ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2022-06-16T16:54:26+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/228Using addanalysis on a run unhides it.2022-06-16T16:54:26+02:00Romain ThervilleUsing addanalysis on a run unhides it.(This explains a lot. How can a run be visible if no one uses "unhide" in the ng6 http logs?)
This can definitely be tested easily, but I'll ask Jules if I need an exemple.(This explains a lot. How can a run be visible if no one uses "unhide" in the ng6 http logs?)
This can definitely be tested easily, but I'll ask Jules if I need an exemple.V3.3Romain 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/226The form to delete projects and runs bugs : there is a '&' in the ng6's password2022-05-10T13:53:23+02:00Romain ThervilleThe form to delete projects and runs bugs : there is a '&' in the ng6's passwordIf there is a '&' in the ng6 user's password, many forms bug on nG6.
The password should be changed again, but an additionnal password is needed:
```
LDAP administrator password:
passwd: Authentication token manipulation error
```If there is a '&' in the ng6 user's password, many forms bug on nG6.
The password should be changed again, but an additionnal password is needed:
```
LDAP administrator password:
passwd: Authentication token manipulation error
```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/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/223Cannot create a new user on TROCADERO2022-04-14T11:10:12+02:00Romain ThervilleCannot create a new user on TROCADEROAdding a new user to the TROCADERO project bugs.
-> No new user in the database.
-> No linking to the project.
![bug_ng6](/uploads/c76ffa23f9410333ffb056359f26e5a1/bug_ng6.png)Adding a new user to the TROCADERO project bugs.
-> No new user in the database.
-> No linking to the project.
![bug_ng6](/uploads/c76ffa23f9410333ffb056359f26e5a1/bug_ng6.png)V3.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/222Format end of sequencing report change2022-12-16T16:21:27+01:00Jules SabbanFormat end of sequencing report changeWith the realese V2.03.2 annoncunced by Nanopore, the end of sequencing report will not be a PDF file, but an HTML file instead.
Make little modification in workflows/ont_qc/__init__.py#L65 script to keep it in files available on nG6.With the realese V2.03.2 annoncunced by Nanopore, the end of sequencing report will not be a PDF file, but an HTML file instead.
Make little modification in workflows/ont_qc/__init__.py#L65 script to keep it in files available on nG6.Jules SabbanJules Sabbanhttps://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/220The reset password mail sent to the users is bugged2023-08-31T14:55:13+02:00Romain ThervilleThe reset password mail sent to the users is bugged"Hi Jerome,
Found the mail with the username and password in the Junk mailbox (happens a lot in our mail system).
I'm a little confused on how to decipher the info about the password. It is something like some ## and a word in-between.
I..."Hi Jerome,
Found the mail with the username and password in the Junk mailbox (happens a lot in our mail system).
I'm a little confused on how to decipher the info about the password. It is something like some ## and a word in-between.
If I copy this into the login page I get an error. "Romain 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/218Warning : In Run -> Analysis -> Download, every ".png" file is excluded from ...2022-04-26T14:02:29+02:00Romain ThervilleWarning : In Run -> Analysis -> Download, every ".png" file is excluded from the listIs it normal? (It's the case for every analysis on nG6.)
See the following :
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/blob/master/ui/nG6/pi1/analyzes/AnalysisTemplate.tpl#L145
@edarnige needs to upload .png images to an analysis...Is it normal? (It's the case for every analysis on nG6.)
See the following :
https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/blob/master/ui/nG6/pi1/analyzes/AnalysisTemplate.tpl#L145
@edarnige needs to upload .png images to an analysis, can we remove this constraint?V3.3Romain 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/215SQL error in ./nG6/src/pymysql/cursors.py2022-12-16T16:21:27+01:00Jules SabbanSQL error in ./nG6/src/pymysql/cursors.pyNew error encountered during illumina_qc :
```
/usr/local/bioinfo/src/nG6/src/pymysql/cursors.py:146: Warning: Data truncated for column 'description' at row 1
result = self._query(query)
```
Maybe related to last plugin nG6 / typo3 ...New error encountered during illumina_qc :
```
/usr/local/bioinfo/src/nG6/src/pymysql/cursors.py:146: Warning: Data truncated for column 'description' at row 1
result = self._query(query)
```
Maybe related to last plugin nG6 / typo3 updates ?Gerald 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/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/212switchspaceid doesn't work right now (project colocation is supposed to be se...2021-07-09T15:21:39+02:00Romain Thervilleswitchspaceid doesn't work right now (project colocation is supposed to be sent to longterm_get)How to find the error?
