ng6 merge requestshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests2020-02-26T13:57:43+01:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/102Merge branch issue#172 with dev2020-02-26T13:57:43+01:00Romain ThervilleMerge branch issue#172 with devUpdate to the workflow addproject
The "project space" field in the form has been made a select field, with
options build dynamically.
issue #172Update to the workflow addproject
The "project space" field in the form has been made a select field, with
options build dynamically.
issue #172V3.2.7Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/101Merge branch Dev with Master2020-02-17T15:07:58+01:00Romain ThervilleMerge branch Dev with MasterMerge to create the tag V3.2.7.
More information on the commits and changes in the corresponding tag.Merge to create the tag V3.2.7.
More information on the commits and changes in the corresponding tag.V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/100Merge branch Issue#171 with dev2020-02-14T17:46:58+01:00Romain ThervilleMerge branch Issue#171 with devUpdate to jflow.min.js and jflow.min.css
- The method to minify jflow's sources to jflow.min.js
(https://github.com/mishoo/UglifyJS2) was to advanced, and generated
errors in the code. We went back below the version 3, to avoid the
scri...Update to jflow.min.js and jflow.min.css
- The method to minify jflow's sources to jflow.min.js
(https://github.com/mishoo/UglifyJS2) was to advanced, and generated
errors in the code. We went back below the version 3, to avoid the
script being broken when minified.
- The JQuery request 'get_user_files' was bugged because it was trying
to reach ng6-test without the port '8080'.
More information in this jflow commit:
jflow@5c505644
issue #171V3.2.7Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/99Merge branch issue#170 with dev2020-02-14T17:46:17+01:00Romain ThervilleMerge branch issue#170 with devUpdate to tx_nG6_pi1.js
The ajax return codes (0,1,2 and 3) cannot be evaluated as strings.
"if (val == '1') {" becomes "if (val == 1) {" .
**Warning : We could also leave this file as it is, and make sure the value returned in AJAX is...Update to tx_nG6_pi1.js
The ajax return codes (0,1,2 and 3) cannot be evaluated as strings.
"if (val == '1') {" becomes "if (val == 1) {" .
**Warning : We could also leave this file as it is, and make sure the value returned in AJAX is a String.
I'm not sure if it is the best solution!**
issue #170V3.2.7Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/94Merge branch Issue#163 with dev2020-02-05T15:46:25+01:00Romain ThervilleMerge branch Issue#163 with devThe links have been updated.The links have been updated.V3.2.7Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/92Merge branch issue#146 with dev2020-01-28T18:06:13+01:00Romain ThervilleMerge branch issue#146 with devThe links has been fixed
In the "Adminsitration > Extend project", projects links have been fixed.
Issue #146The links has been fixed
In the "Adminsitration > Extend project", projects links have been fixed.
Issue #146V3.2.7Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/90Merge branch issue#154 with dev2020-01-22T15:56:09+01:00Romain ThervilleMerge branch issue#154 with devUpdate for the project view
The projects count has been updated to ignore the hidden projects if
they do not appear in the list.
issue #154Update for the project view
The projects count has been updated to ignore the hidden projects if
they do not appear in the list.
issue #154V3.2.6Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/89Merge branch issue#157 with dev2020-01-22T15:56:28+01:00Romain ThervilleMerge branch issue#157 with devCorrection du workflow addproject
1 import was missing to use the new data type "ng6space".
(So the space selection is a nice dropdown menu, instead of a simple
textfield.)
issue #157Correction du workflow addproject
1 import was missing to use the new data type "ng6space".
(So the space selection is a nice dropdown menu, instead of a simple
textfield.)
issue #157V3.2.6Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/88Merge branch Issue#151 with master2020-01-15T16:58:19+01:00Romain ThervilleMerge branch Issue#151 with masterThere was a typo in class.tx_nG6_eid.php.
A few indentations have been fixed.There was a typo in class.tx_nG6_eid.php.
