ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2018-06-27T18:32:33+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/1Mail de relance2018-06-27T18:32:33+02:00Celine NoirotMail de relanceProposer un mail de relance, une fois que la purge déjà été demandéeProposer un mail de relance, une fois que la purge déjà été demandéeV3.1 - Purge2018-04-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/2Purge : somme par projet incoherente2018-06-19T15:08:13+02:00Celine NoirotPurge : somme par projet incoherenteLa somme des données "purgeables" n'est pas coherente dans le table de puge.La somme des données "purgeables" n'est pas coherente dans le table de puge.V3.1 - PurgeClaire KuchlyClaire Kuchly2018-04-18https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/3Infos générales sur la page purge2018-06-19T15:14:21+02:00Celine NoirotInfos générales sur la page purgeDonner l'information de :
- la somme totale "purgeable"
- le nombre total de projets
correspondant aux projets filtrés.Donner l'information de :
- la somme totale "purgeable"
- le nombre total de projets
correspondant aux projets filtrés.V3.1 - PurgeClaire KuchlyClaire Kuchly2018-04-18https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/4ONT_QC analysis : Fast5archive component bug with multiple runs2018-03-30T10:38:47+02:00Maxime MannoONT_QC analysis : Fast5archive component bug with multiple runsIf a run has been launch many times, it has multiple subdirectory of raw data that we have to tar with différents namesIf a run has been launch many times, it has multiple subdirectory of raw data that we have to tar with différents namesV3.3 - ONT_QC analysisMaxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/6Update of the picardtools2018-08-02T13:07:23+02:00Audrey GibertUpdate of the picardtoolsWe have picardtools 1.88
we want to test v2.14 on SLURMWe have picardtools 1.88
we want to test v2.14 on SLURMV3.2 - SlurmAudrey GibertAudrey Gibert2018-04-27https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/7Update of Samtools2018-08-01T09:19:30+02:00Maxime MannoUpdate of SamtoolsOn Genotoul we use samtools v1.1
We want to use the v1.3.1 on genologin (for the momentOn Genotoul we use samtools v1.1
We want to use the v1.3.1 on genologin (for the momentV3.2 - SlurmMaxime MannoMaxime Manno2018-04-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/8Metacharacter "&" in password creates a bug2019-09-12T09:27:13+02:00Audrey GibertMetacharacter "&" in password creates a bugWhen "&" is in the password, the registered password stops just before the "&" :
Example:
if "hgff&ld" is written,
the registered password in the database is "hgff"When "&" is in the password, the registered password stops just before the "&" :
Example:
if "hgff&ld" is written,
the registered password in the database is "hgff"V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/5Bug ng6_cli status --all and on the interface2018-08-28T14:15:51+02:00Maxime MannoBug ng6_cli status --all and on the interfaceAfter the upgrade of nG6_Git, the command ng6_cli status --all did not workAfter the upgrade of nG6_Git, the command ng6_cli status --all did not workV3.2 - SlurmClaire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/9Regenerate a password for users added by the project manager2020-01-22T16:22:03+01:00Audrey GibertRegenerate a password for users added by the project managerFor now, there is no possibility for a user added by the project manager to regenerate their password.
=> It has to be addedFor now, there is no possibility for a user added by the project manager to regenerate their password.
=> It has to be addedRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/11Correct list of id analyse and run stored in db for a purge demand2018-08-02T14:55:49+02:00Celine NoirotCorrect list of id analyse and run stored in db for a purge demandWhen purge was created, a bug stored all values of a project
Correct the list of analyse id and run id before launching the purge
Think to also remove the purge id field to the analyses and the runsWhen purge was created, a bug stored all values of a project
Correct the list of analyse id and run id before launching the purge
Think to also remove the purge id field to the analyses and the runsV3.1 - PurgeCeline NoirotCeline Noirot2018-06-29https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/13flag project which all runs and analyses are purgeable2018-07-18T15:48:10+02:00Claire Kuchlyflag project which all runs and analyses are purgeableV3.1 - PurgeClaire KuchlyClaire Kuchly2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/14[purge] : for projet who has no administror : mail sent to all users project2018-08-28T14:39:30+02:00Claire Kuchly[purge] : for projet who has no administror : mail sent to all users projectV3.1 - PurgeCeline NoirotCeline Noirot2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/15purge: add extension by lab2018-06-21T17:27:34+02:00Celine Noirotpurge: add extension by labAdd the posibility to extend by lab.Add the posibility to extend by lab.V3.1 - PurgeCeline NoirotCeline Noirot2018-06-29https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/16generate script to compute storage size for extention2019-07-23T14:15:59+02:00Celine Noirotgenerate script to compute storage size for extentionV3.1 - Purge2018-06-29https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/12Add visualisation and compute of stored/purged size per group/lab2018-07-18T15:48:10+02:00Celine NoirotAdd visualisation and compute of stored/purged size per group/labAdd visualisation of stored/purged size per group/lab
Generate a table and a graphics.Add visualisation of stored/purged size per group/lab
Generate a table and a graphics.V3.1 - PurgeCeline NoirotCeline Noirot2018-06-29https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/17Add project extention2018-07-18T15:48:10+02:00Celine NoirotAdd project extentionIf a project has a obsolete run (not all), all its run or analysis can be extentedIf a project has a obsolete run (not all), all its run or analysis can be extentedV3.1 - PurgeCeline NoirotCeline Noirot2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/18List all project even not obsolete2018-06-28T18:11:30+02:00Celine NoirotList all project even not obsoleteList all project in purge management to enable the extention for the projects of a complete lab.List all project in purge management to enable the extention for the projects of a complete lab.V3.1 - PurgeCeline NoirotCeline Noirot2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/19Bug project view nb run / analyse / size2018-06-20T16:49:27+02:00Celine NoirotBug project view nb run / analyse / size![ng6-project-bug](/uploads/a9a4a23eb23a55520cae49a853623d8e/ng6-project-bug.png)![ng6-project-bug](/uploads/a9a4a23eb23a55520cae49a853623d8e/ng6-project-bug.png)V3.1 - Purge2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/20Bug purge managment view : total purgeable size false2018-06-21T13:25:30+02:00Celine NoirotBug purge managment view : total purgeable size false![prod-ng6](/uploads/a65c6c3e0444eda15926e004995a55b6/prod-ng6.png)![prod-ng6](/uploads/a65c6c3e0444eda15926e004995a55b6/prod-ng6.png)V3.1 - Purgehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/21Delete Analyse or run from project view or run view2018-08-14T14:13:03+02:00Celine NoirotDelete Analyse or run from project view or run viewIf the user enter an existing user on unix server, and this user do not have permission, the return is true/ok but the directory is not deleted
![image](/uploads/3b6913146624e853d83c524a728a59e4/image.png)If the user enter an existing user on unix server, and this user do not have permission, the return is true/ok but the directory is not deleted
![image](/uploads/3b6913146624e853d83c524a728a59e4/image.png)V3.2 - Slurm2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/22Do not extend run/analyse if date is lower than retention_date2018-06-25T18:51:40+02:00Celine NoirotDo not extend run/analyse if date is lower than retention_dateWhen extend a project entirely, do not change date if it's lower than the retention_dateWhen extend a project entirely, do not change date if it's lower than the retention_dateV3.1 - PurgeCeline NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/23Add total project size in purge demand email2018-06-27T16:32:07+02:00Celine NoirotAdd total project size in purge demand emailV3.1 - PurgeCeline NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/24deletion of demand purge don't work2018-06-29T15:54:26+02:00Celine Noirotdeletion of demand purge don't workReturn always error unable to delete.Return always error unable to delete.V3.1 - PurgeClaire KuchlyClaire Kuchly2018-06-29https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/25after extending a part of project values in Data overview project are false2018-06-29T16:43:21+02:00Celine Noirotafter extending a part of project values in Data overview project are false![image](/uploads/cf5fda99787f29d34f38d5d4f20656a7/image.png)![image](/uploads/cf5fda99787f29d34f38d5d4f20656a7/image.png)V3.1 - PurgeCeline NoirotCeline Noirot2018-06-28https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/26Erreur dans la console ZeroClipboard.min.map2018-08-28T14:18:21+02:00Celine NoirotErreur dans la console ZeroClipboard.min.mapVerifier l'url de ZeroClipboard dans les js de jflow.
