ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2019-09-10T11:58:20+02:00https://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/32add manual for purging data2018-08-02T14:57:31+02:00Gerald Salingerald.salin@inra.fradd manual for purging dataV4 - MaintenanceClaire KuchlyClaire Kuchlyhttps://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/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/233add support to typo3 v112022-10-07T17:07:41+02:00Gerald Salingerald.salin@inra.fradd support to typo3 v11typo3 v10 is maintained until beginning of 2023.
typo3 V11 is maintained until october 2024.
https://typo3.org/cms/roadmap/maintenance-releases
update nG6 extension source code to be compatible with typo3 V11typo3 v10 is maintained until beginning of 2023.
typo3 V11 is maintained until october 2024.
https://typo3.org/cms/roadmap/maintenance-releases
update nG6 extension source code to be compatible with typo3 V11V3.4Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/148Add the duplicat rate without alignment in all illumina workflow2022-12-16T16:21:27+01:00Claire KuchlyAdd the duplicat rate without alignment in all illumina workflowAll the pipeline must have the duplication rate of all the samples : it must be a mandatory analysis.
Add to ng6workflow.pyAll the pipeline must have the duplication rate of all the samples : it must be a mandatory analysis.
Add to ng6workflow.pyClaire KuchlyClaire Kuchly2019-12-31https://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/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/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/185Adding a warning to prevent users from lauching 20+ direct url downloads at t...2022-12-16T16:21:28+01:00Romain ThervilleAdding a warning to prevent users from lauching 20+ direct url downloads at the same timeThis morning, the nG6 virtual server had a 40+ load average.
The cause seems to be a big number of direct downloads (urldownload method) from a single user.
We should add a warning like:
"If you need to recover a large number of files, ...This morning, the nG6 virtual server had a 40+ load average.
The cause seems to be a big number of direct downloads (urldownload method) from a single user.
We should add a warning like:
"If you need to recover a large number of files, please copy the links and only launch 2 to 3 downloads at the same time (Either with the wget command, or with your web browser). Thank you."Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/246allow to create symlinks on genobioinfo2023-11-14T05:38:23+01:00Gerald Salingerald.salin@inra.frallow to create symlinks on genobioinfoallow to choose the server where to create the cymbolic links (genologin pr genobioinfo)allow to choose the server where to create the cymbolic links (genologin pr genobioinfo)V3.4.3Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/200allow to display all entries of a datatable in an analysis2021-04-28T16:30:55+02:00Gerald Salingerald.salin@inra.frallow to display all entries of a datatable in an analysisV3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://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/122changes to NG6's database structure should appear in a .sql file2019-10-14T16:19:52+02:00Romain Thervillechanges to NG6's database structure should appear in a .sql fileWe should change the MO and check that all changes to the databse structure do appear in /bin/ng6_database.sql (Or find a better way not to miss those changes).We should change the MO and check that all changes to the databse structure do appear in /bin/ng6_database.sql (Or find a better way not to miss those changes).V3.2.6https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/71clean pipeline outputs if succeeded2018-09-06T15:09:01+02:00Gerald Salingerald.salin@inra.frclean pipeline outputs if succeededallow the deletion of files in the worflow output dir to save dik spaceallow the deletion of files in the worflow output dir to save dik spaceV4 - Maintenancehttps://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/33correct source indent (tabs/white space) for all files2019-08-29T14:11:18+02:00Gerald Salingerald.salin@inra.frcorrect source indent (tabs/white space) for all filesV4 - MaintenanceRomain ThervilleRomain Thervillehttps://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/128Discard some email adress from purge email.2019-09-20T10:27:40+02:00Celine NoirotDiscard some email adress from purge email.Add a list a emails address to discard from purge email.
To be configure as "email_from"
Eg:
plugin.tx_nG6_pi6.email_to_discard = ctd@inra.fr,ng6-support@inra.fr
Remove thoses email from the list of destinator of the emailAdd a list a emails address to discard from purge email.
To be configure as "email_from"
Eg:
plugin.tx_nG6_pi6.email_to_discard = ctd@inra.fr,ng6-support@inra.fr
Remove thoses email from the list of destinator of the emailV3.2.6Romain ThervilleRomain Thervillehttps://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 - Slurm