Commits · c4df83bc0e712b5e60cf411eb9026364d14f1a31 · deep_genome / cedalion · GitLab

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 4 commits
- Return None,None when constructing a map (#45) · b44ed5e2
  Thomas Van Parys authored Nov 07, 2018
  
  b44ed5e2
- Template example correction · a2cf93a9
  Thomas Van Parys authored Nov 07, 2018
  
  a2cf93a9
- Store nextflow.config in git repo as a template · 47bf422c
  Thomas Van Parys authored Nov 07, 2018
  
  47bf422c
- Make venv location configurable (fixes #46) · 4ef2daf1
  Thomas Van Parys authored Nov 07, 2018
  
  4ef2daf1
31 Oct, 2018 3 commits
- Don't strip away leading and trailing value characters (double quotes) (#44) · 9fd7a44b
  Thomas Van Parys authored Oct 31, 2018
  
  9fd7a44b
- Update annotation header with tabs (#44) · f815b29c
  Thomas Van Parys authored Oct 31, 2018
  
  f815b29c
- Plaza annotation files are TAB separated now (fixes #44) · 2f284c67
  Thomas Van Parys authored Oct 31, 2018
  
  2f284c67
30 Oct, 2018 1 commit
- Use the channel object for storing the newSpeciesId (#43) · e0d07ccb
  Thomas Van Parys authored Oct 30, 2018
  
  e0d07ccb
25 Oct, 2018 5 commits
- Add indexes on a sorted list instead of on a stream (fixes #41) · 288d0e66
  Thomas Van Parys authored Oct 25, 2018
  
  288d0e66
- Use new plaza API interface · 55dd7ebb
  Thomas Van Parys authored Oct 25, 2018
  
  55dd7ebb
- Sort species on Cedalion ID (name) before creating species.txt (fixes #41) · 4c19885e
  Thomas Van Parys authored Oct 25, 2018
  
  4c19885e
- Let orthofinder read from the same species.txt as the other processes (#41) · 601103cb
  Thomas Van Parys authored Oct 25, 2018
  
  601103cb
- Memory retry policy for Explore Features · b3d39d70
  Thomas Van Parys authored Oct 25, 2018
  
  b3d39d70
23 Oct, 2018 2 commits
- And slightly more memory for EF (fixes #35) · cab0778a
  Thomas Van Parys authored Oct 23, 2018
  
  cab0778a
- EF process did not define a maximum time (#35) · 0a456842
  Thomas Van Parys authored Oct 23, 2018
  
  0a456842
18 Oct, 2018 2 commits
- Used fixed memory req for EF again (#36) · 6fae46b1
  Thomas Van Parys authored Oct 18, 2018
  
  6fae46b1
- Catch KeyError instead of generic Exception when gene not found (#34) · fdd558d2
  Thomas Van Parys authored Oct 18, 2018
  
  fdd558d2
17 Oct, 2018 2 commits
- Merge branch 'thpar_ef_data' · 63e2eecc
  Thomas Van Parys authored Oct 17, 2018
  
  63e2eecc
- case typo · 72daae6c
  Thomas Van Parys authored Oct 17, 2018
  
  72daae6c