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Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 23 19:20:54 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: HEAD, caBIG-05Apr06-00, caBIG-13Feb06-00, 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_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, 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_2008_0924, rast_rel_2008_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21, 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_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, 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, rast_release_2008_09_29
Changes since 1.37: +151 -0 lines
Diff to previous 1.37
changes to support dynamic sims and updates

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 7 23:11:10 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.36: +1 -1 lines
Diff to previous 1.36
fixes to salvage code

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 5 01:09:56 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.35: +16 -5 lines
Diff to previous 1.35
fixes to extract_genomes, salvage_subsystem_rows and initialize_alignments_for_subsystems

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 3 22:15:09 2006 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.34: +4 -3 lines
Diff to previous 1.34
fixes to extract_genomes to support CloseStrainSets

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 31 17:31:54 2005 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.33: +12 -0 lines
Diff to previous 1.33
fixes to extract_genomes for AbstractFuncCoupling

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 23 19:27:26 2005 UTC (13 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.32: +5 -0 lines
Diff to previous 1.32
fixes to extract_genomes

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 18:56:37 2005 UTC (13 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.31: +17 -0 lines
Diff to previous 1.31
Add license words.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Nov 5 22:59:44 2005 UTC (14 years ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.30: +15 -4 lines
Diff to previous 1.30
fixes to extract_genomes

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Nov 5 14:02:39 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.29: +51 -33 lines
Diff to previous 1.29
fixes to extract_genomes

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 31 18:18:16 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.28: +229 -10 lines
Diff to previous 1.28
nonfunctional extract_genomes.pl

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 28 01:21:51 2005 UTC (14 years ago) by overbeek
Branch: MAIN
Changes since 1.27: +95 -480 lines
Diff to previous 1.27
bug in chromosomal clusters

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 21 13:04:49 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-dataload-0
Changes since 1.26: +78 -14 lines
Diff to previous 1.26
make Sprout optional in sigs.cgi

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 20 02:37:22 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.25: +32 -20 lines
Diff to previous 1.25
fixes to call_starts

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 17 20:00:37 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
CVS Tags: Root-bobdev_news, efrank-preMakefileToStandardMk, merge-bobdev_news-1, merge-bobdev_news-2, merge-bodev_news-3, merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2, merge-trunktag-bodev_news-3
Branch point for: Branch-bobdev_news
Changes since 1.24: +18 -1 lines
Diff to previous 1.24
fixes to extract_genomes

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 29 14:47:46 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.23: +3 -3 lines
Diff to previous 1.23
add fig_specific_sequences

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 29 03:41:49 2005 UTC (14 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.22: +2 -2 lines
Diff to previous 1.22
fixes to extract_genome

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 15 02:04:34 2004 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.21: +19 -5 lines
Diff to previous 1.21
allow set of seeks to cores for bbhs

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Nov 21 02:56:15 2004 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.20: +23 -5 lines
Diff to previous 1.20
fix strange situation in indexing subsystems

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 10 21:27:49 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.19: +1 -2 lines
Diff to previous 1.19
changes in extraction scripts

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 5 14:57:59 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.18: +23 -1 lines
Diff to previous 1.18
untested changes to extract_genomes - copy-all-but in Global

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 4 19:47:24 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.17: +1 -1 lines
Diff to previous 1.17
add some files to extracted Global

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 27 16:15:28 2004 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.16: +1 -1 lines
Diff to previous 1.16
minor fix to support deletion of genomes from a subsystem

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 16 15:26:37 2004 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +14 -7 lines
Diff to previous 1.15
Modified to avoid crashes due to file-permission problems, and to have more informative error-msgs. -- /gdp

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 20 20:59:37 2004 UTC (15 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +11 -1 lines
Diff to previous 1.14
add %identity to similarities and fix a bug in extract_genomes

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 7 22:01:21 2004 UTC (15 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.13: +1 -0 lines
Diff to previous 1.13
Fix bug in bbh extraction.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 2 10:36:14 2004 UTC (15 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +9 -5 lines
Diff to previous 1.12
make corrections to extract_genomes

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 31 23:05:20 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +1 -1 lines
Diff to previous 1.11
fix to extract_genomes

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 31 01:54:43 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +4 -1 lines
Diff to previous 1.10
fix filenames with parens in extract_genomes

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 29 14:08:58 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +42 -0 lines
Diff to previous 1.9
untested changes to extract_genomes

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 10 02:11:29 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +1 -2 lines
Diff to previous 1.8
handle more varied specification of genomes on extract_genomes

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 1 18:41:58 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +93 -1 lines
Diff to previous 1.7
added copying of Subsystems and Assignments

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 29 08:16:45 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +8 -1 lines
Diff to previous 1.6
Added test for existence of SimGen data; now skips copy attempt rather than aborting if it does not exist. -- /gdp

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 24 21:57:26 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +2 -2 lines
Diff to previous 1.5
Fixed incorrect argument list declarations in sub copy_fasta and sub copy_fasta_and_formatdb. -- /gdp

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jan 31 10:37:44 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +1 -1 lines
Diff to previous 1.4
fix format of file for extract

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 6 23:08:26 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +2 -2 lines
Diff to previous 1.3
fix in extract_genomes

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 20 21:08:43 2003 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +21 -36 lines
Diff to previous 1.2
fixed issues relating to addition/deletion of genomes

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 3 19:39:29 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
CVS Tags: delong-01, delong-02
Changes since 1.1: +26 -8 lines
Diff to previous 1.1

fixed a bunch of changes

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 1 20:46:40 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-00, V00-00-01

Makefile:
	get it to work with the release tools

All the rest:
	had to rename foo to foo.pl so that makefiles could recognize
	perl source from, say, Makefiles and READMEs

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