Issues · vidjil / vidjil

New issue

Garder les fichiers bruts tels qu'uploadés ?

#3624 · created Nov 09, 2018 by Mikaël Salson !-reflexion #-quality server-hosting server-pre-process
- CLOSED
- 1
- 4
updated Mar 17, 2021
`compute_extra` plante s'il n'y a pas de clone

#3626 · created Nov 13, 2018 by Mikaël Salson !!-bug *-go priority-4-week server server-task.py
- CLOSED
- 1
- 0
updated Nov 13, 2018
Compilation sous Fedora

#3629 · created Nov 23, 2018 by Mathieu Giraud cpp-compiler
- CLOSED
- 9
updated Nov 23, 2018
Docker : Ne pas modifier les permissions sur les répertoires

#3638 · created Nov 29, 2018 by Mikaël Salson !-important #-crisis-prevention server-backup server-docker
- CLOSED
- 1
- 2
updated Dec 03, 2018
Les étiquettes en abscisse de la grille peuvent être rognées

#3641 · created Nov 30, 2018 by Mikaël Salson Amiens-next Amiens-Nordine client client-axis client-ergonomy client-grid client-responsive user-request
- CLOSED
- 1
- 1
updated Dec 06, 2018
Refactor normalisation

#3644 · created Nov 30, 2018 by Mathieu Giraud *-go Boldrini-Brasil client-normalization dev-refactor
- CLOSED
- 2
- 1
updated Dec 28, 2018
Extend normalization with custom normalized_reads

#3645 · created Nov 30, 2018 by Mathieu Giraud *-go Boldrini-Brasil client repseq-formats
- CLOSED
- 5
updated Dec 28, 2018
Pre-/post- options in fuse to implement a post-process

#3647 · created Nov 30, 2018 by Mathieu Giraud *-go Boldrini-Brasil server server-fuse
- CLOSED
- 1
updated Dec 11, 2020
Enable to switch between normalized_reads and other modes of normalization (including no normalization)

#3648 · created Nov 30, 2018 by Mathieu Giraud Boldrini-Brasil client client-normalization
- CLOSED
- 3
updated Mar 22, 2019
Vidjil-algo : des tests échouent sur plusieurs slaves

#3652 · created Dec 05, 2018 by Mikaël Salson Algo 2018.12 !-important cpp cpp-compiler dev-ci dev-tests priority-4-week
- CLOSED
- 13
updated Mar 05, 2019
.gitlab-ci.yml: releaser les germlines par un job manual depuis gitlab

#3656 · created Dec 12, 2018 by Mathieu Giraud bio-germlines dev-ci dev-gitlab
- CLOSED
- 1
- 0
updated Oct 20, 2020
Enlever les choix "External" et "Expected" s'il ne sont pas pertinents

#3661 · created Dec 21, 2018 by Mathieu Giraud Boldrini-Brasil client-normalization
- CLOSED
- 1
- 0
updated Dec 31, 2018
Afficher dans getHtmlInfo les valeurs normalized_reads

#3662 · created Dec 21, 2018 by Mathieu Giraud Boldrini-Brasil client-normalization
- CLOSED
- 1
- 0
updated Dec 28, 2018
Réparer une normalization_list affichant la liste des derniers clones normalisés en NORM_EXPECTED

#3666 · created Dec 28, 2018 by Mathieu Giraud *-go client-normalization
- CLOSED
- 2
- 3
updated Jan 16, 2019
clone.getSize2() et normalisation, possible doublon

#3667 · created Dec 28, 2018 by Mathieu Giraud client-grid client-normalization dev-dead-code
- CLOSED
- 2
- 2
updated Jan 16, 2019
Déployer prod-client sur app par gitlab

#3668 · created Dec 31, 2018 by Mathieu Giraud *-go dev-gitlab
- CLOSED
- 0
updated Jan 04, 2019
Mettre à jour d3.js

#3670 · created Jan 10, 2019 by Mathieu Giraud *-go client dev-robust
- CLOSED
- 7
updated Jan 29, 2020
Import .tsv AIRR depuis fuse.py

#3673 · created Jan 10, 2019 by Mathieu Giraud Déploiement 2020.06 Dec 20, 2019 !-important *-go repseq-formats-airr repseq-platform server-fuse
- CLOSED
- 1
- 8
updated Sep 28, 2020
test-browser-unit ne passe pas sur dev

#3679 · created Jan 15, 2019 by Mathieu Giraud dev-gitlab
- CLOSED
- 2
updated Jan 15, 2019
test-server-unit ne passe pas sur lego

