2)
+
+**Merged pull requests:**
+
+- Use second best hits [\#17](https://github.com/sanger-pathogens/circlator/pull/17) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.13.1](https://github.com/sanger-pathogens/circlator/tree/v0.13.1) (2015-05-29)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v0.13.0...v0.13.1)
+
+**Merged pull requests:**
+
+- Minimus2 error typos [\#16](https://github.com/sanger-pathogens/circlator/pull/16) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.13.0](https://github.com/sanger-pathogens/circlator/tree/v0.13.0) (2015-05-28)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v0.12.1...v0.13.0)
+
+**Merged pull requests:**
+
+- Use nucmer diagdiff [\#15](https://github.com/sanger-pathogens/circlator/pull/15) ([martinghunt](https://github.com/martinghunt))
+- Add wrapper for minimus2 pipeline [\#14](https://github.com/sanger-pathogens/circlator/pull/14) ([martinghunt](https://github.com/martinghunt))
+- Update readme [\#12](https://github.com/sanger-pathogens/circlator/pull/12) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.12.1](https://github.com/sanger-pathogens/circlator/tree/v0.12.1) (2015-05-21)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v0.12.0...v0.12.1)
+
+**Merged pull requests:**
+
+- Fix usage typos [\#11](https://github.com/sanger-pathogens/circlator/pull/11) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.12.0](https://github.com/sanger-pathogens/circlator/tree/v0.12.0) (2015-05-20)
+[Full Changelog](https://github.com/sanger-pathogens/circlator/compare/v0.2.0...v0.12.0)
+
+**Merged pull requests:**
+
+- Write final FASTG file [\#10](https://github.com/sanger-pathogens/circlator/pull/10) ([martinghunt](https://github.com/martinghunt))
+- Tidy output and usage [\#9](https://github.com/sanger-pathogens/circlator/pull/9) ([martinghunt](https://github.com/martinghunt))
+- add circularised to column to merge log [\#8](https://github.com/sanger-pathogens/circlator/pull/8) ([martinghunt](https://github.com/martinghunt))
+- trim reads kept from contig ends [\#7](https://github.com/sanger-pathogens/circlator/pull/7) ([martinghunt](https://github.com/martinghunt))
+- Use spades graph [\#6](https://github.com/sanger-pathogens/circlator/pull/6) ([martinghunt](https://github.com/martinghunt))
+- Do not break reads [\#5](https://github.com/sanger-pathogens/circlator/pull/5) ([martinghunt](https://github.com/martinghunt))
+
+## [v0.2.0](https://github.com/sanger-pathogens/circlator/tree/v0.2.0) (2015-04-16)
+**Merged pull requests:**
+
+- make default merge less permissive [\#4](https://github.com/sanger-pathogens/circlator/pull/4) ([martinghunt](https://github.com/martinghunt))
+- Add option to not fix start of some contigs [\#3](https://github.com/sanger-pathogens/circlator/pull/3) ([martinghunt](https://github.com/martinghunt))
+- Include default genes fa [\#2](https://github.com/sanger-pathogens/circlator/pull/2) ([martinghunt](https://github.com/martinghunt))
+- Initial version [\#1](https://github.com/sanger-pathogens/circlator/pull/1) ([martinghunt](https://github.com/martinghunt))
+
+
=====================================
Dockerfile
=====================================
@@ -0,0 +1,28 @@
+# This container will install Circlator from master
+#
+FROM debian:testing
+
+ENV BUILD_DIR=/opt/circlator
+
+# Install the dependancies
+RUN apt-get update -qq && apt-get install -y python python3-pip git wget unzip zlib1g-dev libncurses5-dev
+
+RUN apt-get install --yes libbz2-dev liblzma-dev
+
+RUN mkdir -p ${BUILD_DIR}
+COPY . ${BUILD_DIR}
+
+RUN cd ${BUILD_DIR} && ./install_dependencies.sh
+ENV PATH ${BUILD_DIR}/build/bwa-0.7.12:${BUILD_DIR}/build/canu-1.4/Linux-amd64/bin/:${BUILD_DIR}/build/prodigal-2.6.2:${BUILD_DIR}/build/samtools-1.3:${BUILD_DIR}/build/MUMmer3.23:${BUILD_DIR}/build/SPAdes-3.7.1-Linux/bin:$PATH
+RUN export PATH
+RUN cd ${BUILD_DIR} && python3 setup.py install
+
+RUN circlator progcheck
+
+CMD echo "Usage: docker run -v \`pwd\`:/var/data -it <IMAGE_NAME> bash" && \
+ echo "" && \
+ echo "This will place you in a shell with your current working directory accessible as /var/data." && \
+ echo "You can then run commands like:" && \
+ echo " circlator all /var/data/assembly.fasta /var/data/reads /var/data/<output_subdirectory>" && \
+ echo "For help, please go to https://github.com/sanger-pathogens/circlator/wiki, or type" && \
+ echo " circlator --help"
=====================================
README.md
=====================================
@@ -1,10 +1,87 @@
-Circlator
-=========
-
+# Circlator
A tool to circularize genome assemblies.
