ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2020-02-11T14:32:56+01:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/169FAQ style is ugly2020-02-11T14:32:56+01:00Celine NoirotFAQ style is uglyDo it less uglyDo it less uglyV3.2.6Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/137The static retention period given in the purge mail has to be computed2020-01-27T17:01:35+01:00Romain ThervilleThe static retention period given in the purge mail has to be computed"Dear user,
The two years data storage period of part or whole Accord-Bio project (1 run(s) and 7 analyse(s)) is ended."
Now that the retention is not a constant anymore, the purge mail text should be updated to give the right retention..."Dear user,
The two years data storage period of part or whole Accord-Bio project (1 run(s) and 7 analyse(s)) is ended."
Now that the retention is not a constant anymore, the purge mail text should be updated to give the right retention period.V3.2.6Romain ThervilleRomain Therville2019-11-21https://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/120add the retention policy to project view2020-01-22T11:28:03+01:00Gerald Salingerald.salin@inra.fradd the retention policy to project viewV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/151Add a space id column in Administration > Mail obsolete project2020-01-16T17:33:08+01:00Romain ThervilleAdd a space id column in Administration > Mail obsolete project- New space_id column
- Replace the "size greater than" filter with a "space_id" selection- New space_id column
- Replace the "size greater than" filter with a "space_id" selectionV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/119add the run/analysis status in the summary table2020-01-10T10:28:33+01:00Gerald Salingerald.salin@inra.fradd the run/analysis status in the summary table![image](/uploads/f8e0cf2161a5f2efae6dc3a467633997/image.png)
@celine.noirot @ckuchly what do you think about it?
this way, the user has directly the information regarding the purge state![image](/uploads/f8e0cf2161a5f2efae6dc3a467633997/image.png)
@celine.noirot @ckuchly what do you think about it?
this way, the user has directly the information regarding the purge stateV3.2.6https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/155Warning on hidden column while create a run, analyse or projet2020-01-10T10:24:43+01:00Celine NoirotWarning on hidden column while create a run, analyse or projet`
ng6-test@ng6-test: /work/ng6-test/jflow_rtherville $python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py addanalysis --admin-login cnoirot --run-id 15165 --data-file /work/ng6-test/jflow_rtherville/test.txt --analysis-name "A...`
ng6-test@ng6-test: /work/ng6-test/jflow_rtherville $python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py addanalysis --admin-login cnoirot --run-id 15165 --data-file /work/ng6-test/jflow_rtherville/test.txt --analysis-name "Analyse de run" --analysis-description "68 + 20 Manech" --analysis-software "GATK..." --analysis-software-options "-" --analysis-software-version "GATK:3.7 - Picard:2.1.1 - Bwa:0.7.15 - Samtools:1.3.1 - FastQC:v0.11.2 - Bcftools:1.3.1"
parsing Makeflow...
checking Makeflow for consistency...
Makeflow has 1 rules.
starting workflow....
submitting job: /work/ng6-test/jflow_rtherville/work/addanalysis/wf000499/.working/153171b866/_Stash/0/0/0/w0000000 none /work/ng6-test/jflow_rtherville/work/addanalysis/wf000499/BasicAnalysis_default/analysis.cfg /work/ng6-test/jflow_rtherville/tmp/tmp22_7y9dk.dump
submitted job 16508
**/save/ng6-test/src/ng6-git-rtherville/src/weaver/../pymysql/cursors.py:146: Warning: Incorrect integer value: 'True' for column 'hidden' at row 1
result = self._query(query)
**
job 16508 completed
nothing left to do.
sending incremental file list
./
test.txt
sent 166 bytes received 34 bytes 400.00 bytes/sec
total size is 61 speedup is 0.30
###########
# Results #
###########
> V3.2.6Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/153The DownloadSymlink workflow bugs when an analysis is an ONT Demultiplex2020-01-10T10:24:16+01:00Romain ThervilleThe DownloadSymlink workflow bugs when an analysis is an ONT Demultiplex**When does it happen?**
From the "download" page, when selecting an entire project that contains a demultiplex ONT analysis.
![2019-12-16_172314](/uploads/d98631c574a688f57a243b4984156f8d/2019-12-16_172314.png)
It's okay when the run ...**When does it happen?**
From the "download" page, when selecting an entire project that contains a demultiplex ONT analysis.