#3682 · created Jan 15, 2019 by Mathieu Giraud dev-gitlab dev-tests server
- CLOSED
- 1
- 2
updated Jan 17, 2019
Mieux documenter --label

#3684 · created Jan 17, 2019 by Mathieu Giraud Algo 2018.12 *-go Boldrini-Brasil cpp cpp-options doc
- CLOSED
- 3
updated Mar 14, 2019
Colorer l'icône de tag multiple lorsque c'est pertinent

#3689 · created Jan 22, 2019 by Mathieu Giraud client client-ergonomy priority-1-low
- CLOSED
- 1
- 1
updated Feb 11, 2019
Divergence entre vmi.js sur ce dépôt sur le dépôt vmi

#3693 · created Jan 31, 2019 by Mikaël Salson !-important client vmi-responsive
- CLOSED
- 6
updated Feb 13, 2019
Tester Chrome dans notre CI

#3695 · created Jan 31, 2019 by Mathieu Giraud !-important *-go dev-ci dev-tests-watir
- CLOSED
- 1
- 17
updated Mar 13, 2019
Le top peut-il descendre en dessous de 50 sans l'intervention de l'utliisateur ?

#3697 · created Feb 04, 2019 by Mikaël Salson +-deploy LIL-Lille client client-ergonomy
- CLOSED
- 2
- 11
updated Feb 28, 2019
Docker : Le mot de passe admin web2py n'est pas persistant

#3698 · created Feb 04, 2019 by Mikaël Salson server server-admin server-docker
- CLOSED
- 1
- 7
updated Jun 01, 2020
FUNCTIONAL_CLIENT_BROWSER_PATH et navigateurs officiellement supportés

#3701 · created Feb 05, 2019 by Mathieu Giraud dev-ci
- CLOSED
- 1
- 1
updated Mar 05, 2019
Plus rien n'apparaît dans la liste

#3702 · created Feb 05, 2019 by Mathieu Giraud LIL-Lille client-cloneList
- CLOSED
- 2
updated Mar 25, 2019
Erreur lors de l'export monitor

#3705 · created Feb 05, 2019 by Thonier Florian !!-bug client client-export client-rapport dev-robust
- CLOSED
- 1
updated Feb 05, 2019
Versionnage des versions de compilateurs utilisés dans l'algo

#3706 · created Feb 05, 2019 by Mathieu Giraud cpp-compiler dev-ci
- CLOSED
- 3
updated Jun 19, 2020
Less dynamique ?

#3708 · created Feb 05, 2019 by Mathieu Giraud !-reflexion client-less-css wont-fix
- CLOSED
- 0
updated Feb 05, 2019
CloneDB : afficher le nombre d'échantillons total

#3715 · created Feb 11, 2019 by Mikaël Salson LIL-Lille app-clonedb client client-ergonomy client-info user-request
- CLOSED
- 1
- 0
updated Nov 21, 2019
Tutoriel : mettre à jour en ajoutant les nouveautés

#3718 · created Feb 11, 2019 by Mikaël Salson com-first-time-user doc priority-4-week
- CLOSED
- 12
updated Nov 22, 2019
Tutoriel : ajouter les choses spécifiques à la CLL

#3719 · created Feb 11, 2019 by Mikaël Salson com-first-time-user doc patho-ALL patho-LLC
- CLOSED
- 1
updated Mar 15, 2019
Les tests serveurs sont cassés

#3722 · created Feb 12, 2019 by Mikaël Salson !!-broken-ci !!-bug !-important dev-ci dev-tests-watir
- CLOSED
- 7
updated Oct 20, 2020
"Unknown nucleotide" dans les tests should-vdj

#3728 · created Feb 12, 2019 by Mathieu Giraud
- CLOSED
- 2
updated Feb 12, 2019
Libération de la mémoire à la fin de Aho

#3729 · created Feb 12, 2019 by Mathieu Giraud cpp-mem cpp-speed dev-policy
- CLOSED
- 1
- 6
updated Mar 04, 2019
Compare sample ne montre pas l'ensemble des données disponibles

#3750 · created Feb 27, 2019 by Thonier Florian !!-bug server-compare-samples
- CLOSED
- 4
updated Feb 28, 2019
Utiliser une version fixe de Web2py

#3752 · created Feb 27, 2019 by Mikaël Salson !-reflexion #-certification dev-policy dev-robust server
- CLOSED
- 1
- 0
updated Feb 27, 2019
Les séquences ne sont plus triées par abondance dans le segmenteur

#3759 · created Feb 28, 2019 by Mikaël Salson !!-bug *-go +-working LIL-Lille client client-aligner client-ergonomy dev-tests
- CLOSED
- 1
- 1
updated Feb 28, 2019
Retirer VIDJIL_DEFAULT_OPTIONS

#3762 · created Feb 28, 2019 by Mathieu Giraud cpp dev-tests-should-get
- CLOSED
- 1
- 3
updated Apr 26, 2019
SampleReads : échantillon aléatoire des reads.