![image](/uploads/b15985622e50feb2ce1856f66dbcb1cc/image.png)Verifier l'url de ZeroClipboard dans les js de jflow.
![image](/uploads/b15985622e50feb2ce1856f66dbcb1cc/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/27Project view : hidden run and analyses are counted2019-09-18T17:27:36+02:00Celine NoirotProject view : hidden run and analyses are countedIn data overview hidden project are counted
![image](/uploads/14b9494bc2aedd913f56bf7bf8c0c025/image.png)In data overview hidden project are counted
![image](/uploads/14b9494bc2aedd913f56bf7bf8c0c025/image.png)V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/28TESTs TODO2018-08-02T14:55:08+02:00Celine NoirotTESTs TODOcategorie 1 : projet fini
categorie 2 : projet open
Cas d'utilisation
MAIL
1. [x] envoie mail pour des projets sans manager
1. [x] envoie mail categorie 1 1.> verifier la liste des run/analyses est correcte
TEST Projet 110 :
Liste...categorie 1 : projet fini
categorie 2 : projet open
Cas d'utilisation
MAIL
1. [x] envoie mail pour des projets sans manager
1. [x] envoie mail categorie 1 1.> verifier la liste des run/analyses est correcte
TEST Projet 110 :
Liste des runs (5):
* 110 1369
* 110 1362
* 110 1368
* 110 1370
* 110 1373
Liste des analyses (15):
* 110 8636
* 110 8633
* 110 8637
* 110 12868
* 110 12865
* 1362 6068
* 1362 6070
* 1369 6089
* 1369 6087
* 1370 6088
* 1370 6090
* 1373 6095
* 1373 6096
* 1368 6083
* 1368 6084
Mail :
Files impacted of:
- runs names: pool-B57-VI (1369), pool-B57-T (1362), pool-A22-T (1368), pool-A22-VI (1370), pool-B57-A22-VI (1373)
- analyses ids: 6089, 6087, 6068, 6070, 6083, 6084, 6088, 6090, 6095, 6096, 8636, 8633, 8637, 12868, 12865
1. [x] envoie mail categorie 2 1.> verifier la liste des run/analyses est correcte et l'icone dans la project vue pour chaque run est correcte
Files impacted of:
- runs names: pool1 (9422), Pool2bis_prob (9662), Pool2bis (9742)
- analyses ids: 36670, 36672, 36673, 36695, 37617, 37627, 37635, 37647
{{uid retention_date mail_sent_date retention_date mail_sent_date
36670 1525384800 1531299983 03/05/2018 11/07/2018
36672 1525384800 1531299983 03/05/2018 11/07/2018
36673 1525384800 1531299983 03/05/2018 11/07/2018
36695 1525384800 1531299983 03/05/2018 11/07/2018
37617 1529445600 1531299983 19/06/2018 11/07/2018
37627 1529445600 1531299983 19/06/2018 11/07/2018
37635 1529445600 1531299983 19/06/2018 11/07/2018
37647 1529445600 1531299983 19/06/2018 11/07/2018
37930 1531260000 0 10/07/2018
37934 1531260000 0 10/07/2018
37937 1531260000 0 10/07/2018
37941 1531260000 0 10/07/2018
}}
1. [x] renvoie d'un mail
PURGE
purge d'un projet complet (categorie1)
1. [x] tester login faux / login sans les droits d'acces / login avec les droit
1. [x] creer de faux repertoires associé verifier la suppression + l'icone dans la project vue pour chaque run est correcte + le data overview
purge d'un projet categorie 2
1. [x] verifier que l'icone dans la project vue pour chaque run est correcte,
1. [x] verifier que l'icone dans la run vue pour chaque analyse est correcte,
1. [x] la non suppression des data non obsolete
EXTENTION
extension catégorie 2
1. [x] option que les runs/analyses obsoletes : date changée et icone changé pour les runs/analyses uniquement concernés
1. [x] option projet complet avec date ok pour tout les runs/analyses
1. [x] option projet complet avec date d'extention pouvant être inférieure a des dates de retention de certain runs non obsolete
extention categorie 1 :
1. [x] verifier modification de tout
1. [x] date inferieur pour certain run/analyse verifier modification de tout sauf les run dont la date est suppérieure
vue all project :
1. [x] etendre un projet n'ayant pas de purge associé
1. [x] verifier que tous les runs/analyses sont bien etendu
1. [x] si la date est inférieure verifier que seulememnt les runs /analyses concernés sont etendus
1. [x] etendre un projet ayant une purge associée
1. [x] verifier que tous les runs/analyses sont bien etendu
1. [x] verifier que la purge est dans l'etat traitée et n'est plus dans la purge view.V3.1 - PurgeClaire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/29Modification du plugin nG6 typo3 pour utilisation sur php7 et typo3 V82018-08-28T14:15:29+02:00Gerald Salingerald.salin@inra.frModification du plugin nG6 typo3 pour utilisation sur php7 et typo3 V8copier/coller du mail ne fonctionne pas très bien.
mise de la procedure de mise à jour du plugin ng6 en PJ[procedure_mise_a_jour_ng6_typo3V8.pdf](/uploads/99473730dc54cc392fe051dc18a6f72e/procedure_mise_a_jour_ng6_typo3V8.pdf)[diffModifn...copier/coller du mail ne fonctionne pas très bien.
mise de la procedure de mise à jour du plugin ng6 en PJ[procedure_mise_a_jour_ng6_typo3V8.pdf](/uploads/99473730dc54cc392fe051dc18a6f72e/procedure_mise_a_jour_ng6_typo3V8.pdf)[diffModifnG6_Typo3_V8](/uploads/899e4ad5977dafc9bf0558339e03f93f/diffModifnG6_Typo3_V8)V3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/31add link and name to runs and analyses and projects in the purge email2019-09-10T11:58:20+02:00Gerald Salingerald.salin@inra.fradd link and name to runs and analyses and projects in the purge emaile.g.
