Unverified Commit 60c2f919 authored by Mihai's avatar Mihai Committed by GitHub
Browse files

Pre repository renaming (#526)

* Update GitHub links

* Clean the about page

* Update dependencies
parent 079c7c62
...@@ -15,7 +15,7 @@ Version 2.0.34 ...@@ -15,7 +15,7 @@ Version 2.0.34
Released on March 15th 2021. Released on March 15th 2021.
- Update article link and point towards the new release website (`#518 - Update article link and point towards the new release website (`#518
<https://github.com/mutalyzer/mutalyzer/pull/518>`_). <https://github.com/mutalyzer/mutalyzer2/pull/518>`_).
Version 2.0.33 Version 2.0.33
...@@ -24,11 +24,11 @@ Version 2.0.33 ...@@ -24,11 +24,11 @@ Version 2.0.33
Released on November 24th 2020. Released on November 24th 2020.
- Update links (`#514 - Update links (`#514
<https://github.com/mutalyzer/mutalyzer/pull/514>`_). <https://github.com/mutalyzer/mutalyzer2/pull/514>`_).
- Improve warning messages (`#513 - Improve warning messages (`#513
<https://github.com/mutalyzer/mutalyzer/pull/513>`_). <https://github.com/mutalyzer/mutalyzer2/pull/513>`_).
- Add legacy crossmapper module (`#508 - Add legacy crossmapper module (`#508
<https://github.com/mutalyzer/mutalyzer/pull/508>`_). <https://github.com/mutalyzer/mutalyzer2/pull/508>`_).
Version 2.0.32 Version 2.0.32
...@@ -37,13 +37,13 @@ Version 2.0.32 ...@@ -37,13 +37,13 @@ Version 2.0.32
Released on December 9th 2019. Released on December 9th 2019.
- Update email address and wiki link (`#498 - Update email address and wiki link (`#498
<https://github.com/mutalyzer/mutalyzer/pull/498>`_). <https://github.com/mutalyzer/mutalyzer2/pull/498>`_).
- Fix erroneous message for mtDNA m. coordinate system (`#497 - Fix erroneous message for mtDNA m. coordinate system (`#497
<https://github.com/mutalyzer/mutalyzer/pull/497>`_). <https://github.com/mutalyzer/mutalyzer2/pull/497>`_).
- Update requirements (`#496 - Update requirements (`#496
<https://github.com/mutalyzer/mutalyzer/pull/496>`_). <https://github.com/mutalyzer/mutalyzer2/pull/496>`_).
- Fix invalid LRG record issue (`#495 - Fix invalid LRG record issue (`#495
<https://github.com/mutalyzer/mutalyzer/pull/495>`_). <https://github.com/mutalyzer/mutalyzer2/pull/495>`_).
Version 2.0.31 Version 2.0.31
...@@ -52,15 +52,15 @@ Version 2.0.31 ...@@ -52,15 +52,15 @@ Version 2.0.31
Released on August 21st 2019. Released on August 21st 2019.
- Update requirements (`#486 - Update requirements (`#486
<https://github.com/mutalyzer/mutalyzer/pull/486>`_). <https://github.com/mutalyzer/mutalyzer2/pull/486>`_).
- Add support for NCBI E-utilities API key (`#485 - Add support for NCBI E-utilities API key (`#485
<https://github.com/mutalyzer/mutalyzer/pull/485>`_). <https://github.com/mutalyzer/mutalyzer2/pull/485>`_).
- Update HGVS descriptions retrieval for SNP converter (`#482 - Update HGVS descriptions retrieval for SNP converter (`#482
<https://github.com/mutalyzer/mutalyzer/issues/482>`_) <https://github.com/mutalyzer/mutalyzer2/issues/482>`_)
- Make file selection mandatory in the batch job web page (`#481 - Make file selection mandatory in the batch job web page (`#481
<https://github.com/mutalyzer/mutalyzer/issues/481>`_). <https://github.com/mutalyzer/mutalyzer2/issues/481>`_).