#3764 · created Feb 28, 2019 by Mikaël Salson !-reflexion *-go Paris-Pitié cpp cpp-representative
- CLOSED
- 1
- 6
updated Jul 28, 2020
Tester d'anciens navigateurs sur un slave à part ?

#3765 · created Feb 28, 2019 by Mathieu Giraud !-reflexion dev-ci dev-tests-watir
- CLOSED
- 1
- 0
updated Oct 04, 2019
Release 2019.03 (recopier sur bioinfo)

#3766 · created Mar 01, 2019 by Mathieu Giraud *-go cpp
- CLOSED
- 25
updated May 07, 2020
CloneDB : mise à jour sur vdb et lil

#3767 · created Mar 01, 2019 by Mathieu Giraud Apr 5, 2019 app-clonedb server-hosting
- CLOSED
- 3
updated Feb 26, 2020
Mettre Jenkins sur une autre branche que dev ?

#3768 · created Mar 01, 2019 by Mathieu Giraud dev-ci
- CLOSED
- 4
updated Aug 27, 2020
Jenkins: enlever Vidjil-{coverage,valgrind-unit} ?

#3769 · created Mar 01, 2019 by Mathieu Giraud *-go dev-ci
- CLOSED
- 7
updated Mar 05, 2019
vidjil-all-slaves cassé

#3771 · created Mar 04, 2019 by Mathieu Giraud !!-broken-ci
- CLOSED
- 4
updated Oct 20, 2020
-c designations

#3772 · created Mar 05, 2019 by Mathieu Giraud Algo 2018.12 bikeshedding cpp-options doc support-policy
- CLOSED
- 1
- 3
updated Mar 06, 2019
Aho et stanford-no-cd.should-get

#3773 · created Mar 05, 2019 by Mathieu Giraud
- CLOSED
- 1
- 6
updated Mar 05, 2019
Les tests fonctionnels client ne plantent pas lorsqu'un test échoue

#3774 · created Mar 05, 2019 by Mikaël Salson dev-tests dev-tests-watir
- CLOSED
- 8
updated Jun 18, 2020
Déploiement 2019.03, -c designations et options names 1 of 2 tasks completed

#3778 · created Mar 06, 2019 by Mathieu Giraud +-deploy app-analyze server
- CLOSED
- 5
updated Mar 15, 2019
should-vdj-to-tap: est-ce que `--ignore_N` fonctionne correctement ?

#3784 · created Mar 07, 2019 by Mikaël Salson !!-bug dev-tests-curated-vdj
- CLOSED
- 2
- 1
updated Oct 24, 2019
Combo -FaW obsolète

#3785 · created Mar 08, 2019 by Mathieu Giraud Algo 2018.12 bikeshedding cpp-options doc server-task.py
- CLOSED
- 1
- 4
updated Mar 12, 2019
FreeBSD cassé, timeout should

#3789 · created Mar 12, 2019 by Mathieu Giraud Algo 2018.12 !!-broken-ci
- CLOSED
- 3
updated Oct 20, 2020
valgrind-functional et representative-random-read-chooser.should-get

#3792 · created Mar 12, 2019 by Mathieu Giraud !!-bug cpp-mem cpp-representative
- CLOSED
- 17
updated Mar 14, 2019
A quoi sert la div data de la div liste

#3793 · created Mar 13, 2019 by Thonier Florian !!-bug !!-crisis LIL-Lille client client-design client-ergonomy priority-5-today
- CLOSED
- 6
updated Mar 13, 2019
Pertinence du format .vdj.fa et documentation

#3795 · created Mar 14, 2019 by Mathieu Giraud Algo 2020.08 bikeshedding doc repseq-formats
- CLOSED
- 1
- 5
updated Jul 30, 2020
Docker vidjil/client : les fichiers de configuration de l'hôte sont-ils pris en compte ?