Files impacted of:
- runs names: 314,315,316,317,735,723,1292,1414,1423,1530,1974,1983
- analyses ids: 1149,1151,1154,1150,1152,1153,1155,1159,1160,1156,1157,1158,3650,3652,3662,3634,3633,3623,3621,3636,3635,5835,5840,5852,5858,585...e.g.
Files impacted of:
- runs names: 314,315,316,317,735,723,1292,1414,1423,1530,1974,1983
- analyses ids: 1149,1151,1154,1150,1152,1153,1155,1159,1160,1156,1157,1158,3650,3652,3662,3634,3633,3623,3621,3636,3635,5835,5840,5852,5858,5855,5845,6309,6310,6311,6313,6314,6320,6321,6382,6381,6380,6379,6378,6383,6758,6757,6759,6763,8532,8539,8544,8547,8559,8568,8571,8582,158V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/34slurm, collectInsertSize error, calling Rscript from the path2018-08-28T14:14:39+02:00Gerald Salingerald.salin@inra.frslurm, collectInsertSize error, calling Rscript from the pathillumina_qc call the CollectInsertSizeMetrics from picard in the workflows/components/insertssizes.py component.
this jar call internally a Rscript command.
Rscript is not in the PATH, so the workflow is in error.
"module load system/R-...illumina_qc call the CollectInsertSizeMetrics from picard in the workflows/components/insertssizes.py component.
this jar call internally a Rscript command.
Rscript is not in the PATH, so the workflow is in error.
"module load system/R-3.4.3" should solve the problem, but we don't manage to exectute it
/tools/java/jre1.8.0_45/bin/java -Xmx2g -jar /usr/local/bioinfo/src/picard-tools/picard-2.18.2/picard.jar CollectInsertSizeMetrics HISTOGRAM_WIDTH=800 VALIDATION_STRINGENCY=LENIENT MINIMUM_PCT=0.01 HISTOGRAM_FILE=/work/ng6-test/jflow_mmanno/work/illumina_qc/wf000059/InsertsSizes_default/Demo_NoIndex_L001.pdf INPUT=/work/ng6-test/jflow_mmanno/work/illumina_qc/wf000059/BWA_default/Demo_NoIndex_L001.bam OUTPUT=/work/ng6-test/jflow_mmanno/work/illumina_qc/wf000059/InsertsSizes_default/Demo_NoIndex_L001.txt 2> /work/ng6-test/jflow_mmanno/work/illumina_qc/wf000059/InsertsSizes_default/Demo_NoIndex_L001.loghttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/35Test pipelines with slurm2019-08-29T14:10:39+02:00Gerald Salingerald.salin@inra.frTest pipelines with slurm* [x] illumina_qc
* #34 : need to add "load module system/R-3.4.3" to the .bashrc file of the user for this pipeline to work
* [x] illumina_rnaseq (without annotation which is buggy)
* [x] illumina_diversity_qc
* [x] gene_diversity
...* [x] illumina_qc
* #34 : need to add "load module system/R-3.4.3" to the .bashrc file of the user for this pipeline to work
* [x] illumina_rnaseq (without annotation which is buggy)
* [x] illumina_diversity_qc
* [x] gene_diversity
* [x] methylseq
* add "TrimGalore.modules = bioinfo/cutadapt-1.14-python-3.4.3" in [components] part of application.properties
* not working, waiting for the new pipeline developped by @celine.noirot with another workflow manager #56
* [x] illumina_matepair
* bug #55 with cutadapt output
* [x] ont_qc
* add "Trim_porechop.modules = compiler/gcc-7.2.0,bioinfo/Porechop-0.2.1" in [components] part of application.properties
* [x] radseq
* [x] download_url
* [x] download_symlink
* [x] download_archive
* [x] addrun
* [x] addproject
* [x] addfiles
* [x] addanalysis
* [x] phiX
* [x] quickstartV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/36unable to deploy a project in the download area2018-08-07T16:05:16+02:00Gerald Salingerald.salin@inra.frunable to deploy a project in the download area![image](/uploads/297600d69ec6285068dba1b06789174f/image.png)![image](/uploads/297600d69ec6285068dba1b06789174f/image.png)V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/38unable to delete runs or analyses from the ui2018-08-08T13:10:18+02:00Gerald Salingerald.salin@inra.frunable to delete runs or analyses from the uierror :
`08-08-18 08:07 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Call to undefined function ssh2_connect() | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/nG6_ui_slurm/class.tx_nG6_eid.php in line 158. Request...error :
`08-08-18 08:07 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Call to undefined function ssh2_connect() | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/nG6_ui_slurm/class.tx_nG6_eid.php in line 158. Requested URL: http://ng6-slurm.toulouse.inra.fr/ng6-mmanno/index.php?eID=tx_nG6&type=delete&del_level=analysis&data_folder=/work/ng6-test/jflow_mmanno/ng6&user_login=ng6-test&user_pwd=ng6L12*&user_id=4&ids=50717`V3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.fr2018-08-28https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/39Purge : Set Email From, in ng6 conf pi6 comme pour pi12019-08-30T10:09:24+02:00Celine NoirotPurge : Set Email From, in ng6 conf pi6 comme pour pi1![image](/uploads/59f957cf14964106c3b4e51914488f29/image.png)![image](/uploads/59f957cf14964106c3b4e51914488f29/image.png)V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/40upgrade jflow2019-08-29T14:26:17+02:00Celine Noirotupgrade jflowModules have been develop in jflow. To have this functionalities in ng6 , jflow must be upgrade.
After update test :
* [x] verifier les workflows avec des parametre exclude = True => convertir en rules.
* [x] tester les modules load
* [x...Modules have been develop in jflow. To have this functionalities in ng6 , jflow must be upgrade.
After update test :
* [x] verifier les workflows avec des parametre exclude = True => convertir en rules.
* [x] tester les modules load
* [x] possibility de parcourir les données du seveur ? A désactiver? ou a été codé dans ng6 ? Maintenant fonctionnelité dans jflow ==> Adapter
* [x] verifier qu’il n’y a plus dans la console d’erreur sur le zeroClipboard et fermer l’issue associée
* [x] migrer la doc la jflowV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/41users linked to a project ndo not appear2018-08-28T14:13:00+02:00Gerald Salingerald.salin@inra.frusers linked to a project ndo not appear![image](/uploads/67b486f36a6584c100cbd996358516ff/image.png)![image](/uploads/67b486f36a6584c100cbd996358516ff/image.png)V3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/42Upgrade jflow: load server file2018-08-09T17:15:33+02:00Celine NoirotUpgrade jflow: load server filecheck how ng6 upload server file.
This functionnality is now in jflowcheck how ng6 upload server file.
