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
Released on March 15th 2021.
- 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
......@@ -24,11 +24,11 @@ Version 2.0.33
Released on November 24th 2020.
- Update links (`#514
<https://github.com/mutalyzer/mutalyzer/pull/514>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/514>`_).
- Improve warning messages (`#513
<https://github.com/mutalyzer/mutalyzer/pull/513>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/513>`_).
- Add legacy crossmapper module (`#508
<https://github.com/mutalyzer/mutalyzer/pull/508>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/508>`_).
Version 2.0.32
......@@ -37,13 +37,13 @@ Version 2.0.32
Released on December 9th 2019.
- 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
<https://github.com/mutalyzer/mutalyzer/pull/497>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/497>`_).
- Update requirements (`#496
<https://github.com/mutalyzer/mutalyzer/pull/496>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/496>`_).
- Fix invalid LRG record issue (`#495
<https://github.com/mutalyzer/mutalyzer/pull/495>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/495>`_).
Version 2.0.31
......@@ -52,15 +52,15 @@ Version 2.0.31
Released on August 21st 2019.
- 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
<https://github.com/mutalyzer/mutalyzer/pull/485>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/485>`_).
- 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
<https://github.com/mutalyzer/mutalyzer/issues/481>`_).
<https://github.com/mutalyzer/mutalyzer2/issues/481>`_).
- Update Travis configuration (`#483
<https://github.com/mutalyzer/mutalyzer/pull/483>`_)
<https://github.com/mutalyzer/mutalyzer2/pull/483>`_)
Version 2.0.30
......@@ -69,11 +69,11 @@ Version 2.0.30
Released on May 24th 2019.
- Update requirements (`#475
<https://github.com/mutalyzer/mutalyzer/pull/475>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/475>`_).
- 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
<https://github.com/mutalyzer/mutalyzer/issues/468>`_).
<https://github.com/mutalyzer/mutalyzer2/issues/468>`_).
Version 2.0.29
......@@ -82,15 +82,15 @@ Version 2.0.29
Released on December 4th 2018.
- 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
<https://github.com/mutalyzer/mutalyzer/pull/458>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/458>`_).
- 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
<https://github.com/mutalyzer/mutalyzer/pull/456>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/456>`_).
- 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
......@@ -99,7 +99,7 @@ Version 2.0.28
Released on June 11th 2018.
- 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
......@@ -108,19 +108,19 @@ Version 2.0.27
Released on May 25th 2018.
- 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
<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
<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
<https://github.com/mutalyzer/mutalyzer/pull/442>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/442>`_).
- 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
<https://github.com/mutalyzer/mutalyzer/pull/437>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/437>`_).
- Add link to website changelog (`#434
<https://github.com/mutalyzer/mutalyzer/pull/434>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/434>`_).
Version 2.0.26
......@@ -129,9 +129,9 @@ Version 2.0.26
Released on July 19th 2017.
- 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
<https://github.com/mutalyzer/mutalyzer/issues/430>`_).
<https://github.com/mutalyzer/mutalyzer2/issues/430>`_).
Version 2.0.25
......@@ -141,7 +141,7 @@ Released on May 17th 2017.
- Fix for batch processor crash when trying to alter an "item" column of the
"batch_queue_items" database table (`#426
<https://github.com/mutalyzer/mutalyzer/pull/426>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/426>`_).
Version 2.0.24
---------------
......@@ -150,7 +150,7 @@ Released on April 12th 2017.
- Fix for SNP converter crash when called with 'rs0' as parameter.
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
......@@ -160,7 +160,7 @@ Released on November 9th 2016.
- Fix for internal server error in the position converter triggered by
non-variant description (`#333
<https://github.com/mutalyzer/mutalyzer/issues/333>`_).
<https://github.com/mutalyzer/mutalyzer2/issues/333>`_).
Version 2.0.22
......@@ -169,7 +169,7 @@ Version 2.0.22
Released on September 20th 2016.
- 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
......@@ -178,7 +178,7 @@ Version 2.0.21
Released on June 24th 2016.
- 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
......@@ -187,11 +187,11 @@ Version 2.0.20
Released on June 22th 2016.
- 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
<https://github.com/mutalyzer/mutalyzer/pull/404>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/404>`_).
- Remove support for GI numbers (`#396
<https://github.com/mutalyzer/mutalyzer/pull/396>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/396>`_).
