ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2019-09-27T09:11:39+02:00https://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/127Purge email should be send to all the users of the project.2019-09-20T11:37:40+02:00Celine NoirotPurge email should be send to all the users of the project.From now, email to alert for a purge has to be sent to all the member, administrator and manager of the project.From now, email to alert for a purge has to be sent to all the member, administrator and manager of the project.V3.2.6Romain 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/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/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/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/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/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/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/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/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/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/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/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/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/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/16generate script to compute storage size for extention2019-07-23T14:15:59+02:00Celine Noirotgenerate script to compute storage size for extentionV3.1 - Purge2018-06-29