#3797 · created Mar 14, 2019 by Mikaël Salson !!-bug server-admin server-docker
- CLOSED
- 1
updated Feb 09, 2021
clang++-4.0 pas présent

#3798 · created Mar 14, 2019 by Mathieu Giraud dev-ci
- CLOSED
- 3
updated Mar 19, 2019
Tutoriel serveur

#3800 · created Mar 14, 2019 by Mathieu Giraud doc-tutorial priority-5-today
- CLOSED
- 2
updated Sep 27, 2020
Le menu upload prend toute la largeur, et même plus

#3805 · created Mar 15, 2019 by Mikaël Salson !!-bug !-important client client-ergonomy client-less-css client-ugly priority-4-week vmi-responsive
- CLOSED
- 1
- 5
updated Mar 28, 2019
get reads: mettre un cursor:pointer sur l'icône

#3808 · created Mar 17, 2019 by Mathieu Giraud *-go client-less-css
- CLOSED
- 1
- 0
updated Mar 18, 2019
filtrer pour ne conserver que les clones taggés

#3810 · created Mar 18, 2019 by Thonier Florian !-reflexion client client-ergonomy feature
- CLOSED
- 1
updated Mar 19, 2019
Les warnings ne sont pas produits avec `-c designations`

#3811 · created Mar 18, 2019 by Mikaël Salson Algo 2020.06 !!-bug !-easy *-go client-warning cpp cpp-finesegmenter
- CLOSED
- 2
- 1
updated Jun 10, 2020
Document diversity measures

#3812 · created Mar 18, 2019 by Mathieu Giraud cpp doc math-stats
- CLOSED
- 0
updated Mar 18, 2019
Lien vers le gitlab dans le menu help

#3820 · created Mar 18, 2019 by Thonier Florian client com dev-gitlab feature user-request
- CLOSED
- 1
- 1
updated Apr 02, 2019
Ajout de métadonnées: des traitement avec les dates associées

#3823 · created Mar 18, 2019 by Thonier Florian
- CLOSED
- 1
updated Mar 19, 2019
Calculer l'index de Morisita

#3830 · created Mar 19, 2019 by Thonier Florian Barcelona-clinic LIL-Immuno bio-immuno cpp essen-uk feature math-stats server-fuse
- CLOSED
- 1
- 9
updated Aug 07, 2020
Avoir des icones avec les informations à divers endroits de l'intercace

#3831 · created Mar 19, 2019 by Thonier Florian
- CLOSED
- 1
updated Mar 19, 2019
Clone en R2 perdu en R1+R2 (+R2)

#3833 · created Mar 19, 2019 by Mathieu Giraud Mar 29, 2019 !-important TOU-Toulouse bio-analyze-more com-vw-vidjil-workshop server-pre-process
- CLOSED
- 1
- 11
updated Mar 28, 2019
Bug avce la fonction align sur le segmenteur

#3834 · created Mar 19, 2019 by Thonier Florian
- CLOSED
- 0
updated Mar 19, 2019
CLI11 / vidjil-algo: --options in.json 1 of 2 tasks completed

#3837 · created Mar 19, 2019 by Mathieu Giraud Algo 2019.04 *-go cpp cpp-options
- CLOSED
- 1
- 1
- 5
updated Apr 02, 2019
Flexible strategy for MRD (and other things)

#3838 · created Mar 19, 2019 by Mathieu Giraud Boldrini-Brasil bio-mrd bio-spikes cpp server-config
- CLOSED
- 9
updated Oct 14, 2019
vidjil-algo: parse 'labels' in `config`

#3839 · created Mar 19, 2019 by Mathieu Giraud Algo 2019.04 *-go cpp cpp-options
- CLOSED
- 1
- 5
updated Apr 02, 2019
Envoyer les emails des participants du workshop

#3841 · created Mar 19, 2019 by Thonier Florian Mar 20, 2019
- CLOSED (MOVED)
- 0
updated Mar 19, 2019
Exporter tous les clones au format AIRR

#3842 · created Mar 19, 2019 by Thonier Florian Déploiement 2020.06 !-easy *-go +-deploy LIL-Immuno bio-immuno client-export essen-uk feature server-config server-speed user-request
- CLOSED
- 18
updated Apr 10, 2020
SAvoir si un clone est relié à un antigen

#3843 · created Mar 19, 2019 by Thonier Florian
- CLOSED
- 0
updated Mar 19, 2019
Exporter les clones dans un format compatible avec d'autres bases de données

#3844 · created Mar 19, 2019 by Thonier Florian Mar 19, 2021
- CLOSED
- 1
updated Mar 19, 2019
Permettre de labeliser un set de clones

#3845 · created Mar 19, 2019 by Thonier Florian
- CLOSED
- 1
updated Mar 20, 2019
clusteriser dans l'intrerface sur la séquence en acides aminés.

