6f00381000
Add license
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2016-04-23 18:05:04 +02:00
536a451510
call explicitely tcsh to workaround a path bug
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2016-04-13 17:32:10 +02:00
f466f5505a
Change tha dash bang of the csh shell scripts
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2016-04-13 16:51:58 +02:00
69434c5b86
Add the latest tcsh able to deal with large PATH (at least 4096)
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2016-04-13 16:21:50 +02:00
756d541a82
Try to solve to "Warning: ridiculously long PATH truncated" message
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generated by the csh shell.
Perhaps will we have to avoid this shell ;-)
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2016-04-13 13:04:28 +02:00
721816ae87
Solve #18
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2016-04-13 12:47:41 +02:00
b55cf31e4b
Patch a bug leading to add extra quote to command line parametters
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2016-02-04 16:00:28 +01:00
b2cc474077
Add the cd-hit program to the binaries
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2016-01-27 13:09:43 +01:00
647695d2a2
Patch a compilation bug for getopt
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Former-commit-id: 361c4e3e00ed587a7d7ca684fa92fafefd3cda83
2016-01-05 17:19:37 +01:00
f39e66d4c1
integrate options in the main script
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2015-12-18 22:05:51 +01:00
99865ad568
Add the standard getopt external command allowing to deal with short and
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long options in scripts
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2015-12-18 11:47:56 +01:00
ab37af3b03
Add the name of the org.annot pipeline in the CDS inference
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2015-12-18 08:56:55 +01:00
a4e053989b
Specify the genetic code during the aragorn call.
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2015-12-18 08:39:48 +01:00
cf54e7dcb1
Close #15 . Actually the bug in intron location was related to a
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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.
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2015-12-18 08:39:04 +01:00
d09a1fc40a
Ignore the build directory
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2015-11-29 19:03:54 +01:00
89c4f17fc4
Patch a bug on the generation of the location of tRNA for gene on
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reverse complement strand with an intron.
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Former-commit-id: 722dc77682ef3da8a746879c52072c46adb9de71
2015-11-28 16:11:14 +01:00
b7282fb30d
minor addition in cds/compare
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2015-11-15 13:13:36 +01:00
2d404b5b24
removed need of R igraph from chlorodb/subdb
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2015-11-14 22:13:55 +01:00
d83201fd2f
minor bug in chlorodb
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2015-11-14 15:16:16 +01:00
a6ee2f0781
corrected bug in ncbiblast src/build-system/Makefile.in.top
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2015-11-14 03:21:51 +01:00
7cffc9b412
corrected compilation bug muscle on linux
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2015-11-14 01:32:11 +01:00
3acb2b4ea0
squared src - added missing portclean targets
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2015-11-14 00:39:04 +01:00
ac6dfb38e0
squared several distro in src - clean target added
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2015-11-14 00:25:39 +01:00
085a5ff2a7
squared muscle
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2015-11-14 00:11:27 +01:00
d52ebf0359
squared hmmer distro
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2015-11-13 23:30:03 +01:00
80d7027d70
clean gawk distro
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2015-11-13 23:00:27 +01:00
6f43ede11e
cds test on core and shell
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2015-11-13 22:41:34 +01:00
405631f527
cds go_test bug fixed
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2015-11-13 22:37:22 +01:00
42707c281c
added test for chlorodb
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2015-11-13 18:53:47 +01:00
13b03062d5
add doc for chlorodb
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2015-11-13 17:55:24 +01:00
e4d6a8484d
cds/tools/chlorodb added
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2015-11-13 17:41:18 +01:00
0d5f0c1f20
summary added in comparison
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2015-11-11 18:51:15 +01:00
9c72a83a92
data sources for chlorodb added
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2015-11-11 15:19:50 +01:00
9b1474ddd5
data sources for chlorodb added
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2015-11-11 15:18:42 +01:00
dd9b23bc77
Merge branch 'master' of git.metabarcoding.org:org-asm/org-annotate
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2015-11-10 22:15:29 +01:00
9108ce75f1
fixed too many partial CDS bug
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2015-11-10 22:15:01 +01:00
262995a486
added cds/tools compare and chrlorodb
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2015-11-10 09:29:05 +01:00
813e3958ba
Change minimum length for considering a match from 1000 to 100.
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2015-11-09 17:35:59 +01:00
32908c6809
remove the debug code
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2015-11-09 17:17:34 +01:00
195739b5f8
Patch bug in the inverted repeats annotation
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Realize the annotation on the normalized chromosome
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2015-11-09 17:03:22 +01:00
58e99a81eb
Run the annotation on the normalized sequence
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2015-11-09 15:34:59 +01:00
ae703c70d6
small modifications for the luke cluster
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2015-11-09 15:27:32 +01:00
8b27f23a8e
change the call to awk
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2015-11-09 14:01:21 +01:00
cf99ca56a4
Patches for the cluster luke
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2015-11-09 13:11:54 +01:00
9d2d60e9f0
Patch config/default.conf for considering a CFLAGS and LDFLAGS locally predefined variables
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2015-11-09 11:35:00 +01:00
d77a0dfe67
added cds/tools/compare
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2015-11-09 01:15:14 +01:00
c3c2be254f
go_pass1 moved to bin
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2015-11-09 00:58:50 +01:00
0066211385
fixed bug : CDS product not quoted
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2015-11-08 20:43:18 +01:00
20a6677b34
Merge branch 'master' of git.metabarcoding.org:org-asm/org-annotate
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2015-11-08 19:54:19 +01:00
2d7006fd6c
corrected Annotation reordering for CDS
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2015-11-08 19:53:19 +01:00