Version 2.0.19
......@@ -200,9 +200,9 @@ Version 2.0.19
Released on June 9th 2016.
- 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
<https://github.com/mutalyzer/mutalyzer/pull/390>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/390>`_).
Version 2.0.18
......@@ -211,13 +211,13 @@ Version 2.0.18
Released on May 23rd 2016.
- 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
<https://github.com/mutalyzer/mutalyzer/pull/363>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/363>`_).
- 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
<https://github.com/mutalyzer/mutalyzer/pull/371>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/371>`_).
Version 2.0.17
......@@ -226,12 +226,12 @@ Version 2.0.17
Released on March 24th 2016.
- 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
<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
<https://github.com/mutalyzer/mutalyzer/pull/356>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/356>`_).
Version 2.0.16
......@@ -240,12 +240,12 @@ Version 2.0.16
Released on February 25th 2016.
- 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>`.
- 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
<https://github.com/mutalyzer/mutalyzer/pull/146>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/146>`_).
.. _changelog_2016_details:
......@@ -274,14 +274,14 @@ Version 2.0.15
Released on January 6th 2016.
- 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
<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
<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
also complete features annotated (`#138
<https://github.com/mutalyzer/mutalyzer/pull/138>`_)
<https://github.com/mutalyzer/mutalyzer2/pull/138>`_)
Version 2.0.14
......@@ -290,24 +290,24 @@ Version 2.0.14
Released on November 9th 2015.
- 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
<https://github.com/mutalyzer/mutalyzer/pull/107>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/107>`_).
- 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
<https://github.com/mutalyzer/mutalyzer/pull/101>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/101>`_).
- 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
<https://github.com/mutalyzer/mutalyzer/pull/74>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/74>`_).
- 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
<https://github.com/mutalyzer/mutalyzer/pull/90>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/90>`_).
- Refactoring of unit tests (`#88
<https://github.com/mutalyzer/mutalyzer/pull/88>`_, `#89
<https://github.com/mutalyzer/mutalyzer/pull/89>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/88>`_, `#89
<https://github.com/mutalyzer/mutalyzer2/pull/89>`_).
Version 2.0.13
......@@ -316,7 +316,7 @@ Version 2.0.13
Released on October 1st 2015.
- 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
......@@ -325,17 +325,17 @@ Version 2.0.12
Released on September 30th 2015.
- 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
<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
<https://github.com/mutalyzer/mutalyzer/pull/78>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/78>`_).
- 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
<https://github.com/mutalyzer/mutalyzer/pull/72>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/72>`_).
- 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
......@@ -344,7 +344,7 @@ Version 2.0.11
Released on August 6th 2015.
- 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
......@@ -354,13 +354,13 @@ Released on July 21st 2015.
- Don't crash the position converter on transcript mappings containing no
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*?)``
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
<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
<https://github.com/mutalyzer/mutalyzer/pull/56>`_).
<https://github.com/mutalyzer/mutalyzer2/pull/56>`_).
Version 2.0.9
......@@ -372,7 +372,7 @@ Released on July 9th 2015.
<https://github.com/LUMC/mutalyzer/pull/52>`_, `#53
<https://github.com/LUMC/mutalyzer/pull/53>`_).
- 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
......
......@@ -9,17 +9,17 @@ Documentation
-------------
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
<http://mutalyzer.readthedocs.org>`_.
<http://mutalyzer2.readthedocs.org>`_.
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
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.
......@@ -31,7 +31,7 @@ reports, bug fixes, unit tests, documentation updates, or anything els you may
come up with.
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
......
......@@ -10,7 +10,7 @@ reports, bug fixes, unit tests, documentation updates, or anything els you may
come up with.
Development of Mutalyzer happens on GitHub:
https://github.com/mutalyzer/mutalyzer
https://github.com/mutalyzer/mutalyzer2
Coding style
......
......@@ -166,7 +166,7 @@ error-prone. Several systems exist to automate this, such as `Puppet`_,
`Chef`_, and `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
webservices, and the batch processor, similar to the setup described above.
......
......@@ -5,11 +5,11 @@
Downloading Mutalyzer
=====================
The Mutalyzer source code is `hosted on GitHub
<https://github.com/mutalyzer/mutalyzer>`_. The recommended way to get the
The Mutalyzer2 source code is `hosted on GitHub
<https://github.com/mutalyzer/mutalyzer2>`_. The recommended way to get the
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
other versions.
