ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2022-05-11T10:29:03+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/227[ont_qc] Change end of sequencing report file2022-05-11T10:29:03+02:00Jules Sabban[ont_qc] Change end of sequencing report fileNanopore has change the end of sequencing report file format from PDF to HTMLNanopore has change the end of sequencing report file format from PDF to HTMLV3.3Jules SabbanJules Sabbanhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/225[Purge] Do not purge the hidden runs and analyses2022-04-26T14:00:23+02:00Romain Therville[Purge] Do not purge the hidden runs and analysesHidden runs and analyzes should be removed from the purge process.
(They will be removed semi-manualy.)Hidden runs and analyzes should be removed from the purge process.
(They will be removed semi-manualy.)V3.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/224Project page : Remove the "Raw data and analysis results use xxx"2022-04-26T14:00:49+02:00Romain ThervilleProject page : Remove the "Raw data and analysis results use xxx"This part of the page is computed on the fly, and does not exclude hidden elements. It can be removed.This part of the page is computed on the fly, and does not exclude hidden elements. It can be removed.V3.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/214add a link to the reinit password interface2021-10-12T08:47:06+02:00Gerald Salingerald.salin@inra.fradd a link to the reinit password interfaceV3.3Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/213upgrade to typo3 v102021-10-12T08:47:15+02:00Gerald Salingerald.salin@inra.frupgrade to typo3 v10V3.3Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/204smarty deprecation warnins2021-05-04T11:48:23+02:00Gerald Salingerald.salin@inra.frsmarty deprecation warninsin backend error viewer :
Core: Error handler (FE): PHP Runtime Deprecation Notice: Function create_function() is deprecated in /usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8/ui/nG6/res/smarty/libs/Smarty.class.php line 742
Core: Er...in backend error viewer :
Core: Error handler (FE): PHP Runtime Deprecation Notice: Function create_function() is deprecated in /usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8/ui/nG6/res/smarty/libs/Smarty.class.php line 742
Core: Error handler (FE): PHP User Notice: function call 'assign_by_ref' is unknown or deprecated, use 'assignByRef' in /usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8/ui/nG6/res/smarty/libs/sysplugins/smarty_internal_data.php line 79V3.2.8.1Gerald 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/199update links2021-04-28T14:46:19+02:00Gerald Salingerald.salin@inra.frupdate linkswith the new typo3 version, links are human readable :
change the index.php?id=XX&WWWWWWW with the corresponding page slug in the source
and have to create redirects in apache for those who access the old linkswith the new typo3 version, links are human readable :
change the index.php?id=XX&WWWWWWW with the corresponding page slug in the source
and have to create redirects in apache for those who access the old linksV3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/198upgrade to run under typo3 v92021-04-28T18:58:29+02:00Gerald Salingerald.salin@inra.frupgrade to run under typo3 v9V3.2.8Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/196mail method : some people does not receive mails sent by ng6-slurm2021-04-28T18:59:38+02:00Gerald Salingerald.salin@inra.frmail method : some people does not receive mails sent by ng6-slurmhttps://ariane.inrae.fr/block/?id=ariane_ticket&table=incident&sys_id=96e56e891bdfec102c571176bd4bcb76https://ariane.inrae.fr/block/?id=ariane_ticket&table=incident&sys_id=96e56e891bdfec102c571176bd4bcb76V3.2.8Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/193The purge process should ignore hidden runs and analyses2021-03-25T14:28:42+01:00Romain ThervilleThe purge process should ignore hidden runs and analysesWe don't want the hidden runs and analyzes to appear in the purge alert mail sent to the research teams.
So they have to be removed from the project's expired components, and excluded from the total storage size.We don't want the hidden runs and analyzes to appear in the purge alert mail sent to the research teams.
So they have to be removed from the project's expired components, and excluded from the total storage size.V3.2.7.5Romain ThervilleRomain Therville2021-03-05https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/189GPDR2021-04-23T15:07:08+02:00Gerald Salingerald.salin@inra.frGPDRadding a user to a project allows any authenticated manager user to access the list of all users, including their password :
![image](/uploads/02075d0ab92873342988603ae9e5c84a/image.png)adding a user to a project allows any authenticated manager user to access the list of all users, including their password :
![image](/uploads/02075d0ab92873342988603ae9e5c84a/image.png)V3.2.8https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/182[Web interface]Improve FAQ accesses2021-09-01T08:59:46+02:00Audrey Gibert[Web interface]Improve FAQ accesses2 ideas on the web interface :
* [x] on a project page, on the top-right corner below the data overview frame : adding a sentence "You can add a collaborator to your project : visit the [NG6 FAQ](https://ng6.toulouse.inra.fr/index.php?id...2 ideas on the web interface :
* [x] on a project page, on the top-right corner below the data overview frame : adding a sentence "You can add a collaborator to your project : visit the [NG6 FAQ](https://ng6.toulouse.inra.fr/index.php?id=57) > How to add a user to my project?