This functionnality is now in jflowV3.2 - SlurmCeline NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/43Fil d'ariane2018-08-09T12:53:19+02:00Celine NoirotFil d'arianeFil d'ariane perdu dans ng6-slurm : ajouter plugin ?
Au passage verifier les plugins installés sur ng6 prod?Fil d'ariane perdu dans ng6-slurm : ajouter plugin ?
Au passage verifier les plugins installés sur ng6 prod?V3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/44jflow upgrade: ng6workflow.py / illumina_qc2018-09-20T14:52:20+02:00Celine Noirotjflow upgrade: ng6workflow.py / illumina_qcPour avoir la liste de tout les workflows,
dans les classes ng6workflow.py les functions suivantes ont été ajoutée dans toutes les classes:
def get_description(self):
"""
Return the workflow description, has to be i...Pour avoir la liste de tout les workflows,
dans les classes ng6workflow.py les functions suivantes ont été ajoutée dans toutes les classes:
def get_description(self):
"""
Return the workflow description, has to be implemented by subclasses
"""
raise ( "BasicNG6Workflow")
def define_parameters(self, function="process"):
"""
Define the workflow parameters, has to be implemented by subclasses
"""
pass
Verifier la necessité de faire ca ?! On ne devrait pas avoir a le faire.V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/45server file : parse directory always present2018-09-10T15:02:55+02:00Celine Noirotserver file : parse directory always present![image](/uploads/940211fc09fa3b8b3c7114a833a7b1a1/image.png)
in jflow, must be desactivate when parameter browse_root_dir is not define.![image](/uploads/940211fc09fa3b8b3c7114a833a7b1a1/image.png)
in jflow, must be desactivate when parameter browse_root_dir is not define.V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/47illumina_rnaseq in error, whereas all is fine2018-08-13T10:42:58+02:00Gerald Salingerald.salin@inra.frillumina_rnaseq in error, whereas all is fineseems the jflow output for the rnaseq pipeline can't be done due to the following error, and the workflow has the status "Failed"
![image](/uploads/d0fdbdcdbe941cff1cc9e12ef0731d93/image.png)seems the jflow output for the rnaseq pipeline can't be done due to the following error, and the workflow has the status "Failed"
![image](/uploads/d0fdbdcdbe941cff1cc9e12ef0731d93/image.png)V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/48be able to set the debug level wanted2018-08-13T10:41:58+02:00Gerald Salingerald.salin@inra.frbe able to set the debug level wantedright now, the debug level is set to "logging.DEBUG" in src/jflwo/__init__.py and in src/ng6/__init__.py
add a config in application.properties to set this levelright now, the debug level is set to "logging.DEBUG" in src/jflwo/__init__.py and in src/ng6/__init__.py
add a config in application.properties to set this levelV3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/49make the width of the page larger2018-08-13T10:42:14+02:00Gerald Salingerald.salin@inra.frmake the width of the page largerchange from 990 to 1200px
to be able to view the data in tables more easilychange from 990 to 1200px
to be able to view the data in tables more easilyGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/50add slurm config parser in jflow2018-08-13T11:33:02+02:00Gerald Salingerald.salin@inra.fradd slurm config parser in jflowin component.py.__init__, add
elif type.lower() == "slurm" :
try:
self.__cpu = int(re.match( r'.*-c\s+(\w+)\s+(\d+)\s?.*', self.batch_options).group(2))
except: pass
try:
...in component.py.__init__, add
elif type.lower() == "slurm" :
try:
self.__cpu = int(re.match( r'.*-c\s+(\w+)\s+(\d+)\s?.*', self.batch_options).group(2))
except: pass
try:
self.__memory = re.match( r'.*--mem=(\d+\S+)\s?.*', self.batch_options).group(1)
except: passV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/51check mem and cpu config for slurm2018-09-17T13:12:44+02:00Gerald Salingerald.salin@inra.frcheck mem and cpu config for slurmMaxime doubted before leaving about the mem and cpu regepx?Maxime doubted before leaving about the mem and cpu regepx?V3.2 - SlurmMaxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/53add test data to ont_qc workflow2018-08-13T11:32:37+02:00Gerald Salingerald.salin@inra.fradd test data to ont_qc workflowhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/54in case of a casava workflow, add logs to the run2018-08-28T14:18:56+02:00Gerald Salingerald.salin@inra.frin case of a casava workflow, add logs to the runwe generate log files while creating casava directory
keep them along with the runs to get the required traceabilitywe generate log files while creating casava directory
keep them along with the runs to get the required traceabilityGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/56no output for methylationExtractor2018-10-16T17:19:32+02:00Gerald Salingerald.salin@inra.frno output for methylationExtractorseems removeduplicate component generates a truncated bam fil :
`Summarising genome-wide cytosine methylation report parameters:
===============================================================
Generating comprehensive genome-wide cytosi...seems removeduplicate component generates a truncated bam fil :
`Summarising genome-wide cytosine methylation report parameters:
===============================================================
Generating comprehensive genome-wide cytosine report
(output format: <Chromosome> <Position> <Strand> <count methylated> <count non-methylated> <C-context> <trinucleotide context> )
Reporting methylation for all cytosine contexts. Be aware that this will generate enormous files
Using zero-based start and 1-based end genomic coordinates (zero-based, half-open; user-defined)
Genome folder was specified as /work/ng6-test/jflow_gsalin/work/methylseq/wf000069/BismarkGenomePreparation_default/
Checking file >>/work/ng6-test/jflow_gsalin/work/methylseq/wf000069/RemoveDuplicate_paired/Histone-1-3_clean.bam<< for signs of file truncation...
Captured error message: '[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes'
[ERROR] The file appears to be truncated, please ensure that there were no errors while copying the file!!! Exiting...
