Commits · 115a1955c5883ffd0909cb05e887f70fa561b6e6 · ORG.Asm / ORG.Annotate

13 Apr, 2016 4 commits
- Change tha dash bang of the csh shell scripts · 115a1955
  Eric Coissac authored Apr 13, 2016
  
  115a1955
- Add the latest tcsh able to deal with large PATH (at least 4096) · 32011d9b
  Eric Coissac authored Apr 13, 2016
  
  32011d9b
- Try to solve to "Warning: ridiculously long PATH truncated" message · 87663c6f
  Eric Coissac authored Apr 13, 2016
```
generated by the csh shell.

Perhaps will we have to avoid this shell ;-)
```
  87663c6f
- Solve #18 · 0ac744e9
  Eric Coissac authored Apr 13, 2016
  
  0ac744e9
04 Feb, 2016 1 commit
- Patch a bug leading to add extra quote to command line parametters · f84fd562
  Eric Coissac authored Feb 04, 2016
  
  f84fd562
27 Jan, 2016 1 commit
- Add the cd-hit program to the binaries · 0ecdb8d9
  Eric Coissac authored Jan 27, 2016
  
  0ecdb8d9
05 Jan, 2016 1 commit
- Patch a compilation bug for getopt · 0ea287f1
  Eric Coissac authored Jan 05, 2016
  
  0ea287f1
18 Dec, 2015 5 commits
- integrate options in the main script · e046ef88
  Eric Coissac authored Dec 18, 2015
  
  e046ef88
- Add the standard getopt external command allowing to deal with short and · 128f0656
  Eric Coissac authored Dec 18, 2015
```
long options in scripts
```
  128f0656
- Add the name of the org.annot pipeline in the CDS inference · 497194fa
  Eric Coissac authored Dec 18, 2015
  
  497194fa
- Specify the genetic code during the aragorn call. · 6f18008c
  Eric Coissac authored Dec 18, 2015
  
  6f18008c
- Close #15. Actually the bug in intron location was related to a · dac4fb73
  Eric Coissac authored Dec 18, 2015
```
misinterpretation of the aragorn output format. Now tRNA, and intron
location are coherent with most of the locations extracted from genbank
file with one or 2 base pairs of difference.
```
  dac4fb73
29 Nov, 2015 1 commit
- Ignore the build directory · 476e4070
  Eric Coissac authored Nov 29, 2015
  
  476e4070
28 Nov, 2015 1 commit
- Patch a bug on the generation of the location of tRNA for gene on · 72990545
  Eric Coissac authored Nov 28, 2015
```
reverse complement strand with an intron.
```
  72990545
15 Nov, 2015 1 commit
- minor addition in cds/compare · e865ea93
  Alain Viari authored Nov 15, 2015
  
  e865ea93
14 Nov, 2015 4 commits
- removed need of R igraph from chlorodb/subdb · 574aace9
  Alain Viari authored Nov 14, 2015
  
  574aace9
- minor bug in chlorodb · 7017655a
  Alain Viari authored Nov 14, 2015
  
  7017655a
- corrected bug in ncbiblast src/build-system/Makefile.in.top · edd07fd7
  Alain Viari authored Nov 14, 2015
  
  edd07fd7
- corrected compilation bug muscle on linux · 87269138
  Alain Viari authored Nov 14, 2015
  
  87269138
13 Nov, 2015 10 commits
- squared src - added missing portclean targets · d233d038
  Alain Viari authored Nov 14, 2015
  
  d233d038
- squared several distro in src - clean target added · ebb0e316
  Alain Viari authored Nov 14, 2015
  
  ebb0e316
- squared muscle · 54638fc7
  Alain Viari authored Nov 14, 2015
  
  54638fc7
- squared hmmer distro · 2d4971fe
  Alain Viari authored Nov 13, 2015
  
  2d4971fe
- clean gawk distro · 5b6234f3
  Alain Viari authored Nov 13, 2015
  
  5b6234f3
- cds test on core and shell · 9be1f2c2
  Alain Viari authored Nov 13, 2015
  
  9be1f2c2
- cds go_test bug fixed · f73133dc
  Alain Viari authored Nov 13, 2015
  
  f73133dc
- added test for chlorodb · 639cbbdc
  Alain Viari authored Nov 13, 2015
  
  639cbbdc
- add doc for chlorodb · 55fd2882
  Alain Viari authored Nov 13, 2015
  
  55fd2882
- cds/tools/chlorodb added · 0579e878
  alain viari authored Nov 13, 2015
  
  0579e878
11 Nov, 2015 3 commits
- summary added in comparison · 9a267727
  alain viari authored Nov 11, 2015
  
  9a267727
- data sources for chlorodb added · 0eb38db3
  alain viari authored Nov 11, 2015
  
  0eb38db3
- data sources for chlorodb added · 4cb93ee2
  alain viari authored Nov 11, 2015
  
  4cb93ee2
10 Nov, 2015 3 commits
- Merge branch 'master' of git.metabarcoding.org:org-asm/org-annotate · 14936719
  alain viari authored Nov 10, 2015
  
  14936719
- fixed too many partial CDS bug · d733a46f
  alain viari authored Nov 10, 2015
  
  d733a46f
- added cds/tools compare and chrlorodb · 31633e6b
  alain viari authored Nov 10, 2015
  
  31633e6b
09 Nov, 2015 5 commits
- Change minimum length for considering a match from 1000 to 100. · 6bd827ca
  Eric Coissac authored Nov 09, 2015
  
  6bd827ca
- remove the debug code · 7a805dc6
  Eric Coissac authored Nov 09, 2015
  
  7a805dc6
- Patch bug in the inverted repeats annotation · 73e4e016
  Eric Coissac authored Nov 09, 2015
```
Realize the annotation on the normalized chromosome
```
  73e4e016
- Run the annotation on the normalized sequence · 48e30ca5
  Eric Coissac authored Nov 09, 2015
  
  48e30ca5
- small modifications for the luke cluster · 55a83611
  Eric Coissac authored Nov 09, 2015
  
  55a83611