Commits · 56335113c60de9e0c1b1439973c3c84e400a6c9f · Mirrors / mutalyzer

Nov 01, 2011

Merge r402 from trunk to browser-link-branch · 56335113

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@404 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

56335113

Convert genomic positions to any transcript · ca585e08

Vermaat authored 13 years ago

Add optional gene argument to the numberConvertion webservice method. If
present, it will convert genomic variants to any transcript of the given
gene, no matter how far away they are located (but on the same chromosome
of course). Fixes #70.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@402 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ca585e08

Oct 21, 2011

Fix url in BED track · df171de1

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@396 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

df171de1

Fix positions in BED track on reverse strand · 892ae9b7

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@395 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

892ae9b7

Oct 20, 2011

Implement BED tracks for Genome Browser · 8402dae3

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@394 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8402dae3

Oct 12, 2011

Properly implement link to variant region in Genome Browser · 3b048179

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@393 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

3b048179

Merge r391 from trunk · 31527758

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@392 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

31527758

Oct 11, 2011

Make install/upgrade scripts a bit more robust · 4e06a57c

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@391 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4e06a57c

Fix Genome Browser link (issue #61) · 6b270da8

Vermaat authored 13 years ago

Link to UCSC Genome Browser now has a more proper implementation. Still todo
is error checking and such.

It uses the same infrastrucure as the position converter and is thus also
limited to variants on transcripts with c. notations.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@390 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6b270da8

Merge r380-r388 from trunk to browser-link-branch · b58561a8

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@389 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b58561a8

Oct 10, 2011

Give an error on protein reference sequences · 18e228a6

Vermaat authored 13 years ago

Until protein reference sequences are supported, give an error with a message
instead of crashing. Fixes #62.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@388 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

18e228a6

Accept IVS locations in Variant_info LOVD interface · 302ba055

Vermaat authored 13 years ago

The fix is a hack, basically copying the same functionality from the
namechecker. I think this should eventually be merged somehow.

Fixes #63


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@387 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

302ba055

Update default Mutalyzer location in cache-sync cronjob · f4a60125

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@386 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f4a60125

Oct 07, 2011

Copy user config from install as root (fixes #64) · cd447389

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@385 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

cd447389

Do apt-get update before installing in pre-install script · d0682e4b

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@384 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

d0682e4b

Oct 06, 2011

Update development notes · 0b6bf436

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@383 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0b6bf436

Oct 05, 2011

Update documentation · e7995ea2

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@382 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e7995ea2

Oct 04, 2011

Fix for migration 001 (set default values) · e12d3c81

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@381 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e12d3c81

Sep 30, 2011

Small documentation update · daf079e9

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@380 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

daf079e9

Quick hack as proof of concept implementation · 46b9c88b

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@379 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

46b9c88b

Create browser-link-branch from trunk · 692f4b15

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@378 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

692f4b15

Open development for 2.0.beta-12 · 13440c94

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@375 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

13440c94

Release 2.0.beta-11 · 1b7fb8f9

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@373 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1b7fb8f9

Merge refactor-mutalyzer-branch back into trunk · f48bd705

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@372 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f48bd705

Fix bug in command line interface · feb61bba

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@371 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

feb61bba

Sep 29, 2011

Rename GenBank Uploader to Reference File Loader · 234ff625

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@370 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

234ff625

Sep 27, 2011

Add HEAD method to /Reference download · f8d9bab7

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@369 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f8d9bab7

Fix crash in VariantInfo (thanks Ivo) · 6f20208c

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@368 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6f20208c

Sep 26, 2011

Implement mod_wsgi daemon mode and zero-downtime upgrades · 9d901c20

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@367 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

9d901c20

New location for Trac · a0d5a066

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@366 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a0d5a066

Sep 20, 2011

Fix uploading non-genbank files · 3fbe50a1

Vermaat authored 13 years ago

- Issue a warning instead of an UD number when a user uploads something
  that is not a genbank file (fixes #59).
- Fix a Heisenbug in the batch job unit tests. Wait a little before
  downloading the batch job results.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@365 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

3fbe50a1

Fix looping over homedirs in post-install script · dc934b6a

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@364 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

dc934b6a

Sep 19, 2011

Fix active menu highlighting on HTTPS · 917ecda7

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@363 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

917ecda7

Fix for getCache webservice unit test · ed8d8c45

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@362 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ed8d8c45

Use NCBI mapping data from older build · a9029121

Vermaat authored 13 years ago

We previously used the NCBI mapping data for the current build, but now a new
build was just released, the mapping data is missing (they are waiting for the
data and it should be up soon).

For now, we just use the mapping data for the archived previous build (it is
the build we were using until now anyway).

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@361 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a9029121

Fix bug in migration script · 85430fb0

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@360 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

85430fb0

Sep 14, 2011

Merge r356 from trunk · 357e229a

Vermaat authored 13 years ago

Added a ping() function to the webservice.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@359 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

357e229a

Sep 13, 2011

Use test mail address in batch unit tests · 1caa029b

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@358 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1caa029b

By default, don't run mapping updates from cron in new installations. · 65b150f8

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@357 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

65b150f8

Sep 11, 2011

Added a ping() function to the webservice. · b24246f5

Laros authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@356 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b24246f5