ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2020-07-15T10:02:05+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/188[IlluminaWF]Hiding some analyses per defaut2020-07-15T10:02:05+02:00Audrey Gibert[IlluminaWF]Hiding some analyses per defautBy default, there is only the "log files" analysis that is hidden :
![image](/uploads/6603fbe0bddccccce2c13a16675d8079/image.png)
We should also hide
* Subset read files
* alignment
* alignmentStats
* InsertSizes
*...By default, there is only the "log files" analysis that is hidden :
![image](/uploads/6603fbe0bddccccce2c13a16675d8079/image.png)
We should also hide
* Subset read files
* alignment
* alignmentStats
* InsertSizes
* DemultiplexStatsV4 - MaintenanceAudrey GibertAudrey Gibert2021-07-01https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/194The Downloadsymlink workflow stays stuck when ng6 ssh user has a rsa passphrase2021-05-04T11:49:20+02:00Romain ThervilleThe Downloadsymlink workflow stays stuck when ng6 ssh user has a rsa passphrase**Symptoms:**
- Creating symbolic links through the web interface results in an infinite loading.
- The associated workflow doesn't end.
- The workflow debug returns the following :
Traceback (most recent call last):
File "/work/ng6/j...**Symptoms:**
- Creating symbolic links through the web interface results in an infinite loading.
- The associated workflow doesn't end.
- The workflow debug returns the following :
Traceback (most recent call last):
File "/work/ng6/jflow/work/downloadsymlink/wf008708/.working/f85edccc0a/_Stash/0/0/0/w0000000", line 86, in <module>
outputs = create_symbolik_link(*new_args)
File "/work/ng6/jflow/work/downloadsymlink/wf008708/.working/f85edccc0a/_Stash/0/0/0/w0000000", line 79, in create_symbolik_link
s.cmd('bash %s'%user_script)
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.4/src/weaver/../ng6/utils.py", line 568, in cmd
return self.ssh_results(pid, f)
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.4/src/weaver/../ng6/utils.py", line 561, in ssh_results
got = self._read(f)
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.4/src/weaver/../ng6/utils.py", line 538, in _read
x = os.read(f, 1024)
**Cause of the problem:**
When lauching an SSH connection with the ng6 user (Python : s = SSH(username, password, server_params[0]) ), a passphrase defined in /home/ng6/.ssh/id_rsa is asked.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 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/207Usergroup with deleted = 1 / Error for "tsime-ngando" 's password sync2021-05-27T14:45:34+02:00Romain ThervilleUsergroup with deleted = 1 / Error for "tsime-ngando" 's password syncThe user "tsime-ngando" has its correct password "xxx" on esitoul.
Its password on nG6 is "yyy" instead.
If we set the right password via the nG6 interface or the database, it is automatically set back to the wrong one "yyy".
So, why do...The user "tsime-ngando" has its correct password "xxx" on esitoul.
Its password on nG6 is "yyy" instead.
If we set the right password via the nG6 interface or the database, it is automatically set back to the wrong one "yyy".
So, why does the synch sets a password different than the one from esitoul?
(See also : https://forgemia.inra.fr/get-plage/e-sitoul_adminscripts/-/blob/master/synchronizeUsers.pl)V4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/208RunStats image paths are wrong for A2P1b-PlaGe-Caille2021-05-20T13:54:56+02:00Romain ThervilleRunStats image paths are wrong for A2P1b-PlaGe-CailleEven after the migration, the filepaths are still '/data_shortterm/' instead of '/data_seqoccin/'.
**TODO:**
```
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/data_shortterm/', '/data_seqoccin/')
WHERE analyze_id IN (
SELECT an...Even after the migration, the filepaths are still '/data_shortterm/' instead of '/data_seqoccin/'.
**TODO:**
```
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/data_shortterm/', '/data_seqoccin/')
WHERE analyze_id IN (
SELECT analyze_id FROM tx_nG6_run_analyze WHERE run_id IN (
SELECT run_id FROM tx_nG6_project_run WHERE project_id = xxx
)
);
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/data_shortterm/', '/data_seqoccin/')
WHERE analyze_id IN (
SELECT analyze_id FROM tx_nG6_project_analyze WHERE project_id = xxx
);
```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/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 Therville