Issues · genotoul-bioinfo / D-GENIES

New issue

Permettre l'input d'un seul fasta et faire de l'auto-alignement

#1 · created Oct 17, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Oct 26, 2017
Analyser le fasta avant de lancer l'alignement pour éviter les traitements trop longs ou donnant des résultats inexploitables

#2 · created Oct 17, 2017 by Floreal Cabanettes 1.0 Jan 19, 2018 New feature
- CLOSED
- 1
updated Jan 25, 2018
Ajouter la possibilité de sélectionner la zone à afficher à partir de 2 listes

#3 · created Oct 18, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Oct 27, 2017
Bug de la stroke width des maps lors du changement d'identité minimale

#4 · created Oct 18, 2017 by Floreal Cabanettes 1.0 Bug
- CLOSED
- 0
updated Oct 26, 2017
Trier les zones

#5 · created Oct 18, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 1
updated Oct 25, 2017
Réglette intensité des limites de chromosomes

#6 · created Oct 18, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Oct 26, 2017
Ajout de l'export

#7 · created Oct 18, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 1
updated Nov 10, 2017
Fix window resize

#8 · created Oct 18, 2017 by Floreal Cabanettes 1.0 Bug
- CLOSED
- 0
updated Oct 26, 2017
Big genomes: filter to keep acceptable in memory

#9 · created Oct 18, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 2
updated Nov 20, 2017
Add results to menu

#10 · created Oct 18, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 1
updated Oct 26, 2017
Set files from URL instead of upload them

#11 · created Oct 23, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Nov 01, 2017
Export : build fasta with sorted and re-ordonned (reversed or not) contigs

#12 · created Oct 23, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Nov 16, 2017
Add possibility to undo a sort

#14 · created Oct 24, 2017 by Floreal Cabanettes 1.0 Enhancement New feature
- CLOSED
- 0
updated Oct 25, 2017
Zoom en sélectionnant la zone à zoomer

#15 · created Oct 25, 2017 by Floreal Cabanettes 1.2 New feature
- CLOSED
- 1
updated Jul 12, 2018
Add a tooltip to show current contig and target on cursor position

#16 · created Oct 26, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Oct 27, 2017
Implement support of compressed fasta files (*.gz)

#17 · created Oct 30, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Oct 30, 2017
Add stats

#18 · created Oct 30, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 1
updated Jan 15, 2018
Concurrent jobs failed

#97 · created Jan 04, 2018 by Floreal Cabanettes 1.0 Bug
- CLOSED
- 1
updated Jan 12, 2018
Must fasta files be stored in gzipped format to keep space?

#19 · created Oct 30, 2017 by Floreal Cabanettes 1.0 Discussion
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- 2
updated Feb 07, 2018
Ménage

#20 · created Oct 31, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 3
updated Nov 20, 2017
Add example run

#21 · created Oct 31, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Feb 20, 2018
Show size of fasta files before upload

#22 · created Nov 01, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Jan 04, 2018
Ajax uploading

#23 · created Nov 01, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Nov 01, 2017
Status : add a bar that progress when job progress

#24 · created Nov 01, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Nov 28, 2017
Status : auto-refresh page periodically

#25 · created Nov 01, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Nov 28, 2017
Add max size for files and check it

#26 · created Nov 01, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 2
updated Dec 18, 2017
Fix bug on small screens for run page

#27 · created Nov 01, 2017 by Floreal Cabanettes 1.0 Bug
- CLOSED
- 0
updated Nov 03, 2017
Gérer les erreurs d'upload

#28 · created Nov 01, 2017 by Floreal Cabanettes 1.0 Bug
- CLOSED
- 0
updated Nov 03, 2017
Send mail on job success/fail

#29 · created Nov 01, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 1
updated Nov 07, 2017
Applications.properties & Wsgi file: change url to be valid in distributed package

#30 · created Nov 01, 2017 by Floreal Cabanettes 1.0 Bug
- CLOSED
- 0
updated Nov 02, 2017
Identité : faire en absolu

#31 · created Nov 02, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Nov 02, 2017
Test Homme VS Singe => passe en mémoire ?