......@@ -34,9 +34,9 @@ Archive downloads
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
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
<https://github.com/mutalyzer/mutalyzer/releases>`_.
<https://github.com/mutalyzer/mutalyzer2/releases>`_.
.. _Git: http://git-scm.com/
......@@ -8,7 +8,7 @@ installation can be found at `mutalyzer.nl <https://mutalyzer.nl>`_.
might be interested in :ref:`deploy_ansible`.
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
......
docutils<0.18
Sphinx
alembic
biopython
......
......@@ -38,7 +38,7 @@ Similarly, ``--redis-uri`` (only one allowed) specifies a Redis server to use
for testing. If unspecified, a mock Redis server is used.
Tests are `run automatically on Travis CI
<https://travis-ci.org/mutalyzer/mutalyzer>`_ with SQLite, PostgreSQL, and
<https://travis-ci.org/mutalyzer/mutalyzer2>`_ with SQLite, PostgreSQL, and
MySQL, for each pull request and push on GitHub.
......
......@@ -155,7 +155,7 @@ class Reference(db.Base):
#: Accession number for this reference, including the version number if
#: applicable (e.g., ``AL449423.14``, ``NM_000059.3``,
#: ``UD_138781341344``).
# See: https://github.com/mutalyzer/mutalyzer/issues/399
# See: https://github.com/mutalyzer/mutalyzer2/issues/399
accession = Column(String(20), nullable=False, index=True, unique=True)
#: MD5 checksum of the reference file.
......
......@@ -1125,7 +1125,7 @@ def import_from_lrgmap_file(assembly, lrgmap_file):
# TODO: Also take protein into account. For example, in LRG_321 (TP53)
# some transcripts occur twice (with different CDSs and different
# protein numbers).
# https://github.com/mutalyzer/mutalyzer/issues/372
# https://github.com/mutalyzer/mutalyzer2/issues/372
return TranscriptMapping.create_or_update(
chromosome, 'lrg', accession, record['gene'], orientation,
record['start'], record['stop'],
......
......@@ -14,50 +14,23 @@ posted to this list via the Google Groups interface or by sending an email
to <a href="mutalyzer@googlegroups.com">mutalyzer@googlegroups.com</a>.
</p>
<p>
Bugs and concrete feature requests may also be filed directly in
the <a href="https://github.com/mutalyzer/mutalyzer/issues">GitHub issue
tracker</a>.
</p>
<p>
If you are a regular user of the Mutalyzer webservices or are maintaining your
own Mutalyzer installation, consider subscribing to
the <a href="https://groups.google.com/forum/#!forum/mutalyzer-announce">Mutalyzer
Announcements mailing list</a>. This is a low-volume mailing list for
announcing updates to Mutalyzer and its infrastructure.
</p>
<p>
If you have a private question or a security related issue to discuss, please
use the private
address <a href="info@mutalyzer.nl">info@mutalyzer.nl</a>.
</p>
<h2>Open Source</h2>
<p>
Mutalyzer is Open Source and available under
the <a href="http://www.gnu.org/licenses/agpl-3.0.html">GNU Affero General
Public License</a>. Please <a href="mailto:info@mutalyzer.nl">contact the
authors</a> if you want to discuss custom licensing.
</p>
<p>
Contributions to Mutalyzer are very welcome! They can be feature requests, bug
reports, bug fixes, unit tests, documentation updates, or anything else you may
come up with.
Public License</a>.
</p>
<p>
Development of Mutalyzer happens on
GitHub: <a href="https://github.com/mutalyzer/mutalyzer">github.com/mutalyzer/mutalyzer</a>
Mutalyzer source code is available on
GitHub: <a href="https://github.com/mutalyzer/mutalyzer2">github.com/mutalyzer/mutalyzer2</a>
</p>
<p>
If you're interested in running your own Mutalyzer installation, please have a
look at
our <a href="https://github.com/mutalyzer/ansible-role-mutalyzer">Mutalyzer
our <a href="https://github.com/mutalyzer/mutalyzer2-ansible-role">Mutalyzer
Ansible role</a> for a completely automated deployment.
</p>
......
......@@ -38,7 +38,7 @@ Please supply an amino acid substitution.
</div>
<div class="form-group button-group">
<input type="submit" class="btn btn-primary" value="Back translate">
<a href="https://github.com/mutalyzer/mutalyzer/wiki/Back-Translator" target="new" class="btn btn-default pull-right">Help</a>
<a href="https://github.com/mutalyzer/mutalyzer2/wiki/Back-Translator" target="new" class="btn btn-default pull-right">Help</a>
</div>
</form>
......
