ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2024-03-11T10:40:45+01:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/245store ngl-bi analysis code in ng6 run2024-03-11T10:40:45+01:00Gerald Salingerald.salin@inra.frstore ngl-bi analysis code in ng6 runto allow the request for raw data path and update reasets path in NGL-Bi
in run table, add a new column ngl-bi-runcode-and-lane
check how to populate it from jflowto allow the request for raw data path and update reasets path in NGL-Bi
in run table, add a new column ngl-bi-runcode-and-lane
check how to populate it from jflowV3.4.5Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://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/167[Sequel2] make available BAM format from addrun2022-12-16T16:21:28+01:00Celine Vandecasteele[Sequel2] make available BAM format from addrunCurrently we can only make available fastq format when we add a run in NG6.
Data size on NG6 should be calculated from bam format.
#149Currently we can only make available fastq format when we add a run in NG6.
Data size on NG6 should be calculated from bam format.
#149Audrey GibertAudrey Giberthttps://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/149[Sequel2] make new qc pipeline for Sequel2 data2022-12-16T16:21:28+01:00Claire Kuchly[Sequel2] make new qc pipeline for Sequel2 dataRaw data from Sequel2 instrument are different from the raw data of the RSII instrument.
We would create new pipeline :
This pipeline take CCS and CLR data.
This pipeline make available for :
* CCS data : subreads.ccs.bam file
* CL...Raw data from Sequel2 instrument are different from the raw data of the RSII instrument.
We would create new pipeline :
This pipeline take CCS and CLR data.
This pipeline make available for :
* CCS data : subreads.ccs.bam file
* CLR data : all files in output directory
Create of one analysis of run_stat.
? Make available fastq file.
?Claire KuchlyClaire Kuchly2020-01-31https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/221[IlluminaWF] Change algo use with BWA for ContaminationSearch analysis2022-12-16T16:21:28+01:00Jules Sabban[IlluminaWF] Change algo use with BWA for ContaminationSearch analysisCurrently, the **ContaminationSearch** analysis for illumina workflows is performed with `bwa aln`.
This algorithm is not optimal for the length of reads we currently have ; so we should use `bwa mem`.
Moreover, in the future pipeli...Currently, the **ContaminationSearch** analysis for illumina workflows is performed with `bwa aln`.
This algorithm is not optimal for the length of reads we currently have ; so we should use `bwa mem`.
Moreover, in the future pipeline under Nextflow we will use ***FastqScreen*** to make this analysis. This tool already use `bwa mem`.
So to have comparable results between the two pipelines, we must change `bwa aln` to `bwa mem`.Jules SabbanJules Sabbanhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/142manage run 10X with samples with custom index that have to be processed like ...2022-12-16T16:21:27+01:00Claire Kuchlymanage run 10X with samples with custom index that have to be processed like 10X samplesLike SOCSMURIS projects : [mantis 4657](https://genomique.genotoul.fr/Mantis/view.php?id=4657), 10X samples and other samples in the same lane with longranger demultiplexing.
Rigth now, only sample with 10X indexes can be analyse with 1...Like SOCSMURIS projects : [mantis 4657](https://genomique.genotoul.fr/Mantis/view.php?id=4657), 10X samples and other samples in the same lane with longranger demultiplexing.
Rigth now, only sample with 10X indexes can be analyse with 10X illumina qc workflow.Claire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/186put the addrawfile component generic for any type of file to be saved2022-12-16T16:21:27+01:00Claire Kuchlyput the addrawfile component generic for any type of file to be savedNow the addrawfile component is only for fastq.gz files or with PacBio data we want to saves bam/xml and json files also.
So we want to add :
* [ ] management of any files to saved
* [ ] add calculation of the number of reads and base...Now the addrawfile component is only for fastq.gz files or with PacBio data we want to saves bam/xml and json files also.
So we want to add :
* [ ] management of any files to saved
* [ ] add calculation of the number of reads and bases for bam filesAudrey GibertAudrey Gibert2020-09-30https://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/239error displaying workflow status if too much runs present2022-11-07T16:33:55+01:00Gerald Salingerald.salin@inra.frerror displaying workflow status if too much runs presenterror in web developper interface of the browser : Request-URI Too Long The requested URL's length exceeds the capacity limit for this server.error in web developper interface of the browser : Request-URI Too Long The requested URL's length exceeds the capacity limit for this server.V3.4.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://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/235Hide and unhide a run2022-10-07T17:07:32+02:00Jules SabbanHide and unhide a runWhen I hide a run : every analysis bellow are hidden too
When I unhide a run : every analysis bellow are unhidden too
The behavouir we want when I unhide a run : nothing at analysis level OR unhide every analysis except 'Log files' ...When I hide a run : every analysis bellow are hidden too
When I unhide a run : every analysis bellow are unhidden too
The behavouir we want when I unhide a run : nothing at analysis level OR unhide every analysis except 'Log files' analysis.
The behavouir we want when I hide a run : nothing at analysis level OR same as now (to be discuss).
---
At analysis level, everything works well.
When I hide an analysis : the run above is no hidden : OK !
When I unhide an analysis : the run above is not unhidden : OK !V3.4Romain ThervilleRomain Thervillehttps://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/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/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/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/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/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/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/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.fr