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/9Regenerate a password for users added by the project manager2020-01-22T16:22:03+01:00Audrey GibertRegenerate a password for users added by the project managerFor now, there is no possibility for a user added by the project manager to regenerate their password.
=> It has to be addedFor now, there is no possibility for a user added by the project manager to regenerate their password.
=> It has to be addedRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/249remove archive option for download2024-03-11T10:40:52+01:00Gerald Salingerald.salin@inra.frremove archive option for downloaddue to url errors. Not so much used (~80 in 3 years, can be replaced by symbolic links or direct download from the downlaod areas of analysis)due to url errors. Not so much used (~80 in 3 years, can be replaced by symbolic links or direct download from the downlaod areas of analysis)V3.4.5Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/248allow to run jflow on genobioinfo2024-01-24T09:46:01+01:00Gerald Salingerald.salin@inra.frallow to run jflow on genobioinfogenologin is out, try to run jflow on genobioinfo :
- copy ng6-slurm:/usr/local/bioinfo/src/nG6 (ln de ng6-V3.4.4) from production to genobioinfo:/work/project/PlaGe/sbsuser/ng6-V3.4.4
- create /work/project/PlaGe/sbsuser/jflowSoftware ...genologin is out, try to run jflow on genobioinfo :
- copy ng6-slurm:/usr/local/bioinfo/src/nG6 (ln de ng6-V3.4.4) from production to genobioinfo:/work/project/PlaGe/sbsuser/ng6-V3.4.4
- create /work/project/PlaGe/sbsuser/jflowSoftware to store software needed by jflow and workflows
- compile/install last version of cctools (7.7). Install it in genobioinfo:/work/project/PlaGe/sbsuser/cctools (first compiled on esitoul-rocky-dev). The current version used on genologin fails on compiling on new infrastructure and compiled version copied on genobioinfo fails to run.
- create ng6 database on esitoul-rocky-dev from a backup (/save/ng6/backup_db)
- update /work/project/PlaGe/sbsuser/ng6-V3.4.4/application.properties for output folders (use /work/user/ng6/xxx)
run addrun workflow on test data failed with python3.6, at pickle.load stage....different tests showed the jflow code only works with python 3.4. Hard to find source code and compile it....I copied if from ng6-slurm scp /tools/python/3.4.3 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser and using it, the pipeline succeeded
`/work/project/PlaGe/sbsuser/Python-3.4.3/bin/python3.4 /work/project/PlaGe/sbsuser/ng6-V3.4.4/bin/ng6_cli.py addrun --project-name REPDEV --name GGTestPython3.4 --description makeflow7 --admin-login CTD --date 16/11/2023 --data-nature gDNA --sequencer aviti --species bos --type lane1 --sample type=se sample-id='V' read1='workflows/illumina_qc/data/casava_directory_test/Project_Demo_project/Sample_Demo/Demo_NoIndex_L001_R2_001.fastq.gz'`
To run illumina_qc workflow, we need specific version of some software and to update application.properties with new software location (but with same version) in /work/project/PlaGe/sbsuser/ng6-V3.4.4
Depending on software, a compilation was required or a simple copy worked :
```
1038 scp -r /usr/local/bioinfo/src/FastQC/FastQC_v0.11.2 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1040 scp -r /usr/local/bioinfo/src/fastq_illumina_filter/fastq_illumina_filter-0.1.tar.gz sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1045 scp -r /usr/local/bioinfo/src/FLASH/FLASH-1.2.6 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1047 scp -r /usr/local/bioinfo/src/FASTX-Toolkit/fastx_toolkit-0.0.14 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1049 scp -r /usr/local/bioinfo/src/STAR-2.7.10a_alpha_220314 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1050 scp -r /usr/local/bioinfo/src/STAR/STAR-2.7.10a_alpha_220314 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1059 scp -r /usr/local/bioinfo/src/STAR/STAR-2.7.10a_alpha_220314 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1060 scp -r /tools/java/jre1.8.0_45 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1062 scp -r /usr/local/bioinfo/src/TrimGalore/0.4.5.zip sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1063 scp -r /usr/local/bioinfo/src/Bismark/bismark_v0.19.0.tar.gz sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1064 scp -r /usr/local/bioinfo/src/bowtie/bowtie2-2.3.4.1-linux-x86_64.zip sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1069 scp -r /usr/local/bioinfo/src/cctools/cctools-6.0.14-x86_64-redhat7 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1079 scp -r /usr/local/bioinfo/src/picard-tools/picard-2.18.2 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1084 scp -r /tools/R/R-3.4.3 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
