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Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 14 14:49:11 2008 UTC (11 years, 6 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_2008_0924, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_rel_2008_11_24, rast_rel_2008_12_18, rast_rel_2009_02_05, rast_release_2008_09_29
Changes since 1.56: +27 -0 lines
Diff to previous 1.56
add pipeline flush support.

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 12 20:14:21 2008 UTC (11 years, 7 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_08_07
Changes since 1.55: +70 -388 lines
Diff to previous 1.55
Rollup of RAST release changes.

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 14 16:08:46 2008 UTC (11 years, 8 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_07_21
Changes since 1.54: +2 -2 lines
Diff to previous 1.54
Fix bug in check_jobs
Job48 checks $FIG_Config::meta_use_db before createing GenomeMetaDB-based metafiles.
MGRAST configs set to use that flag.

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 18 17:40:14 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.53: +13 -4 lines
Diff to previous 1.53
Restrict RP to run on amd64 hosts only.

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 3 19:16:13 2008 UTC (11 years, 10 months ago) by mkubal
Branch: MAIN
Changes since 1.52: +4 -2 lines
Diff to previous 1.52
sets attribute_computation_running correctly, really this time it works

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 3 13:08:24 2008 UTC (11 years, 10 months ago) by mkubal
Branch: MAIN
Changes since 1.51: +4 -5 lines
Diff to previous 1.51
sets attribute_computation_running correctly

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 2 15:33:15 2008 UTC (11 years, 10 months ago) by mkubal
Branch: MAIN
Changes since 1.50: +9 -9 lines
Diff to previous 1.50
all attribute stages run before marking attribute stage as complete

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 2 15:06:13 2008 UTC (11 years, 10 months ago) by mkubal
Branch: MAIN
Changes since 1.49: +7 -7 lines
Diff to previous 1.49
removed return 1 after individual attribute stages within sub compute_attributes

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 23 16:12:24 2008 UTC (11 years, 10 months ago) by mkubal
Branch: MAIN
Changes since 1.48: +7 -7 lines
Diff to previous 1.48
fix

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 21 17:16:21 2008 UTC (11 years, 10 months ago) by mkubal
Branch: MAIN
Changes since 1.47: +13 -11 lines
Diff to previous 1.47
runs attribute computation if DONE file exists and import.action set to import

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 20 17:06:47 2008 UTC (11 years, 10 months ago) by mkubal
Branch: MAIN
Changes since 1.46: +2 -1 lines
Diff to previous 1.46
set import.action for attribute computations

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 13 18:14:05 2008 UTC (11 years, 10 months ago) by wilke
Branch: MAIN
Changes since 1.45: +17 -101 lines
Diff to previous 1.45
insert check after compute_attributes

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 13 16:37:32 2008 UTC (11 years, 10 months ago) by wilke
Branch: MAIN
Changes since 1.44: +2 -2 lines
Diff to previous 1.44
bug fixed

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 13 16:30:33 2008 UTC (11 years, 10 months ago) by wilke
Branch: MAIN
Changes since 1.43: +116 -4 lines
Diff to previous 1.43
new version of computing attributes for import jobs

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 12 21:12:53 2008 UTC (11 years, 11 months ago) by wilke
Branch: MAIN
Changes since 1.42: +1 -1 lines
Diff to previous 1.42
computing of attributes also for jobs marked as import

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 5 14:13:22 2008 UTC (11 years, 11 months ago) by mkubal
Branch: MAIN
Changes since 1.41: +287 -25 lines
Diff to previous 1.41
v2

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 15 01:25:41 2008 UTC (12 years, 1 month ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18
Changes since 1.40: +22 -4 lines
Diff to previous 1.40
more userobj method name workarounds

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 11 21:56:05 2008 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.39: +1 -1 lines
Diff to previous 1.39
doh, actually set the metadata value.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 11 21:52:45 2008 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.38: +55 -0 lines
Diff to previous 1.38
bugfix.

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 11 21:45:26 2008 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.37: +1 -1 lines
Diff to previous 1.37
Add support for deadline scheduling & job export.

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 8 20:58:51 2008 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.36: +49 -0 lines
Diff to previous 1.36
Add support for submitting SGE deadline.

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 6 23:51:19 2008 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.35: +4 -3 lines
Diff to previous 1.35
fxi errors

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 6 22:16:37 2008 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.34: +114 -186 lines
Diff to previous 1.34
Support lustre work directory.

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 2 15:12:22 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.33: +25 -25 lines
Diff to previous 1.33
Remove Cello & Phobius stages.

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 31 17:14:29 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.32: +15 -0 lines
Diff to previous 1.32
Add disk freespace check.