#32 · created Nov 02, 2017 by Floreal Cabanettes 1.0 Test
- CLOSED
- 5
updated Nov 09, 2017
Distribution du programme

#33 · created Nov 02, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 1
updated Feb 22, 2018
Stockage des données sous forme compressée

#34 · created Nov 02, 2017 by Floreal Cabanettes 1.0 Enhancement Won't fix
- CLOSED
- 2
updated Feb 07, 2018
Export : ajout de l'export d'un tableau contenant les correspondances query-target sur la diagonale

#35 · created Nov 02, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Nov 20, 2017
Export : exporter les contigs assemblés selon la référence

#36 · created Nov 02, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 2
updated Feb 06, 2018
Check of uploaded extension not done (or does not cause any error)

#37 · created Nov 02, 2017 by Floreal Cabanettes 1.0 Bug
- CLOSED
- 0
updated Nov 03, 2017
Add global exception handler to catch all exception and pass job on error every time

#38 · created Nov 02, 2017 by Floreal Cabanettes 1.0 Bug Enhancement
- CLOSED
- 0
updated Nov 08, 2017
Do the index after the map, if this one has not failed

#39 · created Nov 02, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Nov 03, 2017
Formulaire de contact

#40 · created Nov 02, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 1
updated Feb 19, 2018
If we have too small blocks on contigs or target, too much memory used because of too much break lines

#41 · created Nov 03, 2017 by Floreal Cabanettes 1.0 Bug
- CLOSED
- 4
updated Nov 03, 2017
Check extensions of files before upload (for local files)

#42 · created Nov 03, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Nov 06, 2017
Handle memory exception from minimap

#43 · created Nov 03, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 1
updated Nov 17, 2017
Vérifier que les fichiers fasta fournis sont valides

#44 · created Nov 06, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 1
updated Dec 05, 2017
Test on very small sequences

#47 · created Nov 07, 2017 by Christophe Klopp 1.0 Support
- CLOSED
- 2
updated Nov 08, 2017
Replace spaces and special chars in job names

#70 · created Nov 08, 2017 by Floreal Cabanettes 1.0 Bug
- CLOSED
- 0
updated Nov 08, 2017
Split of contigs: when to do that?

#71 · created Nov 09, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 2
updated Dec 05, 2017
If more than 75% of contigs have length < 1% of the full fasta, do the sort automatically

#72 · created Nov 09, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Jan 29, 2018
Timeout if sort is too long

#73 · created Nov 09, 2017 by Floreal Cabanettes 1.0 Bug
- CLOSED
- 3
updated Nov 14, 2017
Menu Download / Install on genotoul hosted version

#74 · created Nov 10, 2017 by Floreal Cabanettes 1.0 Feb 23, 2018 Done New feature
- CLOSED
- 2
updated Feb 23, 2018
Export pictures with current zoom applied

#75 · created Nov 10, 2017 by Floreal Cabanettes 1.1 Enhancement
- CLOSED
- 1
updated Apr 11, 2018
Change restore zoom color

#76 · created Nov 10, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Nov 17, 2017
Revoir le système de notifications

#77 · created Nov 10, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Nov 13, 2017
input file names in the mail

#78 · created Nov 15, 2017 by Christophe Klopp 1.0 Enhancement
- CLOSED
- 4
updated Nov 17, 2017
Mettre le target avant le query dans le formulaire

#79 · created Nov 15, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Nov 17, 2017
Déterminer les paramètres influençant la consommation mémoire / processeur et être capable de les prédire

#80 · created Nov 16, 2017 by Floreal Cabanettes 1.3 Test
- 1
updated Jul 14, 2018
Disable sort on all-vs-all mode

#81 · created Nov 16, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Nov 17, 2017
API Rest pour attaquer l'appli via une autre application

#82 · created Nov 17, 2017 by Floreal Cabanettes 1.3 New feature
- 1
updated Jul 14, 2018
Scheduler local pour les soumissions de jobs locaux