A few indentations have been fixed.V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/85Merge branch issue #151 with master2020-01-15T13:35:21+01:00Romain ThervilleMerge branch issue #151 with masterA function was missing from the last commit + merge,
get_available_space_ids() from tx.nG6_utils.php.
issue #151A function was missing from the last commit + merge,
get_available_space_ids() from tx.nG6_utils.php.
issue #151V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/80Merge branch issue#129.2 with master2020-01-08T17:53:39+01:00Romain ThervilleMerge branch issue#129.2 with masterBig update for the switch_space_id workflow
-The workflow now handles empty (no data) runs and analyzes, and more
errors.
-A lot of user cases have been tested.
issue #129Big update for the switch_space_id workflow
-The workflow now handles empty (no data) runs and analyzes, and more
errors.
-A lot of user cases have been tested.
issue #129V3.2.6Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/79Merge branch Issues#143 with master2020-01-08T17:56:04+01:00Romain ThervilleMerge branch Issues#143 with masterIt's due to bug with the older version :
- just R1 and R2 files are used for analyses (ContaminationSearch, FastQC etc ... )
- R1, R2 and I1 after illuminaFilter if it's done are saved
- not impacted illlumina_qc analysis
Change : ...It's due to bug with the older version :
- just R1 and R2 files are used for analyses (ContaminationSearch, FastQC etc ... )
- R1, R2 and I1 after illuminaFilter if it's done are saved
- not impacted illlumina_qc analysis
Change :
- ng6_workflow
- add new function in utils for catch R1,R2 and I1 files after illuminafilter
- add new files to manage in smarty viszualisation
(Replaces the merge !68)V3.2.6https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/78#155 convert bool to int to avaoid warning2020-01-08T17:30:39+01:00Celine Noirot#155 convert bool to int to avaoid warningcorrect warningcorrect warningV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/75Merge branch issue#153 with master2020-01-06T11:28:58+01:00Romain ThervilleMerge branch issue#153 with masterUtils.py update
The get_directories_structure_and_content() function has been reworked
to make the projects, runs and analyzes names normalization way more
consistent. This will solve the differences between sources and
destinations in ...Utils.py update
The get_directories_structure_and_content() function has been reworked
to make the projects, runs and analyzes names normalization way more
consistent. This will solve the differences between sources and
destinations in this function.
issue #153V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/74Merge branch issue#150 with master2020-01-06T11:29:35+01:00Romain ThervilleMerge branch issue#150 with masterThe expired projects table's design has been fixed.
issue #150The expired projects table's design has been fixed.
issue #150V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/72Merge issue#129 with master2019-12-09T13:23:18+01:00Romain ThervilleMerge issue#129 with master- I have removed the "local = True" parameter to execute the workflow on
the computing cluster instead of ng6's host.
(It was a test parameter, only meant for testing.)
issue #129- I have removed the "local = True" parameter to execute the workflow on
the computing cluster instead of ng6's host.
(It was a test parameter, only meant for testing.)
issue #129V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/66Merge branch Issue#129 with master2019-11-19T09:32:54+01:00Romain ThervilleMerge branch Issue#129 with masterV3.2.6Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/65#141 change REGEX to display pictures from FASTQC analysis from new2019-11-13T15:26:01+01:00Claire Kuchly#141 change REGEX to display pictures from FASTQC analysis from newstorage spacesstorage spacesV3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/63#139 debug2019-11-13T15:25:44+01:00Claire Kuchly#139 debugDebug number of reads add to saved files for illumina ng6 workflow.Debug number of reads add to saved files for illumina ng6 workflow.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/merge_requests/62[demultiplexont.py]2019-10-28T13:22:00+01:00Audrey Gibert[demultiplexont.py]Script was incorrect for long time processing seqkit
-> Now : postprocess waits the end of job in the process partScript was incorrect for long time processing seqkit
-> Now : postprocess waits the end of job in the process partV3.2.6Romain ThervilleRomain Therville