`
and then, no data loaded in the database
![image](/uploads/54888793e98cfb2c0651d64e496e1a7e/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/57[illumina_diversity_qc] no blastn on genologin2018-12-20T18:26:55+01:00Gerald Salingerald.salin@inra.fr[illumina_diversity_qc] no blastn on genologinwith module load bioinfo/blast-2.2.26
we can only access blastall blastclust blastpgpwith module load bioinfo/blast-2.2.26
we can only access blastall blastclust blastpgphttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/58BasicAnalysis Analysis has no template2018-08-14T09:39:48+02:00Gerald Salingerald.salin@inra.frBasicAnalysis Analysis has no templateerror in typo3 while displayng the basicnalysis analysis : no template found
a template with name BasicAnalyze.tpl was foudn, renamed iterror in typo3 while displayng the basicnalysis analysis : no template found
a template with name BasicAnalyze.tpl was foudn, renamed itV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/59Update project description from web site doesn't work2018-08-14T13:39:36+02:00Gerald Salingerald.salin@inra.frUpdate project description from web site doesn't workerror in the logs : `tx_nG6_eid update_db_field
14-08-18 08:00 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Too few arguments to function tx_nG6_db::update_field(), 4 passed in /save/ng6-test/src/ng6-git-gsalin/ui/nG6/clas...error in the logs : `tx_nG6_eid update_db_field
14-08-18 08:00 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Too few arguments to function tx_nG6_db::update_field(), 4 passed in /save/ng6-test/src/ng6-git-gsalin/ui/nG6/class.tx_nG6_eid.php on line 266 and exactly 5 expected | ArgumentCountError thrown in file /save/ng6-test/src/ng6-git-gsalin/ui/nG6/lib/class.tx_nG6_db.php in line 47. Requested URL: http://ng6-slurm.toulouse.inra.fr/ng6-mmanno/index.php?eID=tx_nG6&type=update_db_field&table=tx_nG6_project&field=description
`https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/60creating a user soes not work2018-08-14T13:39:36+02:00Gerald Salingerald.salin@inra.frcreating a user soes not worklog :
` tx_nG6_eid add_user
14-08-18 08:32 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Class 'tx_saltedpasswords_salts_factory' not found | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/ui/nG6/lib/class.tx_nG6_u...log :
` tx_nG6_eid add_user
14-08-18 08:32 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Class 'tx_saltedpasswords_salts_factory' not found | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/ui/nG6/lib/class.tx_nG6_utils.php in line 243. Requested URL: http://ng6-slurm.toulouse.inra.fr/ng6-mmanno/index.php?eID=tx_nG6&type=add_user&username=roboyer&first_name=Rox%C3%A9ne&last_name=Boyer&password=tfGdFAn4Kr&email=gerald.salin@inra.fr&creator=4&title=GENO&organism=INRA&location=Toulouse&project_id=88&right=0&pid=2&add_user_email=Dear%20%23%23%23USER_FIRST_NAME%23%23%23%20%23%23%23USER_LAST_NAME%23%23%23%2C%0AYou%20have%20now%20acccess%20to%20the%20%23%23%23PROJECT_NAME%23%23%23%20project%20%28%23%23%23PROJECT_DESCRIPTION%23%23%23%29%20accessible%20once%20logged%20in%20by%20the%20following%20url%3A%20%23%23%23PROJECT_LINK%23%23%23%0AThe%20NG6%20team%0APS%3A%20this%20is%20an%20automatic%20e-mail%20message%20generated%20by%20the%20NG6%20system.%20Please%20DO%20NOT%20RESPOND%20to%20this%20e-mail%20because%20the%20mail%20box%20is%20unattended.&add_user_title=[NG6]%20You%20have%20been%20added%20to%20a%20project&create_user_email=Dear%20%23%23%23USER_FIRST_NAME%23%23%23%20%23%23%23USER_LAST_NAME%23%23%23%2C%0APlease%20find%20bellow%20your%20login/password%20required%20to%20log%20into%20the%20NG6%20system%20%28%23%23%23PROJECT_LINK%23%23%23%29%3A%20%0A%20%20%20-%20login%3A%20%23%23%23USER_LOGIN%23%23%23%0A%20%20%20-%20password%3A%20%23%23%23USER_PASSWORD%23%23%23%0AThe%20NG6%20team%0APS%3A%20this%20is%20an%20automatic%20e-mail%20message%20generated%20by%20the%20NG6%20system.%20Please%20DO%20NOT%20RESPOND%20to%20this%20e-mail%20because%20the%20mail%20box%20is%20unattended.&create_user_title=[NG6]%20Account%20creation&from_email=support@ng6.toulouse.inra.fr&project_url=http%3A//ng6-slurm.toulouse.inra.fr/ng6-mmanno/index.php%3Fid%3D55%26tx_nG6_pi1%255Bproject_id%255D%3D88&send_an_email=true
`https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/61update user form, data is not loaded2018-08-14T13:39:42+02:00Gerald Salingerald.salin@inra.frupdate user form, data is not loaded![image](/uploads/7614712925c7139278b1a0d19068bc78/image.png)![image](/uploads/7614712925c7139278b1a0d19068bc78/image.png)V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/62no let users with updatable_password = 0 reset their password2018-08-14T13:39:50+02:00Gerald Salingerald.salin@inra.frno let users with updatable_password = 0 reset their passwordsynchronized users should not be able to reset their passaord in ng6
cf fe_users.updatable_passwordsynchronized users should not be able to reset their passaord in ng6
cf fe_users.updatable_passwordV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/64Test pipelines with slurm with real data2018-12-20T18:27:43+01:00Maxime MannoTest pipelines with slurm with real data* [x] illumina_qc
* [x] illumina_rnaseq (without annotation which is buggy)
* [x] illumina_diversity_qc
* [ ] gene_diversity
* [ ] illumina_matepair
* [x] ont_qc
* [ ] radseq
* [x] download_url
* [x] download_symlink
* [x] down...* [x] illumina_qc
* [x] illumina_rnaseq (without annotation which is buggy)
* [x] illumina_diversity_qc
* [ ] gene_diversity
* [ ] illumina_matepair
* [x] ont_qc
* [ ] radseq
* [x] download_url
* [x] download_symlink
* [x] download_archiveV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/65workflows monitoring not working on ng62018-10-22T13:10:03+02:00Gerald Salingerald.salin@inra.frworkflows monitoring not working on ng6connecte as admin on ng6
go to ADMINISTRATIOn > workflows monitoring
after few seconds, seems jflow server is not reachable....whereas the workflow status on the runs is working well....
![image](/uploads/67802eca658b20942873a2fbda5562d1...connecte as admin on ng6
go to ADMINISTRATIOn > workflows monitoring
after few seconds, seems jflow server is not reachable....whereas the workflow status on the runs is working well....
![image](/uploads/67802eca658b20942873a2fbda5562d1/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/66add a way to align illumina reads against a subset of reads2018-09-06T13:56:45+02:00Gerald Salingerald.salin@inra.fradd a way to align illumina reads against a subset of readswith novaseq/hiseq data, the alignment step can be very time consuming.
think of a way to only align a subset of the reads, giving a workflow argument, e.g. --align-subset-reads
some source code is available in the extract_random_seq f...with novaseq/hiseq data, the alignment step can be very time consuming.
think of a way to only align a subset of the reads, giving a workflow argument, e.g. --align-subset-reads
some source code is available in the extract_random_seq function of SubSetAssignation componentV3.2 - SlurmClaire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/67jflow server not reachable with https2018-09-17T09:30:12+02:00Gerald Salingerald.salin@inra.frjflow server not reachable with httpsaccessing ng6-slurm with https make the jflow server not accessible due to security reason (accessing http://ng6-slurm:8080)
changing to https://ng6-slurm:8080 does not solve the problem...another one is raisedaccessing ng6-slurm with https make the jflow server not accessible due to security reason (accessing http://ng6-slurm:8080)
changing to https://ng6-slurm:8080 does not solve the problem...another one is raisedV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/68add md5sum for raw data in all pipelines2018-09-07T12:07:23+02:00Gerald Salingerald.salin@inra.fradd md5sum for raw data in all pipelinesV3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/69Add a super admin ng6 who can see all projects2019-09-27T13:14:15+02:00Claire KuchlyAdd a super admin ng6 who can see all projectshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/70enhance disk usage with concatenatefilesgroups2018-09-17T09:30:51+02:00Gerald Salingerald.salin@inra.frenhance disk usage with concatenatefilesgroupsto limit the disk usage in illumina pipelines, do not store the output of ConcatenateFilesGroups component in its out output folder, but rather in the run.get_work_directory() folder.