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 23 19:18:19 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.31: +21 -0 lines
Diff to previous 1.31
Add veronika-mail when jobs finish.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 23 19:07:06 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.30: +19 -2 lines
Diff to previous 1.30
Add server name to the error email

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 12 21:33:39 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.29: +2 -2 lines
Diff to previous 1.29
Don't submit non-TL jobs to the TL queue.

Index attributes after new attributes have been created.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 11 21:17:03 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.28: +204 -14 lines
Diff to previous 1.28
Make the attribute computation part of the pipeline dependent on the submit-to-seed or submit-for-JGI status.

Run critica & glimmer if submit.JGI is true.

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 11 17:02:11 2007 UTC (12 years, 6 months ago) by mkubal
Branch: MAIN
Changes since 1.27: +110 -0 lines
Diff to previous 1.27
adding PHOBIUS and CELLO scripts

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 10 20:50:55 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.26: +21 -2 lines
Diff to previous 1.26
Disable contig splitting, quality check, and correction when keep_genecalls is enabled.

Ensure that *.running is set to "no" in all rp_* scripts, both on normal exit and in &fatal.

Fix error returns for failed quality check execution.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 5 17:24:56 2007 UTC (12 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.25: +41 -8 lines
Diff to previous 1.25
Mantis integration.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 25 19:01:52 2007 UTC (12 years, 6 months ago) by mkubal
Branch: MAIN
Changes since 1.24: +56 -0 lines
Diff to previous 1.24
added pfam attribute generation

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 4 20:40:44 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.23: +2 -2 lines
Diff to previous 1.23
fix typo, activate email to actual user

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 4 20:26:16 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.22: +17 -7 lines
Diff to previous 1.22
add check for failed check_neighborhood

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 4 20:19:13 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.21: +159 -8 lines
Diff to previous 1.21
add error message mail (currently set to mail to bob to not spam the users during initial run)

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 1 16:44:23 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.20: +1 -1 lines
Diff to previous 1.20
fix queue name for scenario run

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 1 16:26:26 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.19: +51 -0 lines
Diff to previous 1.19
Add scenario computation.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 1 16:01:14 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.18: +17 -3 lines
Diff to previous 1.18
Rollup of changes for the new RAST install.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 31 17:02:01 2007 UTC (12 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.17: +50 -0 lines
Diff to previous 1.17
new stuf

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 11 21:57:55 2007 UTC (12 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.16: +4 -4 lines
Diff to previous 1.16
change email references from 48-hour to RAST

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 9 20:48:00 2007 UTC (12 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.15: +1 -1 lines
Diff to previous 1.15
invoke second pass of assess_gene_call_quality with the -no-fatal flag

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 28 17:14:51 2007 UTC (13 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.14: +1 -1 lines
Diff to previous 1.14
bugfix

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 27 21:00:27 2007 UTC (13 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.13: +13 -11 lines
Diff to previous 1.13
move email support to Job48
remove stopligth status
make quality_check set up correction.status and correction.request if corrections needed

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 15 17:29:30 2007 UTC (13 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.12: +6 -6 lines
Diff to previous 1.12
check_jobs.pl

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 6 16:53:40 2007 UTC (13 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.11: +1 -0 lines
Diff to previous 1.11
add missing use

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 2 22:17:20 2007 UTC (13 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.10: +69 -1 lines
Diff to previous 1.10
add/fix email and automatic continuation support

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 2 16:42:52 2007 UTC (13 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.9: +6 -2 lines
Diff to previous 1.9
use FIG_Config for jobs direcotry(backend)

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 1 20:03:54 2007 UTC (13 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.8: +152 -2 lines
Diff to previous 1.8
rollup of 48hr fixes

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 18 20:15:28 2007 UTC (13 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.7: +42 -0 lines
Diff to previous 1.7
doh. put autoassign logic back in.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 15 21:43:51 2007 UTC (13 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.6: +30 -13 lines
Diff to previous 1.6
Add bbhs support,changes to postproc sims to compute expanded sims the new way

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 4 21:15:37 2006 UTC (13 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.5: +2 -1 lines
Diff to previous 1.5
48-hr updates.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 1 21:39:11 2006 UTC (13 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.4: +31 -17 lines
Diff to previous 1.4
48hr fixes

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 30 20:18:23 2006 UTC (13 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.3: +44 -3 lines
Diff to previous 1.3
create and index expanded sims in the postproc; use them in FIGV::sims.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 22 21:01:42 2006 UTC (13 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.2: +396 -8 lines
Diff to previous 1.2
48hr mods

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 14 19:18:14 2006 UTC (13 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.1: +29 -0 lines
Diff to previous 1.1
add qstat

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 14 17:26:14 2006 UTC (13 years, 4 months ago) by olson
Branch: MAIN
Adding some utility stuff and the start of the master-check script.

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