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Revision 1.31 - (view) (download) (annotate) - [select for diffs]
Thu Nov 14 17:26:37 2013 UTC (5 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: HEAD, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.30: +4 -4 lines
Diff to previous 1.30
Fix the broken stuff (bob commented out some lines erroneously)

Revision 1.30 - (view) (download) (annotate) - [select for diffs]
Tue Nov 12 21:53:27 2013 UTC (6 years ago) by olson
Branch: MAIN
Changes since 1.29: +8 -3 lines
Diff to previous 1.29
Support for annotation flow from CoreSEED to PubSEED.

Revision 1.29 - (view) (download) (annotate) - [select for diffs]
Mon Jun 11 20:26:12 2012 UTC (7 years, 5 months ago) by golsen
Branch: MAIN
Changes since 1.28: +1 -1 lines
Diff to previous 1.28
Makefile update adding -lm for CFLAGS

Revision 1.28 - (view) (download) (annotate) - [select for diffs]
Mon Jun 11 20:09:00 2012 UTC (7 years, 5 months ago) by golsen
Branch: MAIN
Changes since 1.27: +2 -2 lines
Diff to previous 1.27
Support for c language components of codon usage work.

Revision 1.27 - (view) (download) (annotate) - [select for diffs]
Wed Aug 3 18:52:11 2011 UTC (8 years, 3 months ago) by disz
Branch: MAIN
CVS Tags: mgrast_dev_10262011, mgrast_dev_12152011, mgrast_release_3_1_2, mgrast_version_3_2, rast_rel_2011_0928
Changes since 1.26: +1 -0 lines
Diff to previous 1.26
Added to_run_new_genomes

Revision 1.26 - (view) (download) (annotate) - [select for diffs]
Tue Jun 14 18:18:17 2011 UTC (8 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08022011, mgrast_dev_08112011, mgrast_release_3_1_1, myrast_rel40
Changes since 1.25: +3 -1 lines
Diff to previous 1.25
Add annotation push script

Revision 1.25 - (view) (download) (annotate) - [select for diffs]
Mon Jun 13 20:27:46 2011 UTC (8 years, 5 months ago) by disz
Branch: MAIN
Changes since 1.24: +1 -1 lines
Diff to previous 1.24
Added to_run_daily.sh

Revision 1.24 - (view) (download) (annotate) - [select for diffs]
Tue Apr 5 16:06:18 2011 UTC (8 years, 7 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_dev_05262011, mgrast_dev_06072011, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0
Changes since 1.23: +1 -1 lines
Diff to previous 1.23
fix R build target. why it works for me and not elsewhere I don't know

Revision 1.23 - (view) (download) (annotate) - [select for diffs]
Thu Jan 6 22:57:05 2011 UTC (8 years, 10 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, myrast_33, rast_rel_2011_0119
Changes since 1.22: +4 -1 lines
Diff to previous 1.22
more expression hacking fixes

Revision 1.22 - (view) (download) (annotate) - [select for diffs]
Mon Apr 19 20:27:00 2010 UTC (9 years, 6 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206
Changes since 1.21: +6 -0 lines
Diff to previous 1.21
copy R scripts too

Revision 1.21 - (view) (download) (annotate) - [select for diffs]
Mon Jun 23 16:39:36 2008 UTC (11 years, 4 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_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_release_2008_09_29
Changes since 1.20: +1 -1 lines
Diff to previous 1.20
add md5 modl

Revision 1.20 - (view) (download) (annotate) - [select for diffs]
Tue Dec 4 20:09:03 2007 UTC (11 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18
Changes since 1.19: +3 -1 lines
Diff to previous 1.19
Rollup of release engineering changes that shoudl  make multi-architecture
installs happier.

Revision 1.19 - (view) (download) (annotate) - [select for diffs]
Wed Apr 11 17:47:15 2007 UTC (12 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.18: +2 -0 lines
Diff to previous 1.18
rollup of metagenome server changes

Revision 1.18 - (view) (download) (annotate) - [select for diffs]
Mon Dec 5 18:56:37 2005 UTC (13 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.17: +17 -0 lines
Diff to previous 1.17
Add license words.

Revision 1.17 - (view) (download) (annotate) - [select for diffs]
Wed Aug 31 21:14:32 2005 UTC (14 years, 2 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-00-00-00, caBIG-dataload-0
Changes since 1.16: +1 -1 lines
Diff to previous 1.16
Added rule for "fastasize.c"

Revision 1.16 - (view) (download) (annotate) - [select for diffs]
Wed Apr 13 02:26:57 2005 UTC (14 years, 7 months ago) by efrank
Branch: MAIN
CVS Tags: Root-bobdev_news, 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 1.15: +15 -49 lines
Diff to previous 1.15
this, combined with head for ReleaseTools should do reasonable thing
for .c code

Revision 1.15 - (view) (download) (annotate) - [select for diffs]
Tue Apr 12 21:19:57 2005 UTC (14 years, 7 months ago) by efrank
Branch: MAIN
Changes since 1.14: +48 -13 lines
Diff to previous 1.14
revert to efrank-preMakefileToStandardMk to set head of cvs state
until i return