#83 · created Nov 20, 2017 by Floreal Cabanettes 1.0 Enhancement New feature
- CLOSED
- 0
updated Nov 21, 2017
Cron pour vérifier les jobs locaux

#84 · created Nov 20, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Nov 21, 2017
Export association table : add info of reverse

#85 · created Nov 20, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Nov 20, 2017
Reverse contigs: do a reverse complement, not just reverse the sequence

#86 · created Nov 20, 2017 by Floreal Cabanettes 1.0 Bug
- CLOSED
- 0
updated Nov 21, 2017
Create a galery on the website to present results with...

#87 · created Dec 01, 2017 by Christophe Klopp 1.0 Enhancement New feature
- CLOSED
- 0
updated Jan 30, 2018
Si on met le même id plus de 2 fois dans la soumission d'un job, ça plante (on passe pas à _3)

#88 · created Dec 04, 2017 by Floreal Cabanettes 1.0 Bug
- CLOSED
- 0
updated Dec 05, 2017
Add cluster submission support

#89 · created Dec 12, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Dec 13, 2017
Add support to local+cluster batch system type

#90 · created Dec 13, 2017 by Floreal Cabanettes 1.0 New feature
- CLOSED
- 0
updated Dec 15, 2017
Change ORM

#91 · created Dec 13, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Dec 13, 2017
Add possibility to associate a link to query / target items

#92 · created Dec 21, 2017 by Floreal Cabanettes 1.3 New feature
- 0
updated Jul 14, 2018
Script capable de soumettre un grand nombre de jobs

#93 · created Dec 21, 2017 by Floreal Cabanettes 1.3 New feature
- 0
updated Jul 14, 2018
Add check on file upload size server side

#94 · created Dec 21, 2017 by Floreal Cabanettes 1.0 Bug Enhancement
- CLOSED
- 0
updated Jan 04, 2018
Catch malformed errors server side and client side

#95 · created Dec 22, 2017 by Floreal Cabanettes 1.0 Bug
- CLOSED
- 1
updated Jan 04, 2018
Prepare big jobs on cluster

#96 · created Dec 22, 2017 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 1
updated Jan 05, 2018
Proposer plusieurs palettes de couleur

#98 · created Jan 04, 2018 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Jan 29, 2018
List of query-target associations table: add coordinates

#99 · created Jan 08, 2018 by Floreal Cabanettes 1.0 Enhancement
- CLOSED
- 0
updated Feb 06, 2018
Permettre le téléchargement d'une page web permettant de visualiser en interactif en local

#100 · created Jan 09, 2018 by Floreal Cabanettes 1.2 New feature
- CLOSED
- 0
updated Jul 13, 2018
match coverage bar of the reference genome

#102 · created Jan 10, 2018 by Christophe Klopp 1.2 Enhancement Won't fix
- CLOSED
- 0
updated Jul 12, 2018
Remove BDD

#103 · created Jan 16, 2018 by Floreal Cabanettes 1.0 Jan 19, 2018 Bug Enhancement 2d
- CLOSED
- 2
updated Jan 23, 2018
Sort: still store sorted version on unsort

#104 · created Jan 17, 2018 by Floreal Cabanettes 1.0 Jan 19, 2018 Enhancement
- CLOSED
- 0
updated Jan 29, 2018
Improve databases

#105 · created Jan 17, 2018 by Floreal Cabanettes 1.0 Jan 18, 2018 Enhancement
- CLOSED
- 0
updated Jan 18, 2018
Fix big data in all-vs-all mode

#106 · created Jan 17, 2018 by Floreal Cabanettes 1.0 Feb 2, 2018 Bug
- CLOSED
- 2
updated Feb 05, 2018
Clean session status links and job status links on clear sessions/jobs and periodically

#107 · created Jan 19, 2018 by Floreal Cabanettes 1.0 Jan 22, 2018 Bug Won't fix
- CLOSED
- 1
updated Jan 23, 2018
Error: MySQL server has gone away