#3847 · created Mar 19, 2019 by Thonier Florian bio-AA client-cluster essen-uk feature
- CLOSED
- 2
updated Mar 21, 2019
Index pour montrer la proportion d'un répertoire à se reconstruire

#3848 · created Mar 19, 2019 by Thonier Florian *-too-vague CRE-Créteil bio-diversity patho-CAR-T
- CLOSED
- 3
updated Jan 27, 2021
Sonar ?

#3858 · created Mar 21, 2019 by Mathieu Giraud dev-ci dev-code-quality dev-policy
- CLOSED
- 1
updated Aug 27, 2020
--no-windows, --no-vidjil, --no-airr ?

#3861 · created Mar 22, 2019 by Mathieu Giraud !-easy Paris-Pitié cpp cpp-export cpp-options
- CLOSED
- 1
- 10
updated Jul 28, 2020
Le bouton log a disparu

#3863 · created Mar 22, 2019 by Thonier Florian !!-bug client
- CLOSED
- 2
updated Mar 25, 2019
Permettre depuis un run de sauter au patient parent d'un sample

#3864 · created Mar 22, 2019 by Thonier Florian client client-ergonomy feature
- CLOSED
- 1
updated Mar 25, 2019
Avoir par défaut la séquence représentative calculée sur un échantillon aléatoire de reads

#3866 · created Mar 25, 2019 by Mikaël Salson Algo 2019.05 !-important *-go +-deploy cpp cpp-representative
- CLOSED
- 21
updated May 24, 2019
Seul les tableaux devrait être scrollables

#3867 · created Mar 25, 2019 by Thonier Florian LIL-Lille client-design server server-ergonomy user-request
- CLOSED
- 2
- 3
updated Mar 30, 2020
Trier automatiquement les clones de la liste

#3870 · created Mar 25, 2019 by Thonier Florian REN-Rennes client client-cloneList client-ergonomy client-settings user-request
- CLOSED
- 1
- 5
updated Mar 18, 2020
Ajouter une etiquette "dimers" dans les tags de clones

#3871 · created Mar 25, 2019 by Thonier Florian !-reflexion client client-ergonomy feature
- CLOSED
- 1
updated Mar 25, 2019
My Account: Pouvoir accéder facilement aux dernières analyses effectuées

#3880 · created Mar 29, 2019 by Anne de Septenville server-my-account
- CLOSED
- 1
- 4
updated Dec 10, 2020
Testing spike-normalization.py

#3886 · created Apr 02, 2019 by Mathieu Giraud Apr 24, 2019 bio-mrd bio-spikes client-normalization dev-tests-should-get
- CLOSED
- 6
updated Jan 19, 2021
Changement de dénomination des clones sans VDJ ?

#3890 · created Apr 02, 2019 by Anne de Septenville Algo 2019.10 !!-bug bio-germlines-pseudo client client-ugly cpp cpp-export
- CLOSED
- 1
- 19
updated Mar 25, 2020
Release 2019.04

#3891 · created Apr 02, 2019 by Mathieu Giraud Algo 2019.04 Apr 3, 2019 cpp
- CLOSED
- 16
updated May 17, 2019
Roadmap à long terme

#3894 · created Apr 03, 2019 by Mathieu Giraud #-quality +-roadmap com dev-policy doc support-policy
- CLOSED
- 2
updated Mar 09, 2020
Genescan gris, sur les smaller clones, et partiellement coloré, dans le client : fuse.py / distributions

#3902 · created Apr 08, 2019 by Mathieu Giraud !-reflexion PAN-Necker Paris-Pitié client-bar client-virtual-clone ec-ngs next-audio user-request
- CLOSED
- 1
- 15
updated Apr 23, 2020
Clustériser sur la représentative et non pas sur la fenêtre

#3904 · created Apr 17, 2019 by Mathieu Giraud !-reflexion cpp-cluster cpp-representative
- CLOSED
- 2
updated Dec 16, 2020
Vérifier qu'un pre-process a le bon nombre de fichiers avant de le soumettre/lancer

#3907 · created Apr 25, 2019 by Mikaël Salson server server-ergonomy server-pre-process server-task.py
- CLOSED
- 1
- 5
updated Mar 09, 2020
Avoir des germline de poulet

#3910 · created May 02, 2019 by Thonier Florian Algo 2021.03 bio-germlines bio-rnaseq bio-species com-first-time-user feature
- CLOSED
- 2
- 8
updated Apr 08, 2021
Fusion de reads avec Flash

#3911 · created May 09, 2019 by Mathieu Giraud Déploiement 2020.06 +-deploy dev-tests-should-get server-config server-docker server-pre-process
- CLOSED
- 1
- 17
updated Mar 20, 2020