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Revision 1.75 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 8 20:32:12 2009 UTC (10 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: HEAD, mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_dev_05262011, mgrast_dev_06072011, mgrast_dev_08022011, mgrast_dev_08112011, mgrast_dev_10262011, mgrast_dev_12152011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0, mgrast_release_3_1_1, mgrast_release_3_1_2, mgrast_version_3_2, myrast_33, myrast_rel40, rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.74: +4 -2 lines
Diff to previous 1.74
use $num_neighbors internally instead of hardwired constant

Revision 1.74 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 18 16:50:06 2009 UTC (10 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.73: +1 -1 lines
Diff to previous 1.73
Use file_head to get just the first line of the genome file.

Revision 1.73 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 14 14:00:12 2009 UTC (10 years, 6 months ago) by gdpusch
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Changes since 1.72: +4 -2 lines
Diff to previous 1.72
Replace embedded newlines with spaces in commands.

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Tue Mar 31 20:49:22 2009 UTC (10 years, 7 months ago) by gdpusch
Branch: MAIN
Changes since 1.71: +2 -1 lines
Diff to previous 1.71
Fixed attempt to rename $restart_tmpD across filesystems.

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Sun Mar 29 18:57:11 2009 UTC (10 years, 7 months ago) by gdpusch
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Changes since 1.70: +9 -5 lines
Diff to previous 1.70
Fixed abort if only a genus is entered.

Revision 1.70 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 24 13:19:19 2008 UTC (10 years, 11 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26
Changes since 1.69: +25 -10 lines
Diff to previous 1.69
Added GLIMMER-3 hooks.

Revision 1.69 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 12 20:14:21 2008 UTC (11 years, 3 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0806, 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_08_07, 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_release_2008_09_29
Changes since 1.68: +0 -2 lines
Diff to previous 1.68
Rollup of RAST release changes.

Revision 1.68 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 17 21:58:00 2008 UTC (11 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_06_18, rast_rel_2008_07_21
Changes since 1.67: +1 -1 lines
Diff to previous 1.67
fix another gc=4 bug

Revision 1.67 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 17 18:32:15 2008 UTC (11 years, 4 months ago) by olson
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Changes since 1.66: +2 -4 lines
Diff to previous 1.66
backfill_gaps and correct_frameshifts expect different flags to set the genetic code.

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Tue Jun 17 16:12:09 2008 UTC (11 years, 4 months ago) by olson
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Changes since 1.65: +11 -2 lines
Diff to previous 1.65
Clean up genetic code option passing (careful with the precedence of . and ?:).

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Mon Jun 9 16:02:48 2008 UTC (11 years, 5 months ago) by gdpusch
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CVS Tags: rast_rel_2008_06_16
Changes since 1.64: +49 -27 lines
Diff to previous 1.64
Added option to specify Checkpoint directory. (defaults to $errD). -- /gdp

Revision 1.64 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 22 19:33:09 2008 UTC (11 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.63: +16 -18 lines
Diff to previous 1.63
shift position of correct_frameshifts in rapid_propagation pipeline

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 23 13:40:24 2008 UTC (11 years, 6 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.62: +8 -3 lines
Diff to previous 1.62
Allow setting VERBOSE and DEBUG for run based on metafile. -- /gdp

Revision 1.62 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 13 17:28:18 2008 UTC (11 years, 9 months ago) by gdpusch
Branch: MAIN
Changes since 1.61: +10 -10 lines
Diff to previous 1.61
Minor changes to loggin msgs. -- /gdp

Revision 1.61 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 13 14:54:27 2008 UTC (11 years, 9 months ago) by gdpusch
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Changes since 1.60: +3 -0 lines
Diff to previous 1.60
Final clean-up. -- /gdp

Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 31 22:18:56 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.59: +0 -3 lines
Diff to previous 1.59
put things back the way they were

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 31 22:11:48 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.58: +3 -0 lines
Diff to previous 1.58
This is a minor, yet earth-shattering, change.

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 31 15:31:39 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.57: +5 -0 lines
Diff to previous 1.57
Put reporting of family directory used in the FigFams constructor, only printed if REPORT_FIGFAM_DETAILS
is specified in the environment.

Make the FIG_Config defaulting work properly for the figfams directory.

