Commits · 905c934e04b4822f598b87feac4f958c4c7ca8d7 · vidjil / vidjil

02 Jun, 2020 6 commits
- Revert ".gitlab-ci.yml: deploy_review{,_server}, manual" · 905c934e
  Mathieu Giraud authored Jun 02, 2020
```
This reverts commit 5b75ad4a.
```
  905c934e
- Merge branch 'hotfix-c/ci-without-cgi' into 'dev' · 582926c8
  Mathieu Giraud authored Jun 02, 2020
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Hotfix: ci without cgi nor review environments

See merge request !713
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  582926c8
- tests: move tests on segmenter-page to external · a5db7556
  Mathieu Giraud authored Jun 02, 2020
  
  a5db7556
- .gitlab-ci.yml: deploy_review{,_server}, manual · 5b75ad4a
  Mathieu Giraud authored Jun 02, 2020
  
  5b75ad4a
- testFiles/segmenter_test.js: no test requiring outside cgi · 7b4bdd27
  Mathieu Giraud authored Jun 02, 2020
  
  7b4bdd27
- Merge branch 'feature-s/fix-web2py-dl-link' into 'dev' · c9eb2d22
  Mathieu Giraud authored Jun 02, 2020
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Fix web2py download link

Closes vdj#1060

See merge request !700
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  c9eb2d22
30 May, 2020 2 commits
- Merge branch 'feature-a/static-L4' into 'dev' · 09d2a6fa
  Mathieu Giraud authored May 30, 2020
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demo/get-sequences: static LIL-L4.fastq.gz

See merge request !710
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  09d2a6fa
- server/Makefile: Fix web2py download link · b5dd6ca9
  Mikaël Salson authored May 26, 2020 and Mathieu Giraud committed May 30, 2020
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Fix vdj#1060
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  b5dd6ca9
29 May, 2020 1 commit
- demo/get-sequences: static LIL-L4.fastq.gz · 3080b03c
  Mathieu Giraud authored May 29, 2020
  
  3080b03c
28 May, 2020 4 commits
- Merge branch 'ci/profiling-for-algo-only' into 'dev' · 523b9f78
  Mikaël Salson authored May 28, 2020
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algo/.gitlab-ci.yml: Missing filter on algo branch name

See merge request !707
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  523b9f78
- Merge branch 'feature-a/3413-detected-instead-of-segmented' into 'dev' · f31d69a2
  Mikaël Salson authored May 28, 2020
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vidjil-algo: detected (instead of segmented)

See merge request !704
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  f31d69a2
- algo/.gitlab-ci.yml: Missing filter on algo branch name · 23717221
  Mikaël Salson authored May 28, 2020
  
  23717221
- Merge branch 'doc/gray-zone' into 'dev' · 17526f8b
  Mikaël Salson authored May 28, 2020
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doc: gray zones, sample graph, cluster

See merge request !699
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  17526f8b
27 May, 2020 13 commits
- Merge branch 'feature-a/2138-backtrack-only-when-improving' into 'dev' · ab5ca697
  Mikaël Salson authored May 27, 2020
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core/segment.cpp: backtrack only when the score is improving, even for 'local' (D)

See merge request !693
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  ab5ca697
- doc: 'detected' reads, or reads with detected recombinations · 97abeacb
  Mathieu Giraud authored May 27, 2020
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see #3413
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  97abeacb
- should-get-tests/: update · 6ef7daff
  Mathieu Giraud authored May 27, 2020
  
  6ef7daff
- repseq_vdj.py: update · ad996aa4
  Mathieu Giraud authored May 27, 2020
  
  ad996aa4
- vidjil.cpp: rename long options to --output-{,un}detected · 12943baa
  Mathieu Giraud authored May 27, 2020
  
  12943baa
- vidjil.cpp: update help strings · da0a38e5
  Mathieu Giraud authored May 27, 2020
  
  da0a38e5
- vidjil.cpp: change output file suffix to .{,un}detected.fa · e34aa009
  Mathieu Giraud authored May 27, 2020
```
See #3143. Follows a75946f9.
```
  e34aa009
- doc: typos · a5031058
  Mathieu Giraud authored May 27, 2020
  
  a5031058
- doc/vidjil-algo.md: more documentation on clustering · e7571ba0
  Mathieu Giraud authored May 26, 2020
  
  e7571ba0
- doc/user.md: clustering, more details, link · e9a8f050
  Mathieu Giraud authored May 26, 2020
  
  e9a8f050
- doc/user.md: sample graph, reword, more details on the gray zone · 8a2360a5
  Mathieu Giraud authored May 26, 2020
  
  8a2360a5
- doc/user.md: +/- concentration, reword, more details · 53f512af
  Mathieu Giraud authored May 26, 2020
  
  53f512af
- Merge branch 'doc/typos' into 'dev' · 7f426d91
  Mathieu Giraud authored May 27, 2020
```
Doc/typos

See merge request !698
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  7f426d91
26 May, 2020 2 commits
- doc/user.md: groups, details, typos · d7f2632b
  Mathieu Giraud authored May 26, 2020
  
  d7f2632b
- doc/vidjil-algo.md: typo internal link · 76e7567c
  Mathieu Giraud authored May 26, 2020
  
  76e7567c
25 May, 2020 1 commit
- doc: typos from ORG → MD conversion · 9eddfc8d
  Mikaël Salson authored May 25, 2020
  
  9eddfc8d
20 May, 2020 11 commits
- Merge branch 'doc/credits' into 'dev' · e3b958d2
  Mathieu Giraud authored May 20, 2020
```
Doc/credits

Closes #4131

See merge request !697
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  e3b958d2
- locus.md: Revert "locus.md: link for validate-links.py" · e840eb7f
  Mathieu Giraud authored May 20, 2020
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As #4131 is fixed, this reverts 86cc9cb5.
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  e840eb7f
- tools/validate-links.py: Use User-Agent to prevent from being blocked of some sites · 9e3da200
  Mikaël Salson authored May 20, 2020
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Fix #4131
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  9e3da200
- doc/credits.md: Make links clickable · b800d85a
  Mikaël Salson authored May 20, 2020
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Thanks @magiraud
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  b800d85a
- doc/credits.md: reorder by name · c912debf
  Mikaël Salson authored May 20, 2020
  
  c912debf
- should-vdj.md: Fix URL · ee2282a7
  Mikaël Salson authored May 20, 2020
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Why was this wrong URL not detected earlier?!
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  ee2282a7
- credits.md: Additional article from 2018 · fc127cbe
  Mikaël Salson authored May 20, 2020
  
  fc127cbe
- credits.md: New publications using Vidjil · 0db705b7
  Mikaël Salson authored May 20, 2020
  
  0db705b7
- Merge branch 'feature-a/918-profiling' into 'dev' · 131363ed
  Mathieu Giraud authored May 20, 2020
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profiling c++

Closes #918

See merge request !686
```
  131363ed
- core/segment.cpp: backtrack only when the score is improving, even for 'local' (D) · f5ff934a
  Mathieu Giraud authored May 19, 2020 and Mikaël Salson committed May 20, 2020
  
  f5ff934a
- .gitlab-ci: Add job to provide CPU/Memory profiling · d36b4ad2
  Mikaël Salson authored Apr 30, 2020
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Fix #918
```
  d36b4ad2