......@@ -108,13 +108,13 @@
<ul class="dropdown-menu">
<li>
<a href="https://github.com/mutalyzer/mutalyzer/wiki/Documentation" target="_blank">Documentation</a>
<a href="https://github.com/mutalyzer/mutalyzer2/wiki/Documentation" target="_blank">Documentation</a>
</li>
<li>
<a href="https://github.com/mutalyzer/mutalyzer/wiki/Mutalyzer-FAQ" target="_blank">FAQ</a>
<a href="https://github.com/mutalyzer/mutalyzer2/wiki/Mutalyzer-FAQ" target="_blank">FAQ</a>
</li>
<li>
<a href="https://github.com/mutalyzer/mutalyzer/wiki/Mutalyzer-Exercise" target="_blank">Exercise</a>
<a href="https://github.com/mutalyzer/mutalyzer2/wiki/Mutalyzer-Exercise" target="_blank">Exercise</a>
</li>
<li>
<a href="https://groups.google.com/forum/#!forum/mutalyzer" target="_blank">Mailing list</a>
......@@ -129,7 +129,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a class="navbar-brand" href="https://github.com/mutalyzer/mutalyzer" target="_blank"><img
<a class="navbar-brand" href="https://github.com/mutalyzer/mutalyzer2" target="_blank"><img
src="{{ url_for('static', filename='images/github_logo.png') }}" title="Mutalyzer on GitHub"></a>
</li>
</ul>
......@@ -185,14 +185,14 @@
{% endif %}
</span>
<br>
<a href="https://github.com/mutalyzer/mutalyzer/blob/master/CHANGES.rst">
<a href="https://github.com/mutalyzer/mutalyzer2/blob/master/CHANGES.rst">
Changelog
</a>
</p>
</div>
<div class="col-md-4">
<p class="text-muted">HGVS nomenclature version {{ nomenclature_version }}
(<a href="https://github.com/mutalyzer/mutalyzer/wiki/HGVS-Mutalyzer-Differences">notes</a>)
(<a href="https://github.com/mutalyzer/mutalyzer2/wiki/HGVS-Mutalyzer-Differences">notes</a>)
<br>
<a href="{{ url_for('website.about') }}#recommended-by" name="recommended-by">
Recommended by
......
......@@ -52,7 +52,7 @@
<div class="form-group">
<input type="submit" class="btn btn-primary" value="Submit batch job">
<a href="https://github.com/mutalyzer/mutalyzer/wiki/Batch-Checkers" target="new" class="btn btn-default pull-right">Help</a>
<a href="https://github.com/mutalyzer/mutalyzer2/wiki/Batch-Checkers" target="new" class="btn btn-default pull-right">Help</a>
<a href="#" onclick="toggle_visibility('help');" class="btn btn-default pull-right">File format help <span class="caret"></span></a>
</div>
</form>
......
......@@ -151,7 +151,7 @@ Please supply a reference sequence and an observed sequence.
</div>
<div class="form-group">
<input type="submit" class="btn btn-primary" value="Extract variant description">
<a href="https://github.com/mutalyzer/mutalyzer/wiki/Description-Extractor" target="new" class="btn btn-default pull-right">Help</a>
<a href="https://github.com/mutalyzer/mutalyzer2/wiki/Description-Extractor" target="new" class="btn btn-default pull-right">Help</a>
</div>
</form>
......
......@@ -61,7 +61,7 @@
<div class="form-group button-group">
<input type="submit" class="btn btn-primary" value="Check variant description">
<a href="https://github.com/mutalyzer/mutalyzer/wiki/Name-Checker" target="new" class="btn btn-default pull-right">Help</a>
<a href="https://github.com/mutalyzer/mutalyzer2/wiki/Name-Checker" target="new" class="btn btn-default pull-right">Help</a>
</div>
</form>
......@@ -96,7 +96,7 @@
{% if parse_error %}
<div class="alert alert-info">
Please note that Mutalyzer does not cover the entire HGVS nomenclature. You can find more information
<a href="https://github.com/mutalyzer/mutalyzer/wiki/HGVS-Mutalyzer-Differences">here</a>.
<a href="https://github.com/mutalyzer/mutalyzer2/wiki/HGVS-Mutalyzer-Differences">here</a>.
</div>
{% endif %}
......