#108 · created Jan 23, 2018 by Floreal Cabanettes 1.0 Jan 26, 2018 Bug
- CLOSED
- 4
updated Jan 29, 2018
Run a job: if we choose a file, and then we switch to URL, the size of the file don't disappear

#109 · created Jan 25, 2018 by Floreal Cabanettes 1.0 Jan 25, 2018 Bug
- CLOSED
- 0
updated Jan 29, 2018
Download of query: remove contigs not present in the index

#110 · created Jan 25, 2018 by Floreal Cabanettes 1.0 Feb 2, 2018 Bug
- CLOSED
- 1
updated Jan 29, 2018
Summary: fail for big data: timeout

#111 · created Jan 31, 2018 by Floreal Cabanettes 1.0 Feb 2, 2018 Bug
- CLOSED
- 0
updated Jan 31, 2018
Add a table beside the gallery items with times and memory usage for all items

#112 · created Jan 31, 2018 by Floreal Cabanettes 1.0 Feb 2, 2018 Enhancement
- CLOSED
- 0
updated Feb 05, 2018
Summary stats failed on big data

#113 · created Jan 31, 2018 by Floreal Cabanettes 1.0 Feb 9, 2018 Bug
- CLOSED
- 0
updated Feb 02, 2018
Standalone version

#114 · created Feb 08, 2018 by Floreal Cabanettes 1.0 Feb 23, 2018 New feature
- CLOSED
- 0
updated Feb 08, 2018
Windows compatibility

#115 · created Feb 08, 2018 by Floreal Cabanettes 1.0 Feb 23, 2018 Done Enhancement
- CLOSED
- 1
updated Feb 22, 2018
Remove "you will receive a mail...." on standalone version

#116 · created Feb 14, 2018 by Floreal Cabanettes 1.0 Feb 23, 2018 Bug
- CLOSED
- 0
updated Feb 15, 2018
Standalone version: problem with treatments which requires mail

#117 · created Feb 14, 2018 by Floreal Cabanettes 1.0 Feb 23, 2018 Bug
- CLOSED
- 0
updated Feb 16, 2018
Sometimes (on windows at least) flask is really long to start. Check flask is already started before launch the browser

#118 · created Feb 14, 2018 by Floreal Cabanettes 1.0 Feb 23, 2018 Bug
- CLOSED
- 0
updated Feb 15, 2018
In standalone mode, load all jobs on startup to add them in the result menu

#119 · created Feb 16, 2018 by Floreal Cabanettes 1.0 Feb 20, 2018 New feature
- CLOSED
- 0
updated Feb 16, 2018
Add a button to delete a job

#120 · created Feb 16, 2018 by Floreal Cabanettes 1.0 Feb 20, 2018 New feature
- CLOSED
- 0
updated Feb 16, 2018
Check XSS and other security breaches

#121 · created Feb 16, 2018 by Floreal Cabanettes 1.0 Feb 23, 2018 Bug
- CLOSED
- 0
updated Feb 19, 2018
Query as reference: do we need to remove noise before

#122 · created Feb 20, 2018 by Floreal Cabanettes Discussion Won't fix
- 1
updated Feb 21, 2018
Ease integration of a new tool

#123 · created Mar 02, 2018 by Floreal Cabanettes 1.1 Apr 6, 2018 Enhancement
- CLOSED
- 2
- 0
updated Apr 03, 2018
Add mashmap tool

#124 · created Mar 02, 2018 by Floreal Cabanettes 1.2 Enhancement
- CLOSED
- 2
- 1
updated Jul 12, 2018
Add analytics logs

#125 · created Mar 14, 2018 by Floreal Cabanettes 1.1 Mar 15, 2018 Enhancement
- CLOSED
- 0
updated Apr 03, 2018
Add alignment file as input instead of query and target

#126 · created Apr 03, 2018 by Floreal Cabanettes 1.1 Apr 6, 2018 New feature
- CLOSED
- 1
- 1
updated Apr 09, 2018