saves a copy step (originally done in AddRawFiles com...to limit the disk usage in illumina pipelines, do not store the output of ConcatenateFilesGroups component in its out output folder, but rather in the run.get_work_directory() folder.
saves a copy step (originally done in AddRawFiles componenent) and limit the disk usage (can represent few hundreds of Gb for novaseq runs)V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/72purge error if directory has a lot of files and folders2018-09-17T09:19:33+02:00Gerald Salingerald.salin@inra.frpurge error if directory has a lot of files and foldersreplace ls $dir | xargs rm -f with find . -exec rm -f {}replace ls $dir | xargs rm -f with find . -exec rm -f {}V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/73problem with gzip 1.5 and 1.9 on the new cluster2018-09-17T09:17:48+02:00Gerald Salingerald.salin@inra.frproblem with gzip 1.5 and 1.9 on the new clusterafter some hours of debugging, we found the 1.5 and 1.9 version of gzip implies problem with the server load. huge peaks (> 1000 of load average) were observed and reproduced in the case of massive jobs using system gzip (on the new slur...after some hours of debugging, we found the 1.5 and 1.9 version of gzip implies problem with the server load. huge peaks (> 1000 of load average) were observed and reproduced in the case of massive jobs using system gzip (on the new slurm cluster).
It was not observed with the sge cluster, using version 1.3.
installing 1.3 gzip version on the new cluster solved the problem, but we have to use get_exec_path("gzip") in the components instead of gzip command lineV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/74ONT-QC bug with l502019-01-04T17:45:19+01:00Maxime MannoONT-QC bug with l50we removed the L50 from the R script, and the workflow need this informationwe removed the L50 from the R script, and the workflow need this informationV3.2.2Maxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/75bug in purge management2018-10-01T13:04:43+02:00Gerald Salingerald.salin@inra.frbug in purge managementpurge management doe not work with new versio of typo3purge management doe not work with new versio of typo3V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/76Admin > Statisctis does not work2018-10-01T13:04:35+02:00Gerald Salingerald.salin@inra.frAdmin > Statisctis does not work> 01-10-18 10:54 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Call to undefined function split() | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/ui/nG6/class.tx_nG6_eid.php in line 808. Requested URL: http://ng6-s...> 01-10-18 10:54 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Call to undefined function split() | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/ui/nG6/class.tx_nG6_eid.php in line 808. Requested URL: http://ng6-slurm.toulouse.inra.fr/ng6-mmanno/index.php?eID=tx_nG6&type=project_distribution&by=title&role=create_user&values=BIA,Bioinfo%20GENOTOULV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/77Process mail demands : delay exceed always to "no"2018-10-01T14:30:06+02:00Gerald Salingerald.salin@inra.frProcess mail demands : delay exceed always to "no"whereas we know some have delay exceededwhereas we know some have delay exceededV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/78"Process mail demands" does not work with new version of typo32018-10-01T14:30:00+02:00Gerald Salingerald.salin@inra.fr"Process mail demands" does not work with new version of typo3no records found
delay_purge is not set in the ajax requestno records found
delay_purge is not set in the ajax requestV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/79bug sending mail for purge demand while user disconnected2018-10-01T19:35:52+02:00Gerald Salingerald.salin@inra.frbug sending mail for purge demand while user disconnectedafter a while, the user is dosconnected from the interface.
we can still send mail for purge management
but the purge_deman_id is 0...after a while, the user is dosconnected from the interface.
we can still send mail for purge management
but the purge_deman_id is 0...V3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/80methyl_seq - template Bismark error displaying2018-10-16T17:19:32+02:00Gerald Salingerald.salin@inra.frmethyl_seq - template Bismark error displaying08-10-18 11:09 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Too few arguments to function smarty_modifier_get_description(), 1 passed in /save/ng6-test/src/ng6-git-gsalin/ui/nG6/res/smarty/templates_c/320094d0cb490e0a640ff2...08-10-18 11:09 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Too few arguments to function smarty_modifier_get_description(), 1 passed in /save/ng6-test/src/ng6-git-gsalin/ui/nG6/res/smarty/templates_c/320094d0cb490e0a640ff26100dfbb61200023b2.file.Bismark.tpl.php on line 159 and exactly 2 expected | ArgumentCountError thrown in file /save/ng6-test/src/ng6-git-gsalin/ui/nG6/res/smarty/libs/plugins/modifier.get_description.php in line 177. Requested URL: http://ng6-slurm.toulouse.inra.fr/ng6-mmanno/index.php?id=55&tx_nG6_pi1%5Banalyze_id%5D=55299&tx_nG6_pi1%5Bproject_id%5D=7&tx_nG6_pi1%5Brun_id%5D=14200
![image](/uploads/1d71ea9dd0f07714692a5d1832293e27/image.png)V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/82Error downloading data with symlink and url2018-10-22T12:59:40+02:00Gerald Salingerald.salin@inra.frError downloading data with symlink and urlcan select data to download bug jflow workflow failed
* for symlink : trying to connect with ssh, but errors in keys in knownhosts. Deleting keys regarding ng6-slurm and 147.99.107.64 solved the problem
* for url : tries to open in the ...can select data to download bug jflow workflow failed
* for symlink : trying to connect with ssh, but errors in keys in knownhosts. Deleting keys regarding ng6-slurm and 147.99.107.64 solved the problem
* for url : tries to open in the browser a url prefix with http instead of httpsV3.2.1https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/84no template for BasicAnalyse2018-10-22T12:59:26+02:00Gerald Salingerald.salin@inra.frno template for BasicAnalysecf Maria.
The template does not exist
copy from BasicAnalysis.tplcf Maria.
The template does not exist
copy from BasicAnalysis.tplV3.2.1https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/85Error addanalysis from graphic interface (firefox)2019-11-12T13:44:01+01:00Maxime MannoError addanalysis from graphic interface (firefox)I tried to launch a new analysis from the interface.
The window poped, but nothing append when I clicked on the "Run" button.
![image](/uploads/d4a6c90188f954c6d4f32c4c562b3a78/image.png)I tried to launch a new analysis from the interface.
The window poped, but nothing append when I clicked on the "Run" button.