- Update Travis configuration (`#483 - Update Travis configuration (`#483
<https://github.com/mutalyzer/mutalyzer/pull/483>`_) <https://github.com/mutalyzer/mutalyzer2/pull/483>`_)
Version 2.0.30 Version 2.0.30
...@@ -69,11 +69,11 @@ Version 2.0.30 ...@@ -69,11 +69,11 @@ Version 2.0.30
Released on May 24th 2019. Released on May 24th 2019.
- Update requirements (`#475 - Update requirements (`#475
<https://github.com/mutalyzer/mutalyzer/pull/475>`_). <https://github.com/mutalyzer/mutalyzer2/pull/475>`_).
- Update documentation links (`#474 - Update documentation links (`#474
<https://github.com/mutalyzer/mutalyzer/pull/474>`_). <https://github.com/mutalyzer/mutalyzer2/pull/474>`_).
- Fix the genbank parser to perform loci objects creation in two steps (`#468 - Fix the genbank parser to perform loci objects creation in two steps (`#468
<https://github.com/mutalyzer/mutalyzer/issues/468>`_). <https://github.com/mutalyzer/mutalyzer2/issues/468>`_).
Version 2.0.29 Version 2.0.29
...@@ -82,15 +82,15 @@ Version 2.0.29 ...@@ -82,15 +82,15 @@ Version 2.0.29
Released on December 4th 2018. Released on December 4th 2018.
- Improve user feedback for incorrect specific locus (`#459 - Improve user feedback for incorrect specific locus (`#459
<https://github.com/mutalyzer/mutalyzer/pull/459>`_). <https://github.com/mutalyzer/mutalyzer2/pull/459>`_).
- Improve some position converter warning (`#458 - Improve some position converter warning (`#458
<https://github.com/mutalyzer/mutalyzer/pull/458>`_). <https://github.com/mutalyzer/mutalyzer2/pull/458>`_).
- Update requirements (`#457 - Update requirements (`#457
<https://github.com/mutalyzer/mutalyzer/pull/457>`_). <https://github.com/mutalyzer/mutalyzer2/pull/457>`_).
- Make API more consistent between UDs and NCs (`#456 - Make API more consistent between UDs and NCs (`#456
<https://github.com/mutalyzer/mutalyzer/pull/456>`_). <https://github.com/mutalyzer/mutalyzer2/pull/456>`_).
- Fix internal server error on IVS variant (`#452 - Fix internal server error on IVS variant (`#452
<https://github.com/mutalyzer/mutalyzer/pull/452>`_). <https://github.com/mutalyzer/mutalyzer2/pull/452>`_).
Version 2.0.28 Version 2.0.28
...@@ -99,7 +99,7 @@ Version 2.0.28 ...@@ -99,7 +99,7 @@ Version 2.0.28
Released on June 11th 2018. Released on June 11th 2018.
- Support for LRG XML schema version 1.9 (`#449 - Support for LRG XML schema version 1.9 (`#449
<https://github.com/mutalyzer/mutalyzer/pull/449>`_). <https://github.com/mutalyzer/mutalyzer2/pull/449>`_).
Version 2.0.27 Version 2.0.27
...@@ -108,19 +108,19 @@ Version 2.0.27 ...@@ -108,19 +108,19 @@ Version 2.0.27
Released on May 25th 2018. Released on May 25th 2018.
- Accept variant descriptions with NC files as references (`#445 - Accept variant descriptions with NC files as references (`#445
<https://github.com/mutalyzer/mutalyzer/pull/445>`_). <https://github.com/mutalyzer/mutalyzer2/pull/445>`_).
- Removed support for pending LRG reference files (`#444 - Removed support for pending LRG reference files (`#444
<https://github.com/mutalyzer/mutalyzer/pull/444>`_). <https://github.com/mutalyzer/mutalyzer2/pull/444>`_).
- Add link to wiki page with differences between Mutalyzer and HGVS (`#443 - Add link to wiki page with differences between Mutalyzer and HGVS (`#443
<https://github.com/mutalyzer/mutalyzer/pull/443>`_). <https://github.com/mutalyzer/mutalyzer2/pull/443>`_).
