ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2020-06-11T17:05:46+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/140"Random password generation" + "send mail" doesn't work with superadmin superCTD2020-06-11T17:05:46+02:00Romain Therville"Random password generation" + "send mail" doesn't work with superadmin superCTDWhen trying to regenerate a random password via the nG6 web interface, when logged as superCTD, no mail is sent to the final user.
We should check if the password is updated, and find out why no mail is sent.When trying to regenerate a random password via the nG6 web interface, when logged as superCTD, no mail is sent to the final user.
We should check if the password is updated, and find out why no mail is sent.V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/139Debug about add raw files due to 10X dev2020-06-15T10:26:45+02:00Claire KuchlyDebug about add raw files due to 10X devhttps://genomique.genotoul.fr/Mantis/view.php?id=4787 : add to raw files all reads and reads filtering.https://genomique.genotoul.fr/Mantis/view.php?id=4787 : add to raw files all reads and reads filtering.V3.2.8Claire KuchlyClaire Kuchly2019-11-07https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/138Display error in a project view : Table can not be sorted by date if the user...2020-04-03T15:58:05+02:00Audrey GibertDisplay error in a project view : Table can not be sorted by date if the user is not administratorMargot Zahm came to us because she can not sorter her project table by date :
![image](/uploads/80b4a32a42ffec62512a7fe598d11911/image.png)
![image](/uploads/f3bccdad743010390191f94004919555/image.png)
Order of dates is random
We could ...Margot Zahm came to us because she can not sorter her project table by date :
![image](/uploads/80b4a32a42ffec62512a7fe598d11911/image.png)
![image](/uploads/f3bccdad743010390191f94004919555/image.png)
Order of dates is random
We could not reproduce her bug because we were logged as CTD and it works perfectly for us...
One lead has been reported with the inspector column of web explorer :
what is sent in member view
![image](/uploads/2d8f69ffb2bbd8d28acc37314637bdeb/image.png)
what is sent in admin view
![image](/uploads/7114492349815c674d45ff5ba62c93f4/image.png)V4 - MaintenanceAudrey GibertAudrey Giberthttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/136Fail to update a user's role on a project2020-06-11T17:08:53+02:00Romain ThervilleFail to update a user's role on a projectOn nG6 (prod), the user 513 was both member and admin on a project.
We should check if another user is concerned, and find why there were 2 rows in 'fe_rights' linking the user to the project.
Kanboard link : https://genomique.genotoul...On nG6 (prod), the user 513 was both member and admin on a project.
We should check if another user is concerned, and find why there were 2 rows in 'fe_rights' linking the user to the project.
Kanboard link : https://genomique.genotoul.fr/kanboard/?controller=TaskViewController&action=show&project_id=18&task_id=1132V4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/130In run view, the blue retention limit message should be hidden for now2019-09-12T13:12:08+02:00Romain ThervilleIn run view, the blue retention limit message should be hidden for nowThis message should stay hidden until the runs an analyzes's retention are corrected in the NG6 database.
(Some users have a false "2 year" retention, instead of "3 months")This message should stay hidden until the runs an analyzes's retention are corrected in the NG6 database.
(Some users have a false "2 year" retention, instead of "3 months")V3.2.5.3Romain ThervilleRomain Therville2019-09-12https://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/125Differences between projet's hidden parameter and its run's hidden parameter2020-06-11T17:09:11+02:00Romain ThervilleDifferences between projet's hidden parameter and its run's hidden parameterSometimes (see exemple), hidden projects have visible analyses. Sometimes they do not.
http://ng6-test.toulouse.inra.fr
Project **FlaxCoreCol**
![2019-09-05_172449](/uploads/82d77c3e33ce35a60eb412286fa9d529/2019-09-05_172449.png)
Proj...Sometimes (see exemple), hidden projects have visible analyses. Sometimes they do not.
http://ng6-test.toulouse.inra.fr
Project **FlaxCoreCol**
![2019-09-05_172449](/uploads/82d77c3e33ce35a60eb412286fa9d529/2019-09-05_172449.png)
Project **FlaxCoreCol** Run **FlaxCoreCol-3** (recent)
![2019-09-05_172520](/uploads/bfbc0dea5ea36649347228321404ebd5/2019-09-05_172520.png)
Project **FlaxCoreCol** Run **FlaxCoreCol-4** (older)
![2019-09-05_172649](/uploads/05b5faaf00dc4f2f9d7ef39d0d8caca9/2019-09-05_172649.png)
(At least the icons are missing, but a check in the database is necessary.)V4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/124Analysis added to a run have no space_id2019-09-27T14:50:59+02:00Romain ThervilleAnalysis added to a run have no space_idError:
python3.4 /usr/local/bioinfo/src/nG6/bin/ng6_cli.py addanalysis
data-file 15/ng6.jobs --analysis-name "Variant calling 88"
analysis-description "68 + 20 Manech" --analysis-software "GATK..."
analysis-software-options "-" --ana...Error:
python3.4 /usr/local/bioinfo/src/nG6/bin/ng6_cli.py addanalysis
data-file 15/ng6.jobs --analysis-name "Variant calling 88"
analysis-description "68 + 20 Manech" --analysis-software "GATK..."
analysis-software-options "-" --analysis-software-version "GATK:3.7
Picard:2.1.1 - Bwa:0.7.15 - Samtools:1.3.1 - FastQC:v0.11.2 -
Bcftools:1.3.1" --admin-login sigenae --project-id 1144
**Error: 'NoneType' object has no attribute 'space_id'**
Origin:
Issue#114
src/ng6/ng6workflow.py
```
if addto == "project": cmpt_object.project = self.project
elif addto == "run": cmpt_object.run = self.runobj
#We replace the default space_id
if cmpt_object.space_id == "default" and cmpt_object.space_id != cmpt_object.run.space_id:
cmpt_object.space_id = cmpt_object.run.space_id
```
We should set the space_id according to the project containing the run, not the run itself.V3.2.5.2Romain ThervilleRomain Thervillehttps://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/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/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 Manno2019-07-31https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/109ftp server architecture2019-08-30T09:27:13+02:00Celine Noirotftp server architectureKeep/generate run/analysis architecture for a project when ftp server will be available.Keep/generate run/analysis architecture for a project when ftp server will be available.V4 - MaintenanceGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/108export metadata2019-08-30T09:27:13+02:00Celine Noirotexport metadataadd a functionality to export all metadata of project, run, analysis.add a functionality to export all metadata of project, run, analysis.V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/105sort order not numeric in contaminationsearch table2019-10-28T15:44:50+01:00Gerald Salingerald.salin@inra.frsort order not numeric in contaminationsearch table![image](/uploads/c5da447e601b3750890b5432d22e18a3/image.png)![image](/uploads/c5da447e601b3750890b5432d22e18a3/image.png)V4 - MaintenanceAudrey GibertAudrey Giberthttps://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/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/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/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.fr