* [x] On the run view, in the Raw Data tab, below the "Retention date" frame : adding "There is a fast way to retrieve your data, more information in the [NG6 FAQ](https://ng6.toulouse.inra.fr/index.php?id=57) > How to get my data?
* [x] On an analysis view, in the Download section, same sentence as above : "You can retrieve your data easily, more information in the [NG6 FAQ](https://ng6.toulouse.inra.fr/index.php?id=57) > How to get my data?
* [x] Be more explicit with the download by URL on windows in the FAQ
- [x] @gsalin : Add a news to signal the information!V3.3Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/179[purge] link analyzes to runs in the email2021-10-12T08:53:41+02:00Gerald Salingerald.salin@inra.fr[purge] link analyzes to runs in the emailFiles impacted of:
• Runs : NemaTools-1 (12035), NemaTools-1 (12336)
• Analyzes : IlluminaFilter (47020), ContaminationSearch (47027), ReadsStats (47035), IlluminaFilter (48330), ContaminationSearch (48338), ReadsStats (48339)
...Files impacted of:
• Runs : NemaTools-1 (12035), NemaTools-1 (12336)
• Analyzes : IlluminaFilter (47020), ContaminationSearch (47027), ReadsStats (47035), IlluminaFilter (48330), ContaminationSearch (48338), ReadsStats (48339)
to be transformed as
Files impacted of:
• Run NemaTools-1 (12035)
Analyzes : IlluminaFilter (47020), ContaminationSearch (47027), ReadsStats (47035),
• Run NemaTools-1 (12336)
Analyzes : IlluminaFilter (48330), ContaminationSearch (48338), ReadsStats (48339)V3.4Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/161A rework of the purge processes is needed2020-03-04T09:25:59+01:00Romain ThervilleA rework of the purge processes is neededWith the new retention, space and migration features, a few new cases have to be handled by the purge system:
* New mail model, for the projects in shortterm storage (4 months), that indicate 1 month in advance that the data are going ...With the new retention, space and migration features, a few new cases have to be handled by the purge system:
* New mail model, for the projects in shortterm storage (4 months), that indicate 1 month in advance that the data are going to be deleted.
No extention is allowed in this case.
* A new CRON that sends the purge mail one month before the data deletion and opens a purge request (Admin > Mail obsolete projects).
* A new CRON (every week) to send to the ng6 administrators the list of the last purge mails sent.V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/146There are hard-coded links in Admin>Extend Project>Project name column2020-06-11T17:01:31+02:00Romain ThervilleThere are hard-coded links in Admin>Extend Project>Project name columnEx: href="index.php?id=3&tx_nG6_pi1[project_id]=1"
The "id=3" has to be recovered from the typo3 "plugin.tx_nG6_pi6.redirection_page" template value.
This is defined in tx_nG6_pi6.js, line 706.
The expected result would be href="index.p...Ex: href="index.php?id=3&tx_nG6_pi1[project_id]=1"
The "id=3" has to be recovered from the typo3 "plugin.tx_nG6_pi6.redirection_page" template value.
This is defined in tx_nG6_pi6.js, line 706.
The expected result would be href="index.php?**id=55**&tx_nG6_pi1[project_id]=1" .V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/129Script/workflow to migrate a list of project to from a space to another2020-11-30T11:30:50+01:00Celine NoirotScript/workflow to migrate a list of project to from a space to anotherDevelop a script to transfert a project from a storage space to another :
- change project space id
- change path of run, analyzes (of the project and of the runs)
- move filesDevelop a script to transfert a project from a storage space to another :
- change project space id
- change path of run, analyzes (of the project and of the runs)
- move filesV3.2.7.5Romain ThervilleRomain Thervillehttps://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/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/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 Manno2019-07-31