- Fix for batch processor crash due to NCBI server timeout (`#442 - Fix for batch processor crash due to NCBI server timeout (`#442
<https://github.com/mutalyzer/mutalyzer/pull/442>`_). <https://github.com/mutalyzer/mutalyzer2/pull/442>`_).
- Update genbank retriever parameters according to NCBI recommendations (`#439 - Update genbank retriever parameters according to NCBI recommendations (`#439
<https://github.com/mutalyzer/mutalyzer/pull/439>`_). <https://github.com/mutalyzer/mutalyzer2/pull/439>`_).
- Update getGeneLocation` to use standard strategy to select mapping (`#437 - Update getGeneLocation` to use standard strategy to select mapping (`#437
<https://github.com/mutalyzer/mutalyzer/pull/437>`_). <https://github.com/mutalyzer/mutalyzer2/pull/437>`_).
- Add link to website changelog (`#434 - Add link to website changelog (`#434
<https://github.com/mutalyzer/mutalyzer/pull/434>`_). <https://github.com/mutalyzer/mutalyzer2/pull/434>`_).
Version 2.0.26 Version 2.0.26
...@@ -129,9 +129,9 @@ Version 2.0.26 ...@@ -129,9 +129,9 @@ Version 2.0.26
Released on July 19th 2017. Released on July 19th 2017.
- Description-extractor dependency updated to version 2.35 (`#429 - Description-extractor dependency updated to version 2.35 (`#429
<https://github.com/mutalyzer/mutalyzer/pull/429>`_). <https://github.com/mutalyzer/mutalyzer2/pull/429>`_).
- Fix for negative cCDSStop due to wrong transcript to protein link (`#430 - Fix for negative cCDSStop due to wrong transcript to protein link (`#430
<https://github.com/mutalyzer/mutalyzer/issues/430>`_). <https://github.com/mutalyzer/mutalyzer2/issues/430>`_).
Version 2.0.25 Version 2.0.25
...@@ -141,7 +141,7 @@ Released on May 17th 2017. ...@@ -141,7 +141,7 @@ Released on May 17th 2017.
- Fix for batch processor crash when trying to alter an "item" column of the - Fix for batch processor crash when trying to alter an "item" column of the
"batch_queue_items" database table (`#426 "batch_queue_items" database table (`#426
<https://github.com/mutalyzer/mutalyzer/pull/426>`_). <https://github.com/mutalyzer/mutalyzer2/pull/426>`_).
Version 2.0.24 Version 2.0.24
--------------- ---------------
...@@ -150,7 +150,7 @@ Released on April 12th 2017. ...@@ -150,7 +150,7 @@ Released on April 12th 2017.
- Fix for SNP converter crash when called with 'rs0' as parameter. - Fix for SNP converter crash when called with 'rs0' as parameter.
SNP converter displays now more warning messages (`#419 SNP converter displays now more warning messages (`#419
<https://github.com/mutalyzer/mutalyzer/issues/419>`_). <https://github.com/mutalyzer/mutalyzer2/issues/419>`_).
Version 2.0.23 Version 2.0.23
...@@ -160,7 +160,7 @@ Released on November 9th 2016. ...@@ -160,7 +160,7 @@ Released on November 9th 2016.
- Fix for internal server error in the position converter triggered by - Fix for internal server error in the position converter triggered by
non-variant description (`#333 non-variant description (`#333
<https://github.com/mutalyzer/mutalyzer/issues/333>`_). <https://github.com/mutalyzer/mutalyzer2/issues/333>`_).
Version 2.0.22 Version 2.0.22
...@@ -169,7 +169,7 @@ Version 2.0.22 ...@@ -169,7 +169,7 @@ Version 2.0.22
Released on September 20th 2016. Released on September 20th 2016.
- Biopython dependency updated to version 1.68 (`#411 - Biopython dependency updated to version 1.68 (`#411
<https://github.com/mutalyzer/mutalyzer/pull/411>`_). <https://github.com/mutalyzer/mutalyzer2/pull/411>`_).