+PLEASE NOTE: we currently do not have the resources to provide support for Circlator, so please do not expect a reply if you flag any issue. Apologies for the inconvenience.
+
+[](http://unmaintained.tech/)
+[](https://travis-ci.org/sanger-pathogens/circlator)
+[](https://github.com/sanger-pathogens/circlator/blob/master/LICENSE)
+[](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0849-0)
+[](http://bioconda.github.io/recipes/circlator/README.html)
+[](https://quay.io/repository/biocontainers/circlator)
+[](https://hub.docker.com/r/sangerpathogens/circlator)
+[](https://hub.docker.com/r/sangerpathogens/circlator)
+[](https://codecov.io/gh/sanger-pathogens/circlator)
+
+## Contents
+ * [Introduction](#introduction)
+ * [Installation](#installation)
+ * [Usage](#usage)
+ * [License](#license)
+ * [Feedback/Issues](#feedbackissues)
+ * [Citation](#citation)
+ * [Further Information](#further-information)
+
+## Introduction
+Circlator will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly.
+
+## Installation
For how to install Circlator, please see the [Circlator website](http://sanger-pathogens.github.io/circlator/).
-For how to use Circlator, please see the [Circlator wiki page](https://github.com/sanger-pathogens/circlator/wiki).
+## Usage
+```
+Usage: circlator <command> [options] <required arguments>
+
+To get minimal usage for a command use:
+circlator command
+
+To get full help for a command use one of:
+circlator command -h
+circlator command --help
+
+
+Available commands:
+
+all Run mapreads, bam2reads, assemble, merge, clean, fixstart
+mapreads Map reads to assembly
+bam2reads Make reads from mapping to be reassembled
+assemble Run assembly using reads from bam2reads
+merge Merge original assembly and new assembly made by assemble
+clean Remove small and completely contained contigs from assembly
+fixstart Change start position of circular sequences
+minimus2 Run the minimus2 based circularisation pipeline
+get_dnaa Download file of dnaA (or other of user's choice) genes
+progcheck Checks dependencies are installed
+test Run Circlator on a small test set
+version Print version and exit
+```
+For more information on how to use Circlator, please see the [Circlator wiki page](https://github.com/sanger-pathogens/circlator/wiki).
+
+## License
+Circlator is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/circlator/blob/master/LICENSE).
+
+## Feedback/Issues
+Please report any issues to the [issues page](https://github.com/sanger-pathogens/circlator/issues) or email circlator-help at sanger.ac.uk.
+
+PLEASE NOTE: we currently do not have the resources to provide support for Circlator, so please do not expect a reply if you flag any issue. Apologies for the inconvenience.
+
+## Citation
+If you use this software please cite:
+
+__Circlator: automated circularization of genome assemblies using long sequencing reads__
+Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: [10.1186/s13059-015-0849-0](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0849-0)
+
+__[BWA](http://arxiv.org/abs/1303.3997):__ Li, H et al. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997.
+
+__[MUMmer](http://genomebiology.com/content/5/2/R12):__ Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).
+
+__[Prodigal](http://www.biomedcentral.com/1471-2105/11/119):__ Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).
+
+__[SAMtools](http://bioinformatics.oxfordjournals.org/content/25/16/2078.abstract):__ Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–9 (2009).
+
+__[SPAdes](http://online.liebertpub.com/doi/abs/10.1089/cmb.2012.0021)__: Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–77 (2012)
-Build status: [](https://travis-ci.org/sanger-pathogens/circlator)
+## Further Information
+For more information on this software see:
+* the [Circlator website](http://sanger-pathogens.github.io/circlator/)
+* the [Circlator wiki page](https://github.com/sanger-pathogens/circlator/wiki)
\ No newline at end of file
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+circlator (1.5.6-1) unstable; urgency=medium
+
+ * Afif removed himself from Uploaders (thanks for your work on this)
+ * Add myself to Uploaders
+ * New upstream version
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+
+ -- Andreas Tille <tille at debian.org> Wed, 31 Jul 2019 14:34:43 +0200
+
circlator (1.5.5-3) unstable; urgency=medium
* Team upload.
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12
=====================================
debian/control
=====================================
@@ -1,8 +1,9 @@
Source: circlator
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
dh-python,
python3-all,
python3-setuptools,
@@ -17,7 +18,7 @@ Build-Depends: debhelper (>= 12~),
bwa (>= 0.7.12),
prodigal,
canu (<< 1.8+dfsg-1) | canu (>= 1.8+dfsg-2)
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/circlator
Vcs-Git: https://salsa.debian.org/med-team/circlator.git
Homepage: http://sanger-pathogens.github.io/circlator/
=====================================
install_dependencies.sh
=====================================
View it on GitLab: https://salsa.debian.org/med-team/circlator/compare/bed53bd47ea848c194a4e7148890c2c9d4e41215...bc4403e15bd73c8caaa2bdc6230f6bf4c7eca778
--
View it on GitLab: https://salsa.debian.org/med-team/circlator/compare/bed53bd47ea848c194a4e7148890c2c9d4e41215...bc4403e15bd73c8caaa2bdc6230f6bf4c7eca778
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