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 26 22:22:45 2008 UTC (11 years, 9 months ago) by gdpusch
Branch: MAIN
Changes since 1.56: +69 -42 lines
Diff to previous 1.56
Fixed bug processing RNA-finder output. -- /gdp

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 21 13:01:48 2008 UTC (11 years, 9 months ago) by gdpusch
Branch: MAIN
Changes since 1.55: +6 -4 lines
Diff to previous 1.55
Mod to save checkpointing dirs to $errD. -- /gdp

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 20 21:55:12 2008 UTC (11 years, 9 months ago) by gdpusch
Branch: MAIN
Changes since 1.54: +76 -52 lines
Diff to previous 1.54
Added checkpointing and restart support. -- /gdp

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 20 18:06:30 2007 UTC (11 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.53: +1 -1 lines
Diff to previous 1.53
fix bad system() invocation

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 20 07:46:24 2007 UTC (11 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.52: +6 -5 lines
Diff to previous 1.52
Fixed typo in invocation of `get_fasta_for_tbl_entries`. -- /gdp

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 11 16:46:44 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.51: +15 -10 lines
Diff to previous 1.51
Added save of "checkpoint" directory for each major stage. -- /gdp

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 11 15:38:10 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.50: +18 -13 lines
Diff to previous 1.50
Added save of "checkpoint" directory for each major stage. -- /gdp

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 9 02:16:35 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.49: +3 -3 lines
Diff to previous 1.49
Minor cosmetic changes. -- /gdp

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 7 22:47:12 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.48: +3 -1 lines
Diff to previous 1.48
Added fetch of (hopefully) human-readable translations of return-codes. -- /gdp

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 7 07:59:55 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.47: +20 -13 lines
Diff to previous 1.47
Added logic to skip backfilling if there are no close genomes. -- /gdp

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 5 23:32:40 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.46: +60 -29 lines
Diff to previous 1.46
Fixed logic error that erroneously skipped `find_genes_in_families` when there were no close genomes. -- /gdp

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 4 20:05:29 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.45: +17 -9 lines
Diff to previous 1.45
Fixed problem with "restart" logic. (Attempt to overwrite the working directory $tmpD with the original data in "raw/$orgID/". -- /gdp

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 4 03:18:29 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.44: +3 -2 lines
Diff to previous 1.44
Fixed problems with genetic-code flags when the value of $code is undefined. -- /gdp

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 3 21:20:12 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.43: +200 -152 lines
Diff to previous 1.43
implement restart for rapid_propagation

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 3 19:46:20 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.42: +4 -0 lines
Diff to previous 1.42
put correct_frameshifts into rapid_propagation

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Mon Dec 3 19:38:38 2007 UTC (11 years, 11 months ago) by gdpusch
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Changes since 1.41: +8 -1 lines
Diff to previous 1.41
Added call to `find_special_proteins` (selenoproteins, etc.). -- /gdp

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 2 15:44:40 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.40: +6 -6 lines
Diff to previous 1.40
Fixed bug in `backfill_gaps` invocation. -- /gdp

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 2 02:11:36 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.39: +1 -1 lines
Diff to previous 1.39
Added calls to RNA-finder & `backfill_gaps`. -- /gdp

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 2 01:49:39 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.38: +140 -56 lines
Diff to previous 1.38
Added calls to RNA-finder & `backfill_gaps`. -- /gdp

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 10 20:38:25 2007 UTC (12 years, 1 month ago) by gdpusch
Branch: MAIN
Changes since 1.37: +42 -37 lines
Diff to previous 1.37
Minor changes to comments. -- /gdp

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 13 19:55:54 2007 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.36: +42 -4 lines
Diff to previous 1.36
move assigned_functions , annotations processing to later pipeline stage

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 1 19:48:33 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.35: +30 -2 lines
Diff to previous 1.35
put neighbor info into metadata

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 1 04:56:16 2007 UTC (12 years, 5 months ago) by gdpusch
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Changes since 1.34: +8 -4 lines
Diff to previous 1.34
Modified to invoke `fig_neighbors_using_figfams` if `find_neighbors` fails. -- /gdp

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Thu May 31 19:25:44 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.33: +1 -0 lines
Diff to previous 1.33
die if no neighbors found, until we fix the sims-based version

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Thu May 31 04:45:41 2007 UTC (12 years, 5 months ago) by olson
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Changes since 1.32: +19 -0 lines
Diff to previous 1.32
use sims to find neighbors in case fam-based method fails

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Thu May 17 12:45:58 2007 UTC (12 years, 6 months ago) by gdpusch
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Changes since 1.31: +3 -1 lines
Diff to previous 1.31
Supress removal of TMP directory if VERBOSE flag is set. -- /gdp

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Wed May 9 20:33:16 2007 UTC (12 years, 6 months ago) by gdpusch
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Changes since 1.30: +11 -2 lines
Diff to previous 1.30
Fixed bug on alternate code parsing. -- /gdp

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Mon May 7 07:15:47 2007 UTC (12 years, 6 months ago) by gdpusch
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Changes since 1.29: +6 -5 lines
Diff to previous 1.29
Moved build_pssm_db.pl --> build_figfam_pssm_db.pl. -- /gdp

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 27 19:14:35 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.28: +21 -4 lines
Diff to previous 1.28
fixes to rapid propagation

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Wed Apr 25 21:14:46 2007 UTC (12 years, 6 months ago) by overbeek
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Changes since 1.27: +2 -2 lines
Diff to previous 1.27
fix to rapid_propagation.pl to place errD correctly