-> Try to migrate any project.
What's the error?
```
Traceback (most recent call last):
File "/work/ng6/jflow/work/switchspaceid/wf000402/.working/b5d9ebb5cd/_Stash/0/0/0/w0000000", line 95, in <module>
out...How to find the error?
-> Try to migrate any project.
What's the error?
```
Traceback (most recent call last):
File "/work/ng6/jflow/work/switchspaceid/wf000402/.working/b5d9ebb5cd/_Stash/0/0/0/w0000000", line 95, in <module>
outputs = migrate_project(*new_args)
File "/work/ng6/jflow/work/switchspaceid/wf000402/.working/b5d9ebb5cd/_Stash/0/0/0/w0000000", line 71, in migrate_project
run_analyzes = run.get_analysis()
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8.1/src/weaver/../ng6/run.py", line 194, in get_analysis
analysis.append(Analysis.get_from_id(analysis_id))
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8.1/src/weaver/../ng6/analysis.py", line 680, in get_from_id
[name, date, description, software, options, version] = t3mysql.select_analysis(id)
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8.1/src/weaver/../ng6/t3MySQLdb.py", line 802, in select_analysis
res = qresult.rows[0]
IndexError: tuple index out of range
```
See the following files:
ng6\src\ng6\t3MySQLdb.py
ng6\src\ng6\analysis.py
(They were not updated recently.)V3.3Romain ThervilleRomain Therville2021-07-16https://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/210switch_space_id workflow fail2021-06-04T10:39:18+02:00Romain Thervilleswitch_space_id workflow failThe switch_space_id workflow fails on nG6 and via bash commands.
**on NG6:**
Error "bad username/password" when entering the correct ng6 credentials.
**using bash commands:**
`python3.4 /usr/local/bioinfo/src/ng6_sources/nG6/bin/ng6_...The switch_space_id workflow fails on nG6 and via bash commands.
**on NG6:**
Error "bad username/password" when entering the correct ng6 credentials.
**using bash commands:**
`python3.4 /usr/local/bioinfo/src/ng6_sources/nG6/bin/ng6_cli.py switch_space_id --project_id "xxx" --space_id "longterm_bioinfo"`
python3.4 not found
`python2.7 /usr/local/bioinfo/src/ng6_sources/nG6/bin/ng6_cli.py switch_space_id --project_id "1713" --space_id "longterm_bioinfo"`
Traceback (most recent call last):
File "/usr/local/bioinfo/src/ng6_sources/nG6/bin/ng6_cli.py", line 27, in <module>
from jflow.workflows_manager import WorkflowsManager
File "/usr/local/bioinfo/src/ng6_sources/nG6/src/jflow/__init__.py", line 23, in <module>
from jflow.config_reader import JFlowConfigReader
File "/usr/local/bioinfo/src/ng6_sources/nG6/src/jflow/config_reader.py", line 24, in <module>
from configparser import RawConfigParser, NoOptionError
ImportError: No module named configparser
The module configparser seems to be missing from the python libs.V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/209Download failed for files with .log extension2021-10-11T18:30:36+02:00Claire KuchlyDownload failed for files with .log extension[Mantis associated](https://genomique.genotoul.fr/Mantis/view.php?id=5158)
Team wants to download the .log files of a Pacbio run but they get an error. After investigation, it seems to be an error due to the security set up after the ha...[Mantis associated](https://genomique.genotoul.fr/Mantis/view.php?id=5158)
Team wants to download the .log files of a Pacbio run but they get an error. After investigation, it seems to be an error due to the security set up after the hacking.
The same file with .txt extension can be downloaded.V3.3Claire KuchlyClaire Kuchly