Version 2.0.21 Version 2.0.21
...@@ -178,7 +178,7 @@ Version 2.0.21 ...@@ -178,7 +178,7 @@ Version 2.0.21
Released on June 24th 2016. Released on June 24th 2016.
- Fix typo in batch SNP converter, causing all batch jobs to stall (`#409 - Fix typo in batch SNP converter, causing all batch jobs to stall (`#409
<https://github.com/mutalyzer/mutalyzer/pull/409>`_). <https://github.com/mutalyzer/mutalyzer2/pull/409>`_).
Version 2.0.20 Version 2.0.20
...@@ -187,11 +187,11 @@ Version 2.0.20 ...@@ -187,11 +187,11 @@ Version 2.0.20
Released on June 22th 2016. Released on June 22th 2016.
- Accept accession number as transcript selector (`#405 - Accept accession number as transcript selector (`#405
<https://github.com/mutalyzer/mutalyzer/pull/405>`_). <https://github.com/mutalyzer/mutalyzer2/pull/405>`_).
- Add legend to the output of runMutalyzer service (`#404 - Add legend to the output of runMutalyzer service (`#404
<https://github.com/mutalyzer/mutalyzer/pull/404>`_). <https://github.com/mutalyzer/mutalyzer2/pull/404>`_).
- Remove support for GI numbers (`#396 - Remove support for GI numbers (`#396
<https://github.com/mutalyzer/mutalyzer/pull/396>`_). <https://github.com/mutalyzer/mutalyzer2/pull/396>`_).
Version 2.0.19 Version 2.0.19
...@@ -200,9 +200,9 @@ Version 2.0.19 ...@@ -200,9 +200,9 @@ Version 2.0.19
Released on June 9th 2016. Released on June 9th 2016.
- Fix reference file loading by URL (`#383 - Fix reference file loading by URL (`#383
<https://github.com/mutalyzer/mutalyzer/pull/383>`_). <https://github.com/mutalyzer/mutalyzer2/pull/383>`_).
- Consider accession version in `getGeneName` webservice method (`#390 - Consider accession version in `getGeneName` webservice method (`#390
<https://github.com/mutalyzer/mutalyzer/pull/390>`_). <https://github.com/mutalyzer/mutalyzer2/pull/390>`_).
Version 2.0.18 Version 2.0.18
...@@ -211,13 +211,13 @@ Version 2.0.18 ...@@ -211,13 +211,13 @@ Version 2.0.18
Released on May 23rd 2016. Released on May 23rd 2016.
- Fixed installation on CentOS 6 (`#358 - Fixed installation on CentOS 6 (`#358
<https://github.com/mutalyzer/mutalyzer/pull/358>`_). <https://github.com/mutalyzer/mutalyzer2/pull/358>`_).
- Auto focus primary form input on page load (`#363 - Auto focus primary form input on page load (`#363
<https://github.com/mutalyzer/mutalyzer/pull/363>`_). <https://github.com/mutalyzer/mutalyzer2/pull/363>`_).
- Check optional argument for ``dup`` (`#369 - Check optional argument for ``dup`` (`#369
<https://github.com/mutalyzer/mutalyzer/pull/369>`_). <https://github.com/mutalyzer/mutalyzer2/pull/369>`_).
- Fixes for chromosome slicing by gene symbol (`#371 - Fixes for chromosome slicing by gene symbol (`#371
<https://github.com/mutalyzer/mutalyzer/pull/371>`_). <https://github.com/mutalyzer/mutalyzer2/pull/371>`_).
Version 2.0.17 Version 2.0.17
...@@ -226,12 +226,12 @@ Version 2.0.17 ...@@ -226,12 +226,12 @@ Version 2.0.17
Released on March 24th 2016. Released on March 24th 2016.
- Position converter now checks for selection of gene/transcript (`#346 - Position converter now checks for selection of gene/transcript (`#346
<https://github.com/mutalyzer/mutalyzer/pull/346>`_). <https://github.com/mutalyzer/mutalyzer2/pull/346>`_).
