vidjil merge requestshttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests2019-10-08T16:02:17+02:00https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/488WIP: Resolve "Meilleur gestion des clones virtuels"2019-10-08T16:02:17+02:00Thonier FlorianWIP: Resolve "Meilleur gestion des clones virtuels"Closes #3945Closes #3945avant-les-congés-2019https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/360core/output.cpp: fix Clone.getWarnings()2018-11-20T12:02:03+01:00Mathieu Giraudcore/output.cpp: fix Clone.getWarnings()Closes #3601.Closes #3601.Algo 2018.09Mikaël SalsonMikaël Salsonhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/276WIP: Resolve "La selection par les labels de certains axes est fausse"2018-08-09T11:24:38+02:00Thonier FlorianWIP: Resolve "La selection par les labels de certains axes est fausse"Closes #2751Closes #2751Web 2017.11https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/245WIP: DO NOT MERGE: Feature a/3295 option names2019-03-12T14:13:09+01:00Mathieu GiraudWIP: DO NOT MERGE: Feature a/3295 option namesSee #3295.
```
Usage: ./vidjil-algo [OPTIONS] reads_file
reads_file reads file, in one of the following formats:
- FASTA (.fa/.fasta, .fa.gz/.fasta.gz)
...See #3295.
```
Usage: ./vidjil-algo [OPTIONS] reads_file
reads_file reads file, in one of the following formats:
- FASTA (.fa/.fasta, .fa.gz/.fasta.gz)
- FASTQ (.fq/.fastq, .fq.gz/.fastq.gz)
- BAM (.bam)
Paired-end reads should be merged before given as an input to vidjil-algo.
Command selection
-c COMMAND command
clones locus detection, window extraction, clone clustering (default command, most efficient, all outputs)
windows locus detection, window extraction
segment detailed V(D)J designation (not recommended)
germlines statistics on k-mers in different germlines
Input
-x, --first-reads INT maximal number of reads to process ('all': no limit, default), only first reads
-X, --sampled-reads INT maximal number of reads to process ('all': no limit, default), sampled reads
Germline presets (at least one -g or -V/(-D)/-J option must be given)
-g, --germline GERMLINES ...
-g <.g FILE>(:FILTER)
multiple locus/germlines, with tuned parameters.
Common values are '-g germline/homo-sapiens.g' or '-g germline/mus-musculus.g'
The list of locus/recombinations can be restricted, such as in '-g germline/homo-sapiens.g:IGH,IGK,IGL'
-g PATH
multiple locus/germlines, shortcut for '-g PATH/homo-sapiens.g',
processes human TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with incomplete/unusal recombinations
-V FILE ... custom V germline multi-fasta file(s)
-D FILE ... custom D germline multi-fasta file(s), analyze into V(D)J components
-J FILE ... custom V germline multi-fasta file(s)
-2 try to detect unexpected recombinations
Limits to report and to analyze clones (second pass)
-r, --min-reads INT=5 minimal number of reads supporting a clone
--min-ratio FLOAT=0 minimal percentage of reads supporting a clone
--max-clones INT maximal number of output clones ('all': no maximum, default)
-y, --max-consensus INT=100 maximal number of clones computed with a consensus sequence ('all': no limit)
-z, --max-designations INT=100
maximal number of clones to be analyzed with a full V(D)J designation ('all': no limit, do not use)
--all reports and analyzes all clones
(--min-reads 1 --min-ratio 0 --max-clones all --max-clones-with-consensus all --max-clones-with-analysis all),
to be used only on very small datasets (for example --all -X 20)
Clone analysis (second pass)
-d, --several-D try to detect several D (experimental)
-3, --cdr3 CDR3/JUNCTION detection (requires gapped V/J germlines)
Detailed output per read (generally not recommended, large files, but may be used for filtering, as in -uu -X 1000)
-U, --out-analyzed output analyzed reads (in .segmented.vdj.fa file)
-u, --out-unanalyzed
-u output unanalyzed reads, gathered by cause, except for very short and 'too few V/J' reads (in *.fa files)
-uu output unanalyzed reads, gathered by cause, all reads (in *.fa files) (use only for debug)
-uuu output unanalyzed reads, all reads, including a .unsegmented.vdj.fa file (use only for debug)
--out-reads output all reads by clones (clone.fa-*), to be used only on small datasets
Output
-o, --out-dir PATH=./out/ output directory
-b, --out-base STRING output basename (by default basename of the input file)
-v, --verbose verbose mode
Help
-h, --help help
-H, --help-advanced help, including advanced and experimental options
The full help is available in the doc/algo.org file.