Revision 1.14 - (view) (download) (annotate) - [select for diffs]
Tue Apr 12 20:43:43 2005 UTC (14 years, 7 months ago) by efrank
Branch: MAIN
CVS Tags: partialStandardMkMigration
Changes since 1.13: +13 -48 lines
Diff to previous 1.13
This largely migrates the makefile to use standard.mk.  In particular,
it moves the .c compilation residue out to $(workdir) so that the
source dir stays clean.

this builds but does not link.  i think there's an md5 dependency that
my local env can't meet?

if this is a disaster, there's a tag efrank-preMakefileToStandardMk on
this package before my work that can be revived.

Revision 1.13 - (view) (download) (annotate) - [select for diffs]
Wed Mar 30 00:09:40 2005 UTC (14 years, 7 months ago) by golsen
Branch: MAIN
CVS Tags: efrank-preMakefileToStandardMk
Changes since 1.12: +1 -1 lines
Diff to previous 1.12
Added fastasize to list of C programs.

Revision 1.12 - (view) (download) (annotate) - [select for diffs]
Wed Mar 9 01:48:24 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.11: +4 -2 lines
Diff to previous 1.11
Fix C compile to find perl includes in the current environment.

Revision 1.11 - (view) (download) (annotate) - [select for diffs]
Tue Mar 8 21:06:04 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.10: +6 -1 lines
Diff to previous 1.10
Add support for computing MD5 checksums for contigs and genomes.

The checksum of a genome is defined as the checksum of its signature file. The signature
file consists of tab-separated lines, one for each contig, ordered by the contig id.
Each line contains the contig ID, the length of the contig in nucleotides, and the
MD5 checksum of the nucleotide data, with uppercase letters forced to lower case.

The signature file is written by index_contigs to
The genome's md5 checksum is written by index_contigs to <genomedir>/MD5SUM.

The md5.c code here is extracted from the Perl Digest::MD5 module. We use the perl
configuration to build it so that it will work correctly on 64-bit architectures.

Revision 1.10 - (view) (download) (annotate) - [select for diffs]
Fri Nov 19 22:02:55 2004 UTC (14 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.9: +3 -0 lines
Diff to previous 1.9
Fix makefiles for change in releasetools.

Revision 1.9 - (view) (download) (annotate) - [select for diffs]
Wed Sep 29 18:22:53 2004 UTC (15 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.8: +2 -0 lines
Diff to previous 1.8
Changes for new toplevel makefile structure.

Revision 1.8 - (view) (download) (annotate) - [select for diffs]
Tue Aug 24 22:11:50 2004 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.7: +19 -1 lines
Diff to previous 1.7
Gary Olsen's optimized database loading code.

This probably needs to be tweaked to use the full path (FIG_Config::bin/<app>), but I
want to get this committed today.

Revision 1.7 - (view) (download) (annotate) - [select for diffs]
Wed Jun 16 16:08:20 2004 UTC (15 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.6: +7 -1 lines
Diff to previous 1.6
Clean up map support.

Revision 1.6 - (view) (download) (annotate) - [select for diffs]
Tue Dec 23 19:20:44 2003 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.5: +2 -4 lines
Diff to previous 1.5
new build structure.

Revision 1.5 - (view) (download) (annotate) - [select for diffs]
Wed Dec 3 02:31:02 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-01, delong-01, delong-02
Changes since 1.4: +17 -3 lines
Diff to previous 1.4

   o removed the files that are generated by configure-env
   o removed FIG_Config.pm from every package where it existed:
     we generate it now.
   o Modified makefiles to all have lib bin clean and test targets
     although some don't do anything
   o Modified makefiles to call configure-env to generate files needed.
     This needs to be improved in the future.

Revision 1.4 - (view) (download) (annotate) - [select for diffs]
Tue Dec 2 23:46:04 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
Changes since 1.3: +0 -2 lines
Diff to previous 1.3

removef all: target.

Revision 1.3 - (view) (download) (annotate) - [select for diffs]
Mon Dec 1 20:58:35 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-00
Changes since 1.2: +1 -1 lines
Diff to previous 1.2

Use PKGNAME macro from the top makefile

Revision 1.2 - (view) (download) (annotate) - [select for diffs]
Mon Dec 1 20:46:40 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
Changes since 1.1: +12 -17 lines
Diff to previous 1.1

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

Revision 1.1.1.1 - (view) (download) (annotate) - [select for diffs] (vendor branch)
Mon Dec 1 16:55:42 2003 UTC (15 years, 11 months ago) by efrank
Branch: initial
CVS Tags: init
Changes since 1.1: +0 -0 lines
Diff to previous 1.1 , to next main 1.31

import


Revision 1.1 - (view) (download) (annotate) - [select for diffs]
Mon Dec 1 16:55:42 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
Branch point for: initial
Initial revision

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