- Update about page and link to `new mailing list - Update about page and link to `new mailing list
<https://groups.google.com/forum/#!forum/mutalyzer>`_ (`#353 <https://groups.google.com/forum/#!forum/mutalyzer>`_ (`#353
<https://github.com/mutalyzer/mutalyzer/pull/353>`_). <https://github.com/mutalyzer/mutalyzer2/pull/353>`_).
- Batch jobs processor is more robust on errors (`#356 - Batch jobs processor is more robust on errors (`#356
<https://github.com/mutalyzer/mutalyzer/pull/356>`_). <https://github.com/mutalyzer/mutalyzer2/pull/356>`_).
Version 2.0.16 Version 2.0.16
...@@ -240,12 +240,12 @@ Version 2.0.16 ...@@ -240,12 +240,12 @@ Version 2.0.16
Released on February 25th 2016. Released on February 25th 2016.
- Fixed transcript naming in mapping webservices (`#147 - Fixed transcript naming in mapping webservices (`#147
<https://github.com/mutalyzer/mutalyzer/pull/147>`_). See below for <https://github.com/mutalyzer/mutalyzer2/pull/147>`_). See below for
:ref:`details <changelog_2016_details>`. :ref:`details <changelog_2016_details>`.
- Support LRG transcripts in the position converter (`#147 - Support LRG transcripts in the position converter (`#147
<https://github.com/mutalyzer/mutalyzer/pull/147>`_). <https://github.com/mutalyzer/mutalyzer2/pull/147>`_).
- Don't report ``ext*?`` when variant RNA has stop codon (`#146 - Don't report ``ext*?`` when variant RNA has stop codon (`#146
<https://github.com/mutalyzer/mutalyzer/pull/146>`_). <https://github.com/mutalyzer/mutalyzer2/pull/146>`_).
.. _changelog_2016_details: .. _changelog_2016_details:
...@@ -274,14 +274,14 @@ Version 2.0.15 ...@@ -274,14 +274,14 @@ Version 2.0.15
Released on January 6th 2016. Released on January 6th 2016.
- Speedup NCBI mapview file import (`#124 - Speedup NCBI mapview file import (`#124
<https://github.com/mutalyzer/mutalyzer/pull/124>`_). <https://github.com/mutalyzer/mutalyzer2/pull/124>`_).
- Parse genbank file without VERSION field (`#126 - Parse genbank file without VERSION field (`#126
<https://github.com/mutalyzer/mutalyzer/pull/126>`_). <https://github.com/mutalyzer/mutalyzer2/pull/126>`_).
- Fix issue where some transcripts would not show in the legend (`#136 - Fix issue where some transcripts would not show in the legend (`#136
<https://github.com/mutalyzer/mutalyzer/pull/136>`_). <https://github.com/mutalyzer/mutalyzer2/pull/136>`_).
- Don't discard complete gene from GenBank file when it has incomplete but - Don't discard complete gene from GenBank file when it has incomplete but
also complete features annotated (`#138 also complete features annotated (`#138
<https://github.com/mutalyzer/mutalyzer/pull/138>`_) <https://github.com/mutalyzer/mutalyzer2/pull/138>`_)
Version 2.0.14 Version 2.0.14
...@@ -290,24 +290,24 @@ Version 2.0.14 ...@@ -290,24 +290,24 @@ Version 2.0.14
Released on November 9th 2015. Released on November 9th 2015.
- E-mail address is now optional in batch job website interface (`#119 - E-mail address is now optional in batch job website interface (`#119
<https://github.com/mutalyzer/mutalyzer/pull/119>`_). <https://github.com/mutalyzer/mutalyzer2/pull/119>`_).
- Use Mailcheck in the batch jobs form (`#107 - Use Mailcheck in the batch jobs form (`#107
<https://github.com/mutalyzer/mutalyzer/pull/107>`_). <https://github.com/mutalyzer/mutalyzer2/pull/107>`_).
- Optional email for batch jobs from webservices (`#104 - Optional email for batch jobs from webservices (`#104
<https://github.com/mutalyzer/mutalyzer/pull/104>`_). <https://github.com/mutalyzer/mutalyzer2/pull/104>`_).