![image](/uploads/d4a6c90188f954c6d4f32c4c562b3a78/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/86downloadsymlink, special characters2019-09-27T09:11:39+02:00Gerald Salingerald.salin@inra.frdownloadsymlink, special characterssome special characters are included in run names (e.g. /, (, )), introducing a bug in the download step (at least creating symlinks)some special characters are included in run names (e.g. /, (, )), introducing a bug in the download step (at least creating symlinks)V3.2.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/88sending email from update user window does not work2018-12-20T18:05:34+01:00Gerald Salingerald.salin@inra.frsending email from update user window does not workno email is sent, no error ion the javascript console....no email is sent, no error ion the javascript console....V3.2.1https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/89run date in tx_ng6_run is wrong2019-02-11T18:36:40+01:00Gerald Salingerald.salin@inra.frrun date in tx_ng6_run is wrongrunning a workflow with a run date D will be displayed D-1dayrunning a workflow with a run date D will be displayed D-1dayV3.2.3https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/90Lost of Porechop version2019-02-11T17:24:49+01:00Maxime MannoLost of Porechop version![2018-11-05_100514](/uploads/c5a7c2dc48cd73b91c20252710124b20/2018-11-05_100514.png)![2018-11-05_100514](/uploads/c5a7c2dc48cd73b91c20252710124b20/2018-11-05_100514.png)V3.2.3Maxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/95Ajout d'analyse à un projet2019-10-21T11:52:25+02:00Philippe BardouAjout d'analyse à un projetImpossible d'ajouter une analyse à un projet via l'interface...
![Sélection_254](/uploads/c87f171a96f549d097dac188e11c7a20/Sélection_254.png)Impossible d'ajouter une analyse à un projet via l'interface...
![Sélection_254](/uploads/c87f171a96f549d097dac188e11c7a20/Sélection_254.png)V3.2.5.2Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/96Extra space between md5 and file name in md5sum.txt2018-12-14T18:44:42+01:00Roxane BoyerExtra space between md5 and file name in md5sum.txtThere are 3 spaces instead of 2 in the md5sum file :
```
3efa244db27854b63b740a31e16e85e6 ESE00019_AAGTCCAA-TACTCATA-AH2MC2BBXY_L002_R1.fastq.gz
ff0510e4615e75a5b5cccac402262e88 ESE00107_GTTCCAAT-GCAGAATT-AH2MC2BBXY_L002_R2.fastq.gz...There are 3 spaces instead of 2 in the md5sum file :
```
3efa244db27854b63b740a31e16e85e6 ESE00019_AAGTCCAA-TACTCATA-AH2MC2BBXY_L002_R1.fastq.gz
ff0510e4615e75a5b5cccac402262e88 ESE00107_GTTCCAAT-GCAGAATT-AH2MC2BBXY_L002_R2.fastq.gz
```
md5sum -c md5sum.txt
md5sum: PLF7_GCCGCG-C28GH_L001_R1.fastq.gz: Aucun fichier ou dossier de ce type
PLF7_GCCGCG-C28GH_L001_R1.fastq.gz : Échec d'ouverture ou de lecture.Roxane BoyerRoxane Boyerhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/97The makeflow command for md5sum is too long for the cluster2019-01-04T11:37:46+01:00Audrey GibertThe makeflow command for md5sum is too long for the clusterThe command for md5sum sent by Makeflow contains the paths of all samples. In 2 of our workflows, there are 672 samples, that is far too long to be accepted for the cluster.
>>>
2018/12/04 12:47:55.67 makeflow[46806] notice: job submis...The command for md5sum sent by Makeflow contains the paths of all samples. In 2 of our workflows, there are 672 samples, that is far too long to be accepted for the cluster.
>>>
2018/12/04 12:47:55.67 makeflow[46806] notice: job submission failed: no output from slurm
couldn't submit batch job, still trying...
>>>V3.2.1Audrey GibertAudrey Gibert2018-12-14https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/98update user not working2018-12-20T18:24:47+01:00Gerald Salingerald.salin@inra.frupdate user not working![image](/uploads/dcc565f70a9e98cc10254b37cca1ac02/image.png)
![image](/uploads/1c0595fae6c3f7a384db569c20874537/image.png)![image](/uploads/dcc565f70a9e98cc10254b37cca1ac02/image.png)
![image](/uploads/1c0595fae6c3f7a384db569c20874537/image.png)V3.2.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/99delete data for a purge demand sometimes does not work2018-12-20T18:03:53+01:00Gerald Salingerald.salin@inra.frdelete data for a purge demand sometimes does not work![image](/uploads/b473a3c59c2274e805d8cf0d8c714dfb/image.png)
the interface is freezed and nothing happens
in case the folder contains a lot of files![image](/uploads/b473a3c59c2274e805d8cf0d8c714dfb/image.png)
the interface is freezed and nothing happens
in case the folder contains a lot of filesV3.2.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/100Read and bases count are sometimes false2019-01-04T11:39:15+01:00Gerald Salingerald.salin@inra.frRead and bases count are sometimes falseSince the last ng6 update, the reads ans bases counts displayed for the runs are false.
AddRawFiles was modified to manage huge number of sample files (#97).
It seems the function counting the reads and bases is run too early.Since the last ng6 update, the reads ans bases counts displayed for the runs are false.
AddRawFiles was modified to manage huge number of sample files (#97).
It seems the function counting the reads and bases is run too early.V3.2.2Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.fr2019-01-10https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/101adapt visualisation of ONT versions (gridion and promethion)2019-01-15T14:01:26+01:00Maxime Mannoadapt visualisation of ONT versions (gridion and promethion)The scripts parse-version for ONT gridion and promethion have been modified. We need to update and adapt the visualisationThe scripts parse-version for ONT gridion and promethion have been modified. We need to update and adapt the visualisationV3.2.3Maxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/102Amélioration de la FAQ2019-08-02T09:42:35+02:00Roxane BoyerAmélioration de la FAQL'onglet FAQ de ng6 devrait peut-être faire peau neuve.
Notamment en ce qui concerne les adaptateurs des séquences Illumina, les informations présentées portent à confusion, et les index Illumina semblent avoir changé (une base en plus a...L'onglet FAQ de ng6 devrait peut-être faire peau neuve.
Notamment en ce qui concerne les adaptateurs des séquences Illumina, les informations présentées portent à confusion, et les index Illumina semblent avoir changé (une base en plus au début et à la fin de la séquence).Roxane BoyerRoxane Boyerhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/103ONT - Bug with gzipped input fastq file2019-06-11T15:13:44+02:00Maxime MannoONT - Bug with gzipped input fastq fileThe new automatised pipeline launch the ont_qc with a gzipped input fastq file, and the analysis failedThe new automatised pipeline launch the ont_qc with a gzipped input fastq file, and the analysis failedV3.2.4Maxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/104loadin icon go on display while an error is raised2019-08-30T13:22:58+02:00Roxane Boyerloadin icon go on display while an error is raisedwhile downloading data with 'symlink', even if an error is raised the message is not displayed and the user has to wait :
![image](/uploads/fb5a7e6c8e7dac37eaac89bd231ce4da/image.png)while downloading data with 'symlink', even if an error is raised the message is not displayed and the user has to wait :
![image](/uploads/fb5a7e6c8e7dac37eaac89bd231ce4da/image.png)V3.2.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/106Configuring different storage space2019-09-06T17:11:30+02:00Celine NoirotConfiguring different storage spaceAdd a workflow parameter to store raw data and processed results in different storage space depending on project (ng6 or seqoccin or labs ?)
