jass merge requestshttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests2019-10-15T11:37:23+02:00https://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/1Using python 3.5 image to build the doc2019-10-15T11:37:23+02:00Bryan BRANCOTTEUsing python 3.5 image to build the docThe image also have make installed, so we just need to install sphinx. Sphinx image also exists, but less official so I prefered using python:3.5 as in https://gitlab.pasteur.fr/hub/12765-viralhostrangedb/blob/master/.gitlab-ci.yml#L133-145The image also have make installed, so we just need to install sphinx. Sphinx image also exists, but less official so I prefered using python:3.5 as in https://gitlab.pasteur.fr/hub/12765-viralhostrangedb/blob/master/.gitlab-ci.yml#L133-145https://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/2Add "Edit on gitlab" link2019-10-15T11:39:17+02:00Bryan BRANCOTTEAdd "Edit on gitlab" linkAdd the link, example can be found at http://hub.pages.pasteur.fr/12765-viralhostrangedb/ and https://gitlab.pasteur.fr/hub/12765-viralhostrangedb/blob/master/doc/conf.py#L72-79Add the link, example can be found at http://hub.pages.pasteur.fr/12765-viralhostrangedb/ and https://gitlab.pasteur.fr/hub/12765-viralhostrangedb/blob/master/doc/conf.py#L72-79https://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/3Deploy only master branch2019-10-15T16:47:22+02:00Bryan BRANCOTTEDeploy only master branchMerge request !1 and !2 are failing due to the CI trying to deploy the webserver with credentials that I do not have. This patch allows to start it only for master.Merge request !1 and !2 are failing due to the CI trying to deploy the webserver with credentials that I do not have. This patch allows to start it only for master.https://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/4rename benchmark files that prevent cloning jass on windows2021-02-05T14:06:41+01:00Cyril NERINrename benchmark files that prevent cloning jass on windowsFix #52Fix #52https://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/5I modified the name of the "*chr*.txt" file because it created problems: it...2021-02-05T16:43:32+01:00Cyril NERINI modified the name of the "*chr*.txt" file because it created problems: it...I modified the name of the "*chr*.txt" file because it created problems: it doesn't work on windows because * is a prohibited symbol.I modified the name of the "*chr*.txt" file because it created problems: it doesn't work on windows because * is a prohibited symbol.Cyril NERINCyril NERINhttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/6to solve problem of the file that contains stars inside its name2021-02-05T17:55:33+01:00Cyril NERINto solve problem of the file that contains stars inside its nameCyril NERINCyril NERINhttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/8Modification of index.html2021-03-03T12:17:54+01:00Cyril NERINModification of index.htmlI modified the index to add a section displaying a link to the jass documents as well as a link to the jass preprint, as Hanna recommended to meI modified the index to add a section displaying a link to the jass documents as well as a link to the jass preprint, as Hanna recommended to meHanna JULIENNEHanna JULIENNEhttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/9fix install in python3.62021-03-12T11:03:18+01:00Hervé MENAGERfix install in python3.6missing hdf5 dep with python3.6
(see #61)missing hdf5 dep with python3.6
(see #61)https://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/11Dev cne2021-04-19T19:02:24+02:00Cyril NERINDev cneHervé MENAGERHervé MENAGERhttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/12make jass installable via pip directly2021-05-05T14:33:35+02:00Hervé MENAGERmake jass installable via pip directly* requirements with a specific syntax in install_requires
* install with `pip install -U "git+https://gitlab.pasteur.fr/statistical-genetics/jass@hmenager-upgrade-deps-patch-98128#egg=jass"`* requirements with a specific syntax in install_requires
* install with `pip install -U "git+https://gitlab.pasteur.fr/statistical-genetics/jass@hmenager-upgrade-deps-patch-98128#egg=jass"`https://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/13Dev cne2021-05-17T14:41:09+02:00Cyril NERINDev cneperformance optimization and new version of manhattan plot (web interface)
FIX #68
FEAT #76
FEAT #77performance optimization and new version of manhattan plot (web interface)
FIX #68
FEAT #76
FEAT #77Cyril NERINCyril NERINhttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/15Increase the length of the column storing Allelle and Snp-id2021-05-17T15:47:37+02:00Hanna JULIENNEIncrease the length of the column storing Allelle and Snp-idhttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/16release 2.12021-05-17T18:27:02+02:00Hanna JULIENNErelease 2.1+ Improve computation time for large number of phenotypes
+ Fix the coding of missing value pattern for more than 19 phenotypes
+ Increasing the number of character for column to allow for non-biallelic SNPs+ Improve computation time for large number of phenotypes
+ Fix the coding of missing value pattern for more than 19 phenotypes
+ Increasing the number of character for column to allow for non-biallelic SNPshttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/18Revert "extend allele length"2021-05-17T18:56:52+02:00Hanna JULIENNERevert "extend allele length"This reverts commit 407bd26524e458421ef04722e779ac97d217a5b3
because of weird characterThis reverts commit 407bd26524e458421ef04722e779ac97d217a5b3
because of weird characterhttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/17extend allele length2021-05-17T20:56:43+02:00Hanna JULIENNEextend allele lengthhttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/19ansible deployment corrections and improvements2021-05-19T20:40:49+02:00Hervé MENAGERansible deployment corrections and improvements- use the right requirements file in ansible
- configure setup of services with 'docker' variable
- use deploy user variable for ownership of config file- use the right requirements file in ansible
- configure setup of services with 'docker' variable
- use deploy user variable for ownership of config fileHervé MENAGERHervé MENAGERhttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/20run ansible turning off docker for live deployment2021-05-19T21:00:30+02:00Hervé MENAGERrun ansible turning off docker for live deploymenthttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/22clean up docker-compose file2021-06-01T16:37:47+02:00Hervé MENAGERclean up docker-compose file- remove commented files
- share local data and code dirs
- autorestart when python code changed- remove commented files
- share local data and code dirs
- autorestart when python code changedHervé MENAGERHervé MENAGERhttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/24replace http by https in jass interface and fix bug on directLink2021-06-01T16:43:11+02:00Cyril NERINreplace http by https in jass interface and fix bug on directLinkCyril NERINCyril NERINhttps://gitlab.pasteur.fr/statistical-genetics/jass/-/merge_requests/25Update requirements.txt2021-06-01T18:08:26+02:00Hervé MENAGERUpdate requirements.txtSpecify properly the connexion source branch and URL for requirements download.Specify properly the connexion source branch and URL for requirements download.