- Process batch jobs grouped by email address (`#101 - Process batch jobs grouped by email address (`#101
<https://github.com/mutalyzer/mutalyzer/pull/101>`_). <https://github.com/mutalyzer/mutalyzer2/pull/101>`_).
- Use interval binning scheme on transcript mappings (`#100 - Use interval binning scheme on transcript mappings (`#100
<https://github.com/mutalyzer/mutalyzer/pull/100>`_). <https://github.com/mutalyzer/mutalyzer2/pull/100>`_).
- Back translator interface (`#74 - Back translator interface (`#74
<https://github.com/mutalyzer/mutalyzer/pull/74>`_). <https://github.com/mutalyzer/mutalyzer2/pull/74>`_).
- Transcript-protein links are now cached in Redis (`#94 - Transcript-protein links are now cached in Redis (`#94
<https://github.com/mutalyzer/mutalyzer/pull/94>`_). <https://github.com/mutalyzer/mutalyzer2/pull/94>`_).
- Added `Ter` as a valid amino acid in the HGVS grammar (`#90 - Added `Ter` as a valid amino acid in the HGVS grammar (`#90
<https://github.com/mutalyzer/mutalyzer/pull/90>`_). <https://github.com/mutalyzer/mutalyzer2/pull/90>`_).
- Refactoring of unit tests (`#88 - Refactoring of unit tests (`#88
<https://github.com/mutalyzer/mutalyzer/pull/88>`_, `#89 <https://github.com/mutalyzer/mutalyzer2/pull/88>`_, `#89
<https://github.com/mutalyzer/mutalyzer/pull/89>`_). <https://github.com/mutalyzer/mutalyzer2/pull/89>`_).
Version 2.0.13 Version 2.0.13
...@@ -316,7 +316,7 @@ Version 2.0.13 ...@@ -316,7 +316,7 @@ Version 2.0.13
Released on October 1st 2015. Released on October 1st 2015.
- Fix query bug in update transcript-protein links (`#85 - Fix query bug in update transcript-protein links (`#85
<https://github.com/mutalyzer/mutalyzer/pull/85>`_). <https://github.com/mutalyzer/mutalyzer2/pull/85>`_).
Version 2.0.12 Version 2.0.12
...@@ -325,17 +325,17 @@ Version 2.0.12 ...@@ -325,17 +325,17 @@ Version 2.0.12
Released on September 30th 2015. Released on September 30th 2015.
- Fix off-by-one in slicing chromosome by gene name (`#79 - Fix off-by-one in slicing chromosome by gene name (`#79
<https://github.com/mutalyzer/mutalyzer/pull/79>`_). <https://github.com/mutalyzer/mutalyzer2/pull/79>`_).
- Document scheme used for all positions and ranges (`#79 - Document scheme used for all positions and ranges (`#79
<https://github.com/mutalyzer/mutalyzer/pull/79>`_). <https://github.com/mutalyzer/mutalyzer2/pull/79>`_).
- Show diff for variant protein from non-reference start codon (`#78 - Show diff for variant protein from non-reference start codon (`#78
<https://github.com/mutalyzer/mutalyzer/pull/78>`_). <https://github.com/mutalyzer/mutalyzer2/pull/78>`_).
- Visualise protein change, also with alternative start (`#72 - Visualise protein change, also with alternative start (`#72
<https://github.com/mutalyzer/mutalyzer/pull/72>`_). <https://github.com/mutalyzer/mutalyzer2/pull/72>`_).
- Translate alternative start to M, also in variant (`#72 - Translate alternative start to M, also in variant (`#72
<https://github.com/mutalyzer/mutalyzer/pull/72>`_). <https://github.com/mutalyzer/mutalyzer2/pull/72>`_).
- Added Baker's yeast (SacCer_Apr2011/sacCer3) assembly (`#73 - Added Baker's yeast (SacCer_Apr2011/sacCer3) assembly (`#73
<https://github.com/mutalyzer/mutalyzer/pull/73>`_). <https://github.com/mutalyzer/mutalyzer2/pull/73>`_).