```
I didn't managed to compile STAR, nor R-3.4.3
- stop here for STAR
- I used last version of R R-4.3.2 > compilation OK > test OK...but had to add 'Rpath = /work/project/PlaGe/sbsuser/jflowSoftware/R-4.3.2/bin/' and modify inserstssizes.py to modify PATH (Rscript is called by picard for CollectMetrics component to generate pdf file)V3.4.4Gerald 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/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/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/234add logging through typo3 in ng6 extension2022-09-27T18:26:23+02:00Gerald Salingerald.salin@inra.fradd logging through typo3 in ng6 extensiondo not use error_log anymore
look at ng6.php code to implement loggingdo not use error_log anymore
look at ng6.php code to implement loggingV3.4https://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/232download symlink finished without error, but no data is available2022-10-06T21:29:54+02:00Gerald Salingerald.salin@inra.frdownload symlink finished without error, but no data is availablein case the analyze name contains some special characters, the output folder and/or the symbolic links can't be created :
mkdir -p -m 755 /outputFolder/Analyse_Demultiplexed_subreads_**(**bam**)**.XXX ;
ln -s /inputFolder/file.xml /outp...in case the analyze name contains some special characters, the output folder and/or the symbolic links can't be created :
mkdir -p -m 755 /outputFolder/Analyse_Demultiplexed_subreads_**(**bam**)**.XXX ;
ln -s /inputFolder/file.xml /outputFolder/file.xml;
avoid these characters in the names of run/analysis/projects or replace them when creating the symlinksV3.4https://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/219Error when updating the database, table tx_nG6_result2022-01-27T17:41:01+01:00Romain ThervilleError when updating the database, table tx_nG6_resultWhen trying to update some filepaths, I made the following mistake:
```
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/data_get/', '/data_seqoccin/');
```
Instead of:
```
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/dat...When trying to update some filepaths, I made the following mistake:
```
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/data_get/', '/data_seqoccin/');
```
Instead of:
```
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/data_get/', '/data_seqoccin/')
WHERE analyze_id = 77699;
```
Result:
All the analysis filepaths were wrong for projects in the longterm_get space.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/217"In days, your data will be deleted." in the purge alert mail2022-01-05T14:31:33+01:00Romain Therville"In days, your data will be deleted." in the purge alert mailThe delay in days should appear in the alert mail.The delay in days should appear in the alert mail.https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/216No space_id filter in Administration->Mail obsolete project->Filter on space2022-01-05T14:31:46+01:00Romain ThervilleNo space_id filter in Administration->Mail obsolete project->Filter on spaceIn the drop-down menu, no option is available:
![ng6_bug](/uploads/47ad79eefd6ce3aaa030751cddf06d7e/ng6_bug.png)In the drop-down menu, no option is available:
![ng6_bug](/uploads/47ad79eefd6ce3aaa030751cddf06d7e/ng6_bug.png)https://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/211Jflow issues2022-11-30T15:59:30+01:00Romain ThervilleJflow issuesLately, we have encountered a lot a failed processes on nG6, and they all seem to revolve around jflow.
I'll put in the issue every jflow error found on ng6.Lately, we have encountered a lot a failed processes on nG6, and they all seem to revolve around jflow.
I'll put in the issue every jflow error found on ng6.V4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/206Login / logout issues2021-05-27T14:45:45+02:00Romain ThervilleLogin / logout issuesAfter a first login, login out or getting disconnected results in a "bad password" error blocking any other connection, with any user.
Clearing the cache, history or cookies doesn't resolve the problem.
It is specific to the browser, ope...After a first login, login out or getting disconnected results in a "bad password" error blocking any other connection, with any user.
Clearing the cache, history or cookies doesn't resolve the problem.
It is specific to the browser, openning a new one allows to connect one user, once.
(Maybe restarting the entire computer works, I haven't tried yet.)V4 - Maintenance