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Wed Apr 25 20:53:38 2007 UTC (12 years, 6 months ago) by overbeek
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Changes since 1.26: +27 -14 lines
Diff to previous 1.26
take existing gene calls in rapid propagation

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Tue Nov 28 17:49:08 2006 UTC (12 years, 11 months ago) by olson
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Changes since 1.25: +3 -1 lines
Diff to previous 1.25
48-hr quality fixes

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Tue Nov 28 17:09:22 2006 UTC (12 years, 11 months ago) by overbeek
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Changes since 1.24: +2 -0 lines
Diff to previous 1.24
initialize evidence and ann in rp directory

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Sat Nov 25 17:20:30 2006 UTC (12 years, 11 months ago) by overbeek
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Changes since 1.23: +1 -1 lines
Diff to previous 1.23
limit functions used for inference of subsystems to proposed*functions

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Sat Nov 25 17:17:47 2006 UTC (12 years, 11 months ago) by overbeek
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Changes since 1.22: +1 -1 lines
Diff to previous 1.22
allow multiple function files in rapid propogation

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Fri Nov 24 20:44:08 2006 UTC (12 years, 11 months ago) by olson
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Changes since 1.21: +7 -3 lines
Diff to previous 1.21
updates to 48 code

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Wed Nov 22 21:01:35 2006 UTC (12 years, 11 months ago) by olson
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Changes since 1.20: +21 -10 lines
Diff to previous 1.20
48hr mods

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Mon Nov 20 20:55:35 2006 UTC (12 years, 11 months ago) by olson
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Changes since 1.19: +6 -1 lines
Diff to previous 1.19
add metadata stetting

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Tue Nov 14 17:35:44 2006 UTC (13 years ago) by olson
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Changes since 1.18: +94 -17 lines
Diff to previous 1.18
Changes for rapid propagation on the cluster.

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Fri Nov 10 21:43:55 2006 UTC (13 years ago) by overbeek
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Changes since 1.17: +2 -2 lines
Diff to previous 1.17
Invoke `assess_gene_call_quality`. -- /gdp

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Sat Oct 28 14:29:09 2006 UTC (13 years ago) by overbeek
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Changes since 1.16: +1 -1 lines
Diff to previous 1.16
Incorporated change to invocation of `promote_orfs_to_pegs`. -- /gdp

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 15 13:46:45 2006 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.15: +2 -0 lines
Diff to previous 1.15
added log of calling subsystems to rapid_propagation

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Sun Oct 15 13:31:41 2006 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.14: +1 -0 lines
Diff to previous 1.14
add rapid subsystem inference to rapid_propagation

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Sat Oct 14 23:59:26 2006 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.13: +8 -5 lines
Diff to previous 1.13
minor fixes to rapid propagation

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Sat Oct 14 21:47:20 2006 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.12: +22 -13 lines
Diff to previous 1.12
package up the steps in rapid propoagation

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Fri Oct 13 20:08:32 2006 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.11: +18 -2 lines
Diff to previous 1.11
add logging to rapid_propagation

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Fri Oct 6 06:08:12 2006 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.10: +1 -1 lines
Diff to previous 1.10
Added missing $newD at renaming assigned_functions to proposed_functions. -- /gdp

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Thu Oct 5 00:28:58 2006 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.9: +4 -4 lines
Diff to previous 1.9
fixes to rapid prop technology and added diffsF.cgi

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 2 15:41:53 2006 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.8: +1 -1 lines
Diff to previous 1.8
Minor cosmetic change. -- /gdp

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 2 15:33:36 2006 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.7: +4 -3 lines
Diff to previous 1.7
Inserted missing output-directory prefix, plus minor cosmetic changes. -- /gdp

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 19 18:40:42 2006 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.6: +2 -2 lines
Diff to previous 1.6
Added logging for final promote ORFs step. -- /gdp

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 19 13:54:58 2006 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.5: +2 -2 lines
Diff to previous 1.5
Minor cosmetic change. -- /gdp

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Tue Sep 19 00:01:45 2006 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.4: +2 -2 lines
Diff to previous 1.4
Modified to save results from both stages of `find_genes_based_on_neighbors`. -- /gdp

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Mon Sep 18 21:12:21 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.3: +10 -8 lines
Diff to previous 1.3
spiff up the lock/unlock stuff

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Mon Sep 18 17:05:22 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.2: +20 -0 lines
Diff to previous 1.2
Added license block; set $SIG{HUP} to "IGNORE." -- /gdp

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 18 02:19:34 2006 UTC (13 years, 1 month ago) by overbeek
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Changes since 1.1: +1 -0 lines
Diff to previous 1.1
promote remaining orfs in rapid_propagation

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Mon Sep 18 00:26:39 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
initial undebugged rapid propagation script

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