Version 2.0.11 Version 2.0.11
...@@ -344,7 +344,7 @@ Version 2.0.11 ...@@ -344,7 +344,7 @@ Version 2.0.11
Released on August 6th 2015. Released on August 6th 2015.
- Fix bug in recognizing ``p.(=)`` (was reported as ``p.?``) (`#65 - Fix bug in recognizing ``p.(=)`` (was reported as ``p.?``) (`#65
<https://github.com/mutalyzer/mutalyzer/pull/65>`_). <https://github.com/mutalyzer/mutalyzer2/pull/65>`_).
Version 2.0.10 Version 2.0.10
...@@ -354,13 +354,13 @@ Released on July 21st 2015. ...@@ -354,13 +354,13 @@ Released on July 21st 2015.
- Don't crash the position converter on transcript mappings containing no - Don't crash the position converter on transcript mappings containing no
exons (`#63 exons (`#63
<https://github.com/mutalyzer/mutalyzer/pull/63>`_). <https://github.com/mutalyzer/mutalyzer2/pull/63>`_).
- Use the notation for an uncertain stop codon, e.g., ``p.(Gln730Profs*?)`` - Use the notation for an uncertain stop codon, e.g., ``p.(Gln730Profs*?)``
instead of ``p.(Gln730Profs*96)`` when a variant results in a frame shift or instead of ``p.(Gln730Profs*96)`` when a variant results in a frame shift or
extension and we don't see a new stop codon in the RNA (`#57 extension and we don't see a new stop codon in the RNA (`#57
<https://github.com/mutalyzer/mutalyzer/pull/57>`_). <https://github.com/mutalyzer/mutalyzer2/pull/57>`_).
- Added Dog (Broad CanFam3.1/canFam3) assembly for position converter (`#56 - Added Dog (Broad CanFam3.1/canFam3) assembly for position converter (`#56
<https://github.com/mutalyzer/mutalyzer/pull/56>`_). <https://github.com/mutalyzer/mutalyzer2/pull/56>`_).
Version 2.0.9 Version 2.0.9
...@@ -372,7 +372,7 @@ Released on July 9th 2015. ...@@ -372,7 +372,7 @@ Released on July 9th 2015.
<https://github.com/LUMC/mutalyzer/pull/52>`_, `#53 <https://github.com/LUMC/mutalyzer/pull/52>`_, `#53
<https://github.com/LUMC/mutalyzer/pull/53>`_). <https://github.com/LUMC/mutalyzer/pull/53>`_).
- Usability improvements in reading DNA for description extractor (`#54 - Usability improvements in reading DNA for description extractor (`#54
<https://github.com/mutalyzer/mutalyzer/pull/54>`_). <https://github.com/mutalyzer/mutalyzer2/pull/54>`_).
Version 2.0.8 Version 2.0.8
......
...@@ -9,17 +9,17 @@ Documentation ...@@ -9,17 +9,17 @@ Documentation
------------- -------------
User documentation can be found on the `wiki User documentation can be found on the `wiki
<https://github.com/mutalyzer/mutalyzer/wiki>`_. <https://github.com/mutalyzer/mutalyzer2/wiki>`_.
Developer documentation is `hosted at Read The Docs Developer documentation is `hosted at Read The Docs
<http://mutalyzer.readthedocs.org>`_. <http://mutalyzer2.readthedocs.org>`_.
Submit your bug reports and feature requests `here Submit your bug reports and feature requests `here
<https://github.com/mutalyzer/mutalyzer/issues>`_. <https://github.com/mutalyzer/mutalyzer2/issues>`_.
If you're interested in running your own Mutalyzer installation, please have a If you're interested in running your own Mutalyzer installation, please have a
look at our `Mutalyzer Ansible role look at our `Mutalyzer Ansible role
<https://github.com/mutalyzer/ansible-role-mutalyzer>`_ for a completely <https://github.com/mutalyzer/mutalyzer2-ansible-role>`_ for a completely
automated deployment. automated deployment.
