Commits · 6fff44004a97b874a56bbc3977fb6de45e5fde3e · deep_genome / cedalion · GitLab

05 Feb, 2019 3 commits
- Add dummy channels to circumvent join matching bug · 6fff4400
  Thomas Van Parys authored Feb 05, 2019
  
  6fff4400
- Make input data validation more lenient towards CDS and GFF3 (#47) · e32b6c67
  Thomas Van Parys authored Feb 05, 2019
  
  e32b6c67
- Disable EF and WGD processes for missing CDS or annotation (#47) · 1210d2b9
  Thomas Van Parys authored Feb 05, 2019
  
  1210d2b9
14 Jan, 2019 1 commit
- Update overview schema · ec28c3e1
  Thomas Van Parys authored Jan 14, 2019
  
  ec28c3e1
04 Jan, 2019 1 commit
- High level process overview scheme · 11089ebb
  Thomas Van Parys authored Jan 04, 2019
  
  11089ebb
19 Dec, 2018 1 commit
- Don't publish Clime input files (fixes #68) · ebab20e2
  Thomas Van Parys authored Dec 19, 2018
  
  ebab20e2
13 Dec, 2018 2 commits
- Merge branch 'master' of https://gitlab.psb.ugent.be/deep_genome/pipeline · 1ea5ca25
  Thomas Van Parys authored Dec 13, 2018
  
  1ea5ca25
- Don't publish the input files for Explore Features (fixes #66) · 61a80e21
  Thomas Van Parys authored Dec 13, 2018
  
  61a80e21
12 Dec, 2018 2 commits
- Make publishing of b2g output xml files optional (fixes #62) · 99ddead0
  Thomas Van Parys authored Dec 12, 2018
  
  99ddead0
- Do not publish clusters and graph files for orthofinder (fixes #61) · 9858bfe6
  Thomas Van Parys authored Dec 12, 2018
  
  9858bfe6
27 Nov, 2018 4 commits
- Allow a storage location and process specific store_ parameters (fixes #38) · f48afa99
  Thomas Van Parys authored Nov 27, 2018
  
  f48afa99
- Less time for WGD ksd again, but double the amount of cores · 63438268
  Thomas Van Parys authored Nov 27, 2018
  
  63438268
- -mp flag requires space · c978aeae
  Thomas Van Parys authored Nov 27, 2018
  
  c978aeae
- Give WGD ksd more time and limit with mp500 flag · 1684342e
  Thomas Van Parys authored Nov 27, 2018
  
  1684342e
22 Nov, 2018 1 commit
- Keep storage off for now · b5478d0c
  Thomas Van Parys authored Nov 22, 2018
  
  b5478d0c
21 Nov, 2018 2 commits
- Added storage parameter. Used on ips and blast all vs all (#38) · e3134618
  Thomas Van Parys authored Nov 21, 2018
  
  e3134618
- Limit numpy threads to 4 in WGD and increase starting mem (#19) · ab40bcb3
  Thomas Van Parys authored Nov 21, 2018
  
  ab40bcb3
20 Nov, 2018 1 commit
- WGD sometimes needs more than 1h. Set it to 5h (#19) · de4ee6c3
  Thomas Van Parys authored Nov 20, 2018
  
  de4ee6c3
19 Nov, 2018 2 commits
- Add resume option to launch script (#19) · c4df83bc
  Thomas Van Parys authored Nov 19, 2018
  
  c4df83bc
- More memory for jobs spread over 4 cpus (#19) · e22b9645
  Thomas Van Parys authored Nov 19, 2018
  
  e22b9645
16 Nov, 2018 7 commits
- Add shebang to launcher (fixes #59) · 541ec443
  Thomas Van Parys authored Nov 16, 2018
  
  541ec443
- Launcher: use CEDALION_HOME env variable (fixes #58) · 47b11f60
  Thomas Van Parys authored Nov 16, 2018
  
  47b11f60
- Escape sed special chars · 219a1045
  Thomas Van Parys authored Nov 16, 2018
  
  219a1045
- plaza api ftp returns latest version and adds version option (fixes #56) · 9bc89054
  Thomas Van Parys authored Nov 16, 2018
  
  9bc89054
- Make linter happy · 765b2492
  Thomas Van Parys authored Nov 16, 2018
  
  765b2492
- Adapt plaza api and launcher to 'year' entry in Plaza (#56) · 84f68594
  Thomas Van Parys authored Nov 16, 2018
  
  84f68594
- Make the linter happy · 50ea9045
  Thomas Van Parys authored Nov 16, 2018
  
  50ea9045
15 Nov, 2018 3 commits
- Let launch script export working directory (fixes #49) · 02f9348c
  Thomas Van Parys authored Nov 15, 2018
  
  02f9348c
- Use PrettyTables in launcher (fixes #50) · f5e729b6
  Thomas Van Parys authored Nov 15, 2018
  
  f5e729b6
- Filter spaces out of gene ids (#55) · e472f8fa
  Thomas Van Parys authored Nov 15, 2018
  
  e472f8fa
14 Nov, 2018 3 commits
- WGD ks_one_v_one slightly more mem to start with · 2c325682
  Thomas Van Parys authored Nov 14, 2018
  
  2c325682
- Set errorStrategy to finish after retrying · d38a9de5
  Thomas Van Parys authored Nov 14, 2018
  
  d38a9de5
- Set time constraints for most processes and reduce mem req for WGD (fixes #54) · e6c2b009
  Thomas Van Parys authored Nov 14, 2018
  
  e6c2b009
12 Nov, 2018 4 commits
- Sort EF null species (fixes #52) · 11546a31
  Thomas Van Parys authored Nov 12, 2018
  
  11546a31
- Sort clime col-species (#52) · 358c693b
  Thomas Van Parys authored Nov 12, 2018
  
  358c693b
- Filter new species id by value (#43) · 62cf8b34
  Thomas Van Parys authored Nov 12, 2018
  
  62cf8b34
- Use xvfb-run to emulate x-server for ev01 (fixes #42) · cba410c7
  Thomas Van Parys authored Nov 12, 2018
  
  cba410c7
08 Nov, 2018 2 commits
- Allow to save back to loaded species file (fixes #48) · 9208393f
  Thomas Van Parys authored Nov 08, 2018
  
  9208393f
- Load optional species file in launcher (#48) · da9e9463
  Thomas Van Parys authored Nov 08, 2018
  
  da9e9463
07 Nov, 2018 1 commit
- Return None,None when constructing a map (#45) · b44ed5e2
  Thomas Van Parys authored Nov 07, 2018
  
  b44ed5e2