![2019-12-16_172314](/uploads/d98631c574a688f57a243b4984156f8d/2019-12-16_172314.png)
It's okay when the run and analyzes are deployed and selected:
![2019-12-16_172422](/uploads/b95a120a14968d72406ad2d2d27e7f77/2019-12-16_172422.png)
**Why?**
In utils.py:
*12-16 13:19 Utils DEBUG get_directories_structure_and_content. src_directories = /save/ng6///data/run/fb3cdcb00, /save/ng6///data/analyze/e3df5acbb, /save/ng6///data/analyze/2753b0457, /save/ng6///data/run/b2e7de531, /save/ng6///data/analyze/ae6d2ec97, /save/ng6///data/analyze/cfec28f91
12-16 13:19 Utils DEBUG get_directories_structure_and_content. dest_directories = /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/RawData, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_RUNStats.64606, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_DemultiplexONT.64608, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/RawData, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_DemultiplexONT.64568, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_RUNStats.64567, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3-Climares-mtplx6-2-PAD92409.16250/Analyse_DemultiplexONT.64608, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3-Climares-mtplx6-2-PAD92409.16250/Analyse_RUNStats.64606, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2-Climares-mtplx6-PAD92409.16245/Analyse_DemultiplexONT.64568, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2-Climares-mtplx6-PAD92409.16245/Analyse_RUNStats.64567*
(The destination tab contains 2 versions of the same runs and analyzes, one with '-' separatores, one with '_'.)
This may be fixed with an update to the download page's javascript call:
http://ng6-test.toulouse.inra.fr:8080//run_workflow?username=ng6-test&password=aCYLKVdYzI8AaTcB%25C2%25A4%25C3%2596%25C3%25B3i%2540%25C3%2598%2515%25C3%25B6%2522&user_directory=/work/ng6-test/jflow_rtherville/&admin_login=CTD&data_id=15032&run_id=15032&analysis_id=57729::-::57730&workflow_class=DownloadSymlink&callback=jQuery111105034437105204775_1576513683378&_=1576513683383
(By removing the analyzes that have no directory.)
The workflow tries the following treatment:
ln -s /save/ng6/data/run/fb3cdcb00 /work/ng6/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/RawData
ln -s /save/ng6/data/analyze/e3df5acbb /work/ng6/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_RUNStats.64606
ln -s /save/ng6/data/analyze/2753b0457 /work/ng6/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_DemultiplexONT.64608
ln -s /save/ng6/data/run/b2e7de531 /work/ng6/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/RawData
ln -s /save/ng6/data/analyze/ae6d2ec97 /work/ng6/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_DemultiplexONT.64568
ln -s /save/ng6/data/analyze/cfec28f91 /work/ng6/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_RUNStats.64567
But fails, BECAUSE /save/ng6/data/analyze/2753b0457 AND /save/ng6/data/analyze/ae6d2ec97 DO NOT EXIST!V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/85Error addanalysis from graphic interface (firefox)2019-11-12T13:44:01+01:00Maxime MannoError addanalysis from graphic interface (firefox)I tried to launch a new analysis from the interface.
The window poped, but nothing append when I clicked on the "Run" button.
![image](/uploads/d4a6c90188f954c6d4f32c4c562b3a78/image.png)I tried to launch a new analysis from the interface.
The window poped, but nothing append when I clicked on the "Run" button.
![image](/uploads/d4a6c90188f954c6d4f32c4c562b3a78/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/126Add a new group superadmin2019-10-29T09:36:55+01:00Celine NoirotAdd a new group superadminDuring purge step, system administrator need to have access to all the project.
*Actually to do so, we add in production a nG6_ADMIN users which is added to all project manually (via sql query during purge process)*
It would be interest...During purge step, system administrator need to have access to all the project.
*Actually to do so, we add in production a nG6_ADMIN users which is added to all project manually (via sql query during purge process)*
It would be interesting to have a new group "superadmin" which give access to all the projects.V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/132AligmentStats : Duplicate output is incorrect2019-10-28T10:44:11+01:00Audrey GibertAligmentStats : Duplicate output is incorrectIn Beestrong>NOVA12>AligmentStats, Duplicate table is almost correct!
[image](/uploads/f69faf5d6173d80430db07b47230557d/image.png)In Beestrong>NOVA12>AligmentStats, Duplicate table is almost correct!
[image](/uploads/f69faf5d6173d80430db07b47230557d/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/134Debug about add index files in sample definition2019-10-28T10:29:19+01:00Claire KuchlyDebug about add index files in sample definitionwith the definition with index files for 10X analysis, error in illumina_qc launched.
in src/ng6/ng6workflow.py
```python
def __preprocess_samples__(self):
samples_ids = []
pidx = 1
nidx = 1
for index, ...with the definition with index files for 10X analysis, error in illumina_qc launched.
in src/ng6/ng6workflow.py
```python
def __preprocess_samples__(self):
samples_ids = []
pidx = 1
nidx = 1
for index, sample in enumerate(self.samples) :
if sample.name :
self.samples_names.append(sample.name)
else :
sample.name = 'SAMPLE_' + str(nidx)
nidx += 1
if sample.sample_id :
if sample.sample_id in samples_ids :
display_error_message( "Sample identifier %s must be uniq ( sample %s ).\n" % sample.sample_id, sample.name )
# add an automatic id for samples
else :
sample.sample_id = 'sample_' + str(pidx)
pidx += 1
samples_ids.append(sample.sample_id)
for rfile in sample.reads1 :
self.reads1_indexes.append(sample.sample_id)
self.reads1.append(rfile)
for rfile in sample.reads2 :
self.reads2_indexes.append(sample.sample_id)
self.reads2.append(rfile)
**for rfile in sample.index :
self.index.append(rfile)**
```Claire KuchlyClaire Kuchly2019-10-24https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/131[ont-qc] Add .pdf file into ng6 analysis for nanopore runs2019-10-25T13:19:41+02:00Roxane Boyer[ont-qc] Add .pdf file into ng6 analysis for nanopore runsThe pdf file would be in the same location than the jflow and the log file. So into /work/sbsuser/data/Nanopore/RUN_REP/jflow.