...@@ -31,7 +31,7 @@ reports, bug fixes, unit tests, documentation updates, or anything els you may ...@@ -31,7 +31,7 @@ reports, bug fixes, unit tests, documentation updates, or anything els you may
come up with. come up with.
Please refer to the documentation for `more information on contributions Please refer to the documentation for `more information on contributions
<http://mutalyzer.readthedocs.org/en/latest/contributing.html>`_. <http://mutalyzer2.readthedocs.org/en/latest/contributing.html>`_.
Copyright Copyright
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...@@ -10,7 +10,7 @@ reports, bug fixes, unit tests, documentation updates, or anything els you may ...@@ -10,7 +10,7 @@ reports, bug fixes, unit tests, documentation updates, or anything els you may
come up with. come up with.
Development of Mutalyzer happens on GitHub: Development of Mutalyzer happens on GitHub:
https://github.com/mutalyzer/mutalyzer https://github.com/mutalyzer/mutalyzer2
Coding style Coding style
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...@@ -166,7 +166,7 @@ error-prone. Several systems exist to automate this, such as `Puppet`_, ...@@ -166,7 +166,7 @@ error-prone. Several systems exist to automate this, such as `Puppet`_,
`Chef`_, and `Ansible`_. `Chef`_, and `Ansible`_.
An automated `deployment of Mutalyzer with Ansible An automated `deployment of Mutalyzer with Ansible
<https://github.com/mutalyzer/ansible-role-mutalyzer>`_ is available on <https://github.com/mutalyzer/mutalyzer2-ansible-role>`_ is available on
GitHub. This includes installation of the website, SOAP and HTTP/RPC+JSON GitHub. This includes installation of the website, SOAP and HTTP/RPC+JSON
webservices, and the batch processor, similar to the setup described above. webservices, and the batch processor, similar to the setup described above.
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...@@ -5,11 +5,11 @@ ...@@ -5,11 +5,11 @@
Downloading Mutalyzer Downloading Mutalyzer
===================== =====================
The Mutalyzer source code is `hosted on GitHub The Mutalyzer2 source code is `hosted on GitHub
<https://github.com/mutalyzer/mutalyzer>`_. The recommended way to get the <https://github.com/mutalyzer/mutalyzer2>`_. The recommended way to get the
Mutalyzer source code is by cloning the `Git`_ repository:: Mutalyzer source code is by cloning the `Git`_ repository::
git clone https://github.com/mutalyzer/mutalyzer.git git clone https://github.com/mutalyzer/mutalyzer2.git
This will give you the current development version. See below for working with This will give you the current development version. See below for working with
other versions. other versions.
...@@ -34,9 +34,9 @@ Archive downloads ...@@ -34,9 +34,9 @@ Archive downloads
If for whatever reason you don't want to use Git, you can download the source If for whatever reason you don't want to use Git, you can download the source
code directly as a zip archive or tarball. The current development version can code directly as a zip archive or tarball. The current development version can
be found from the `project homepage be found from the `project homepage
<https://github.com/mutalyzer/mutalyzer>`_. Archive downloads for release versions <https://github.com/mutalyzer/mutalyzer2>`_. Archive downloads for release versions
can be found on the `releases page can be found on the `releases page
<https://github.com/mutalyzer/mutalyzer/releases>`_. <https://github.com/mutalyzer/mutalyzer2/releases>`_.
.. _Git: http://git-scm.com/ .. _Git: http://git-scm.com/
...@@ -8,7 +8,7 @@ installation can be found at `mutalyzer.nl <https://mutalyzer.nl>`_. ...@@ -8,7 +8,7 @@ installation can be found at `mutalyzer.nl <https://mutalyzer.nl>`_.
might be interested in :ref:`deploy_ansible`. might be interested in :ref:`deploy_ansible`.
This is the developer documentation for Mutalyzer. User documentation can be This is the developer documentation for Mutalyzer. User documentation can be
found on the `wiki <https://github.com/mutalyzer/mutalyzer/wiki>`_. found on the `wiki <https://github.com/mutalyzer/mutalyzer2/wiki>`_.
Managing Mutalyzer Managing Mutalyzer
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