ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2019-01-04T11:37:46+01:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/97The makeflow command for md5sum is too long for the cluster2019-01-04T11:37:46+01:00Audrey GibertThe makeflow command for md5sum is too long for the clusterThe command for md5sum sent by Makeflow contains the paths of all samples. In 2 of our workflows, there are 672 samples, that is far too long to be accepted for the cluster.
>>>
2018/12/04 12:47:55.67 makeflow[46806] notice: job submis...The command for md5sum sent by Makeflow contains the paths of all samples. In 2 of our workflows, there are 672 samples, that is far too long to be accepted for the cluster.
>>>
2018/12/04 12:47:55.67 makeflow[46806] notice: job submission failed: no output from slurm
couldn't submit batch job, still trying...
>>>V3.2.1Audrey GibertAudrey Gibert2018-12-14https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/98update user not working2018-12-20T18:24:47+01:00Gerald Salingerald.salin@inra.frupdate user not working![image](/uploads/dcc565f70a9e98cc10254b37cca1ac02/image.png)
![image](/uploads/1c0595fae6c3f7a384db569c20874537/image.png)![image](/uploads/dcc565f70a9e98cc10254b37cca1ac02/image.png)
![image](/uploads/1c0595fae6c3f7a384db569c20874537/image.png)V3.2.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/88sending email from update user window does not work2018-12-20T18:05:34+01:00Gerald Salingerald.salin@inra.frsending email from update user window does not workno email is sent, no error ion the javascript console....no email is sent, no error ion the javascript console....V3.2.1https://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.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/82Error downloading data with symlink and url2018-10-22T12:59:40+02:00Gerald Salingerald.salin@inra.frError downloading data with symlink and urlcan select data to download bug jflow workflow failed
* for symlink : trying to connect with ssh, but errors in keys in knownhosts. Deleting keys regarding ng6-slurm and 147.99.107.64 solved the problem
* for url : tries to open in the ...can select data to download bug jflow workflow failed
* for symlink : trying to connect with ssh, but errors in keys in knownhosts. Deleting keys regarding ng6-slurm and 147.99.107.64 solved the problem
* for url : tries to open in the browser a url prefix with http instead of httpsV3.2.1https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/84no template for BasicAnalyse2018-10-22T12:59:26+02:00Gerald Salingerald.salin@inra.frno template for BasicAnalysecf Maria.
The template does not exist
copy from BasicAnalysis.tplcf Maria.
The template does not exist
copy from BasicAnalysis.tplV3.2.1https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/80methyl_seq - template Bismark error displaying2018-10-16T17:19:32+02:00Gerald Salingerald.salin@inra.frmethyl_seq - template Bismark error displaying08-10-18 11:09 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Too few arguments to function smarty_modifier_get_description(), 1 passed in /save/ng6-test/src/ng6-git-gsalin/ui/nG6/res/smarty/templates_c/320094d0cb490e0a640ff2...08-10-18 11:09 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Too few arguments to function smarty_modifier_get_description(), 1 passed in /save/ng6-test/src/ng6-git-gsalin/ui/nG6/res/smarty/templates_c/320094d0cb490e0a640ff26100dfbb61200023b2.file.Bismark.tpl.php on line 159 and exactly 2 expected | ArgumentCountError thrown in file /save/ng6-test/src/ng6-git-gsalin/ui/nG6/res/smarty/libs/plugins/modifier.get_description.php in line 177. Requested URL: http://ng6-slurm.toulouse.inra.fr/ng6-mmanno/index.php?id=55&tx_nG6_pi1%5Banalyze_id%5D=55299&tx_nG6_pi1%5Bproject_id%5D=7&tx_nG6_pi1%5Brun_id%5D=14200
![image](/uploads/1d71ea9dd0f07714692a5d1832293e27/image.png)V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/79bug sending mail for purge demand while user disconnected2018-10-01T19:35:52+02:00Gerald Salingerald.salin@inra.frbug sending mail for purge demand while user disconnectedafter a while, the user is dosconnected from the interface.
we can still send mail for purge management
but the purge_deman_id is 0...after a while, the user is dosconnected from the interface.