It would be named report.pdfThe pdf file would be in the same location than the jflow and the log file. So into /work/sbsuser/data/Nanopore/RUN_REP/jflow.
It would be named report.pdfV3.2.6Audrey GibertAudrey Giberthttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/121purge email configuration2019-10-24T09:38:56+02:00Gerald Salingerald.salin@inra.frpurge email configurationcheck the recipient field, I think there were multiple copies of support.ng6 in the last purge session.check the recipient field, I think there were multiple copies of support.ng6 in the last purge session.V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/95Ajout d'analyse à un projet2019-10-21T11:52:25+02:00Philippe BardouAjout d'analyse à un projetImpossible d'ajouter une analyse à un projet via l'interface...
![Sélection_254](/uploads/c87f171a96f549d097dac188e11c7a20/Sélection_254.png)Impossible d'ajouter une analyse à un projet via l'interface...
![Sélection_254](/uploads/c87f171a96f549d097dac188e11c7a20/Sélection_254.png)V3.2.5.2Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/135Actions on ng6 users2019-10-21T10:12:58+02:00Romain ThervilleActions on ng6 users- Create super CTD (plage user, superadmin group)
- Delete the user nG6_ADMIN (and revoke its rights on every project)
- Telling Didier about it- Create super CTD (plage user, superadmin group)
- Delete the user nG6_ADMIN (and revoke its rights on every project)
- Telling Didier about itV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/122changes to NG6's database structure should appear in a .sql file2019-10-14T16:19:52+02:00Romain Thervillechanges to NG6's database structure should appear in a .sql fileWe should change the MO and check that all changes to the databse structure do appear in /bin/ng6_database.sql (Or find a better way not to miss those changes).We should change the MO and check that all changes to the databse structure do appear in /bin/ng6_database.sql (Or find a better way not to miss those changes).V3.2.6https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/133[10X] Add index files to the files return by ng6workflow.py2019-10-09T14:36:00+02:00Claire Kuchly[10X] Add index files to the files return by ng6workflow.pyIl faudrait que lorsque ng6workflow.py lors de l'illumina_process cela retourne également le fichier d'index filtré.
`return fastqilluminafilter, filtered_read1_files, filtered_read2_files, saved_files, concatenatefastq`
`return fastqi...Il faudrait que lorsque ng6workflow.py lors de l'illumina_process cela retourne également le fichier d'index filtré.
`return fastqilluminafilter, filtered_read1_files, filtered_read2_files, saved_files, concatenatefastq`
`return fastqilluminafilter, filtered_read1_files, filtered_read2_files, filtered_index_files, saved_files, concatenatefastq`Claire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/124Analysis added to a run have no space_id2019-09-27T14:50:59+02:00Romain ThervilleAnalysis added to a run have no space_idError:
python3.4 /usr/local/bioinfo/src/nG6/bin/ng6_cli.py addanalysis
data-file 15/ng6.jobs --analysis-name "Variant calling 88"
analysis-description "68 + 20 Manech" --analysis-software "GATK..."
analysis-software-options "-" --ana...Error:
python3.4 /usr/local/bioinfo/src/nG6/bin/ng6_cli.py addanalysis
data-file 15/ng6.jobs --analysis-name "Variant calling 88"
analysis-description "68 + 20 Manech" --analysis-software "GATK..."
analysis-software-options "-" --analysis-software-version "GATK:3.7
Picard:2.1.1 - Bwa:0.7.15 - Samtools:1.3.1 - FastQC:v0.11.2 -
Bcftools:1.3.1" --admin-login sigenae --project-id 1144
**Error: 'NoneType' object has no attribute 'space_id'**
Origin:
Issue#114
src/ng6/ng6workflow.py
```
if addto == "project": cmpt_object.project = self.project
elif addto == "run": cmpt_object.run = self.runobj
#We replace the default space_id
if cmpt_object.space_id == "default" and cmpt_object.space_id != cmpt_object.run.space_id:
cmpt_object.space_id = cmpt_object.run.space_id
```
We should set the space_id according to the project containing the run, not the run itself.V3.2.5.2Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/69Add a super admin ng6 who can see all projects2019-09-27T13:14:15+02:00Claire KuchlyAdd a super admin ng6 who can see all projects