```Algo 2018.09https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/122Resolve "Remplacer les presets avec « clone consensus length » par « clone av...2017-11-24T13:40:03+01:00Thonier FlorianResolve "Remplacer les presets avec « clone consensus length » par « clone average length » ?"Closes #2704Closes #2704Web 2017.11https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/119WIP: Resolve "Axes et value en string : bug lors du passage en « clone averag...2017-11-20T16:52:31+01:00Thonier FlorianWIP: Resolve "Axes et value en string : bug lors du passage en « clone average read length » en mode bar"Closes #2703Closes #2703Web 2017.11https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1428Draft: #5249 download 502 error2024-02-19T17:01:48+01:00CHESNIN ClementDraft: #5249 download 502 errorCHESNIN ClementCHESNIN Clementhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1424Draft: #5244 Better deal with tasks status, including in pre-process2024-02-19T17:04:33+01:00CHESNIN ClementDraft: #5244 Better deal with tasks status, including in pre-processCHESNIN ClementCHESNIN Clementhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1420should-get-tests/top-per-locus.should: fix valgrind test2024-02-05T13:57:52+01:00Mathieu Giraudshould-get-tests/top-per-locus.should: fix valgrind testau-dessus de !1398au-dessus de !1398https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1395Doc details2024-01-19T16:06:54+01:00Mathieu GiraudDoc detailshttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1375Draft: py4web; task.py; add a reconnect in run_fuse function2023-12-11T11:49:49+01:00THONIER FlorianDraft: py4web; task.py; add a reconnect in run_fuse functionWithout this reconnect, the functiuon don't have a corect acces to current state of the db and that allow errorWithout this reconnect, the functiuon don't have a corect acces to current state of the db and that allow errorhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1372Draft: Feature s/api ci fix2023-12-07T17:10:45+01:00THONIER FlorianDraft: Feature s/api ci fixCette banche repart du dernier commit de !1347 avant le merge et ou le test api fonctionnait.
Elle a peut-être été rebasée.Cette banche repart du dernier commit de !1347 avant le merge et ou le test api fonctionnait.
Elle a peut-être été rebasée.https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1323Docker; better use of environnement variable.2023-12-08T14:58:04+01:00THONIER FlorianDocker; better use of environnement variable.Use an .env file that will contain all variable
Use variable directly by entrypoint of some docker image to not have to manually modify values in filesUse an .env file that will contain all variable
Use variable directly by entrypoint of some docker image to not have to manually modify values in fileshttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1317Update prod-server for Lille2023-07-13T16:43:23+02:00THONIER FlorianUpdate prod-server for LilleBased on release 2023-04 of vidjil server (+ 2 hotfix)Based on release 2023-04 of vidjil server (+ 2 hotfix)https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1315Draft: cypress, fix error of unavailable type on firefox2023-05-10T14:29:37+02:00THONIER FlorianDraft: cypress, fix error of unavailable type on firefoxQuick fix of error on warning view that don't update.Quick fix of error on warning view that don't update.https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1306Draft: Hotfix upload file2023-03-30T12:03:45+02:00THONIER FlorianDraft: Hotfix upload filehttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1296docker/vidjil-client/conf: recompile cgi2023-03-23T15:48:37+01:00Mathieu Girauddocker/vidjil-client/conf: recompile cgi
Comme !1293, mais avec feature-sct, juste pour voir
Comme !1293, mais avec feature-sct, juste pour voirhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1294Resolve "docker-compose, use env and more config for mysql"2023-06-19T10:47:23+02:00THONIER FlorianResolve "docker-compose, use env and more config for mysql"Closes #5127Closes #5127Mikaël SalsonMikaël Salsonhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1287Draft: Don't rebuild docker images2023-11-28T12:09:59+01:00Mikaël SalsonDraft: Don't rebuild docker imagesFix #4951Fix #4951https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/1282Draft: get reads; return correct result file, update client part for name of ...2023-01-19T10:44:56+01:00Thonier FlorianDraft: get reads; return correct result file, update client part for name of downloaded fileLink to #5070Link to #5070