we can still send mail for purge management
but the purge_deman_id is 0...V3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/77Process mail demands : delay exceed always to "no"2018-10-01T14:30:06+02:00Gerald Salingerald.salin@inra.frProcess mail demands : delay exceed always to "no"whereas we know some have delay exceededwhereas we know some have delay exceededV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/78"Process mail demands" does not work with new version of typo32018-10-01T14:30:00+02:00Gerald Salingerald.salin@inra.fr"Process mail demands" does not work with new version of typo3no records found
delay_purge is not set in the ajax requestno records found
delay_purge is not set in the ajax requestV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/75bug in purge management2018-10-01T13:04:43+02:00Gerald Salingerald.salin@inra.frbug in purge managementpurge management doe not work with new versio of typo3purge management doe not work with new versio of typo3V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/76Admin > Statisctis does not work2018-10-01T13:04:35+02:00Gerald Salingerald.salin@inra.frAdmin > Statisctis does not work> 01-10-18 10:54 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Call to undefined function split() | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/ui/nG6/class.tx_nG6_eid.php in line 808. Requested URL: http://ng6-s...> 01-10-18 10:54 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Call to undefined function split() | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/ui/nG6/class.tx_nG6_eid.php in line 808. Requested URL: http://ng6-slurm.toulouse.inra.fr/ng6-mmanno/index.php?eID=tx_nG6&type=project_distribution&by=title&role=create_user&values=BIA,Bioinfo%20GENOTOULV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/26Erreur dans la console ZeroClipboard.min.map2018-08-28T14:18:21+02:00Celine NoirotErreur dans la console ZeroClipboard.min.mapVerifier l'url de ZeroClipboard dans les js de jflow.
![image](/uploads/b15985622e50feb2ce1856f66dbcb1cc/image.png)Verifier l'url de ZeroClipboard dans les js de jflow.
![image](/uploads/b15985622e50feb2ce1856f66dbcb1cc/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/5Bug ng6_cli status --all and on the interface2018-08-28T14:15:51+02:00Maxime MannoBug ng6_cli status --all and on the interfaceAfter the upgrade of nG6_Git, the command ng6_cli status --all did not workAfter the upgrade of nG6_Git, the command ng6_cli status --all did not workV3.2 - SlurmClaire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/41users linked to a project ndo not appear2018-08-28T14:13:00+02:00Gerald Salingerald.salin@inra.frusers linked to a project ndo not appear![image](/uploads/67b486f36a6584c100cbd996358516ff/image.png)![image](/uploads/67b486f36a6584c100cbd996358516ff/image.png)V3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/21Delete Analyse or run from project view or run view2018-08-14T14:13:03+02:00Celine NoirotDelete Analyse or run from project view or run viewIf the user enter an existing user on unix server, and this user do not have permission, the return is true/ok but the directory is not deleted
![image](/uploads/3b6913146624e853d83c524a728a59e4/image.png)If the user enter an existing user on unix server, and this user do not have permission, the return is true/ok but the directory is not deleted
![image](/uploads/3b6913146624e853d83c524a728a59e4/image.png)V3.2 - Slurm2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/61update user form, data is not loaded2018-08-14T13:39:42+02:00Gerald Salingerald.salin@inra.frupdate user form, data is not loaded![image](/uploads/7614712925c7139278b1a0d19068bc78/image.png)![image](/uploads/7614712925c7139278b1a0d19068bc78/image.png)V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/47illumina_rnaseq in error, whereas all is fine2018-08-13T10:42:58+02:00Gerald Salingerald.salin@inra.frillumina_rnaseq in error, whereas all is fineseems the jflow output for the rnaseq pipeline can't be done due to the following error, and the workflow has the status "Failed"
![image](/uploads/d0fdbdcdbe941cff1cc9e12ef0731d93/image.png)seems the jflow output for the rnaseq pipeline can't be done due to the following error, and the workflow has the status "Failed"
![image](/uploads/d0fdbdcdbe941cff1cc9e12ef0731d93/image.png)V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/38unable to delete runs or analyses from the ui2018-08-08T13:10:18+02:00Gerald Salingerald.salin@inra.frunable to delete runs or analyses from the uierror :
`08-08-18 08:07 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Call to undefined function ssh2_connect() | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/nG6_ui_slurm/class.tx_nG6_eid.php in line 158. Request...error :
`08-08-18 08:07 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Call to undefined function ssh2_connect() | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/nG6_ui_slurm/class.tx_nG6_eid.php in line 158. Requested URL: http://ng6-slurm.toulouse.inra.fr/ng6-mmanno/index.php?eID=tx_nG6&type=delete&del_level=analysis&data_folder=/work/ng6-test/jflow_mmanno/ng6&user_login=ng6-test&user_pwd=ng6L12*&user_id=4&ids=50717`V3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.fr2018-08-28https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/11Correct list of id analyse and run stored in db for a purge demand2018-08-02T14:55:49+02:00Celine NoirotCorrect list of id analyse and run stored in db for a purge demandWhen purge was created, a bug stored all values of a project
Correct the list of analyse id and run id before launching the purge
Think to also remove the purge id field to the analyses and the runsWhen purge was created, a bug stored all values of a project
Correct the list of analyse id and run id before launching the purge
Think to also remove the purge id field to the analyses and the runsV3.1 - PurgeCeline NoirotCeline Noirot2018-06-29