Warn:
- Quality control must be keep even if storage space is deleted, must be store in in ng6 ...Add a workflow parameter to store raw data and processed results in different storage space depending on project (ng6 or seqoccin or labs ?)
Warn:
- Quality control must be keep even if storage space is deleted, must be store in in ng6 space ?
- Think to handle data purge (do not delete if it's in rented space), check administration purge.
Code :
- web interface:
- storage info is stored in application.properties and db
- file eg: run_view.tmpl use relative path : `{$link=(('fileadmin'|cat:$runs[key($runs)].directory)|cat:'/')|cat:$file}`
- statistics storage space: check and define how to handle those spaces
- jflow code :
- application.properties will contain new section for storage space defined py project/lab name
- the storage space name is linked to a project
- functions get_save_directory() ... has to be adapted
- db must contain storage space name
- filesystem
- web interface: create symbolic link in fileadmin directory on different spaces
- adding new storage space, create symbolic link (look at how is done in jflow for [storage] section
- only project table has new attribute storage spaceV3.2.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/107handle limit storage period/date depending on storage space parameter2019-08-30T17:25:07+02:00Celine Noirothandle limit storage period/date depending on storage space parameterData storage period depend on kind of project (eg seqoccin), this should be a workflow parameter.
To ensure the user do not set period value, the period has to be set in application.properties.
- For rented space validate how to set en...Data storage period depend on kind of project (eg seqoccin), this should be a workflow parameter.
To ensure the user do not set period value, the period has to be set in application.properties.
- For rented space validate how to set end of storage date
![image](/uploads/dcb383c6dea62c2d9ededd61a85fe433/image.png)
- end of storage date could depend on a date or a period depending on storage space name
```
[space_default]
retention_period = 3m
path=/ng6
[space_default_old]
retention_period = 2y
path=/ng6
[space_seqoc]
# pour un espace donnee : deux parametre exclusif retention_date != retention_period
retention_date=12/03/2021
#retention_period = 2year
path=/seqoc
```
- Add retention_time parameter in application.properties.example
V3.2.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/110handle several data space2019-09-06T17:11:30+02:00Celine Noirothandle several data spaceFor seqOccIn project need to handle several project space.
To do:
* [x] handle different space when add run/analyse/project ...
* [x] handle different retention date thanks to space_id
* [x] handle spaces in download plugin
Validatio...For seqOccIn project need to handle several project space.
To do:
* [x] handle different space when add run/analyse/project ...
* [x] handle different retention date thanks to space_id
* [x] handle spaces in download plugin
Validation to be checked :
* [x] addproject with default space
* [x] addproject with specific space
* [x] addrun to a project with a specific space -> run data are in space ?
* [x] addanalysis to a project with a specific space -> analysis data are in space ?
* [x] addanalysis to a run with a specific space -> analysis data are in space ?V3.2.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/111[ont-qc] Adding logs to ont-qc analysis2019-07-23T09:22:06+02:00Maxime Manno[ont-qc] Adding logs to ont-qc analysis#### It should have log files from :
* [x] the Merkaat pipeline log
* [x] final status run summary log#### It should have log files from :
* [x] the Merkaat pipeline log
* [x] final status run summary logV3.2.4Maxime MannoMaxime Manno2019-07-31https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/112[ont-qc] Adding new analysis : Demultiplex Stat for ONT2021-03-25T13:39:09+01:00Maxime Manno[ont-qc] Adding new analysis : Demultiplex Stat for ONT#### We need to change the current demultiplex stat analysis management : :metal:
**What will change ?** replacement of porechop by Qcat, creation of a new analysis
* [x] Create new component
* [x] Create new template
* [x] Add seqki...#### We need to change the current demultiplex stat analysis management : :metal:
**What will change ?** replacement of porechop by Qcat, creation of a new analysis
* [x] Create new component
* [x] Create new template
* [x] Add seqkit stats logs for all the samples (included the unmappaed files)
* [x] Add fastq files only for the barcodes added into the pool
* [x] Add Qcat and Seqkit path and oprions into the application.propertiesV4 - MaintenanceMaxime MannoMaxime Manno2019-08-31https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/113[ont_qc] Add N90 and 5 longest reads informations2019-07-24T09:39:10+02:00Maxime Manno[ont_qc] Add N90 and 5 longest reads informationsV3.2.3.1Maxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/114The analyse data do not end up in the right directory2019-08-06T15:25:20+02:00Romain ThervilleThe analyse data do not end up in the right directoryAfter an analyze run, some files are in the right directory, but most are not.
REPDEV project, Run ont_qc (30-07-19) :
http://ng6-test.toulouse.inra.fr/fileadmin/data_seqoccin/run/db3b81bfe/md5sum.txt
http://ng6-test.toulouse.inra.fr/f...After an analyze run, some files are in the right directory, but most are not.
REPDEV project, Run ont_qc (30-07-19) :
http://ng6-test.toulouse.inra.fr/fileadmin/data_seqoccin/run/db3b81bfe/md5sum.txt
http://ng6-test.toulouse.inra.fr/fileadmin/data_seqoccin/run/db3b81bfe/test.fastq.gz
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/RunStats_archive.tar.gz
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_cumulyield.png
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_channelbases.png
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_channelreads.png
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_distribquality.png
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_distriblength_bybases.png
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample.sequencing_summary.txt
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_seqrate.png
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_distriblength.pngV3.2.4Romain ThervilleRomain Therville2019-08-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/116Custom message for purged data2019-08-30T13:23:46+02:00Romain ThervilleCustom message for purged dataWe need another message, replacing "Results folder not synchronized yet... " when the data has been purged.We need another message, replacing "Results folder not synchronized yet... " when the data has been purged.V3.2.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/117Add duplication stat to alignmentStat analyze2019-08-30T13:23:44+02:00Claire KuchlyAdd duplication stat to alignmentStat analyzeV3.2.5Natacha FaivreNatacha Faivrehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/118create a documentation to explain how to add storage space2022-10-06T21:22:15+02:00Gerald Salingerald.salin@inra.frcreate a documentation to explain how to add storage spaceV3.4https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/119add the run/analysis status in the summary table2020-01-10T10:28:33+01:00Gerald Salingerald.salin@inra.fradd the run/analysis status in the summary table![image](/uploads/f8e0cf2161a5f2efae6dc3a467633997/image.png)
@celine.noirot @ckuchly what do you think about it?
this way, the user has directly the information regarding the purge state![image](/uploads/f8e0cf2161a5f2efae6dc3a467633997/image.png)
@celine.noirot @ckuchly what do you think about it?
this way, the user has directly the information regarding the purge stateV3.2.6https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/120add the retention policy to project view2020-01-22T11:28:03+01:00Gerald Salingerald.salin@inra.fradd the retention policy to project viewV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/121purge email configuration2019-10-24T09:38:56+02:00Gerald Salingerald.salin@inra.frpurge email configurationcheck the recipient field, I think there were multiple copies of support.ng6 in the last purge session.check the recipient field, I think there were multiple copies of support.ng6 in the last purge session.V3.2.6Romain ThervilleRomain Therville