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removing defunct files

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1 parent f5ed6a2 commit fff94f9533cf188ff71e7d1035431b11a7ae20a5 @lstein lstein committed Oct 17, 2008
Showing with 253 additions and 286 deletions.
  1. +2 −0 Build.PL
  2. +0 −17 MANIFEST
  3. +3 −0 MANIFEST.SKIP
  4. +4 −4 conf/GBrowse.conf
  5. +0 −54 conf/Gbrowse_karyotype.conf
  6. +172 −91 install_util/GBrowseInstall.pm
  7. +72 −115 install_util/GuessDirectories.pm
  8. +0 −5 pkg_config.in
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@@ -51,6 +51,8 @@ for my $arg (keys %{$build->private_props}) {
$build->config_data($arg=>$value);
}
+$build->add_build_element('conf');
+$build->add_build_element('htdocs');
$build->create_build_script;
exit 0;
View
@@ -3,19 +3,11 @@ bin/sync-bioperl.sh
Build.PL
cgi-bin/gbrowse
cgi-bin/gbrowse_details
-cgi-bin/gbrowse_drag
-cgi-bin/gbrowse_gff_autocomplete
cgi-bin/gbrowse_img
-cgi-bin/gbrowse_karyotype
-cgi-bin/gbrowse_not
-cgi-bin/gbrowse_seqfeature_autocomplete
-cgi-bin/gbrowse_syn
-cgi-bin/gbrowset
cgi-bin/README
Changes
conf/enzymes.txt
conf/GBrowse.conf
-conf/Gbrowse_karyotype.conf
conf/languages/de.pm
conf/languages/en.pm
conf/languages/es.pm
@@ -87,7 +79,6 @@ conf/templates/default/set_track_options_controls.tt2
conf/templates/default/slider.tt2
conf/templates/default/sourcemenu.tt2
conf/templates/default/start_section.tt2
-conf/templates/default/trackstable.bak.tt2
conf/templates/default/trackstable.tt2
conf/templates/default/uploadedfiles.tt2
conf/templates/default/uploadtable.tt2
@@ -189,7 +180,6 @@ docs/tutorial/conf_files/volvox5.conf
docs/tutorial/conf_files/volvox_final.conf
docs/tutorial/conf_files/volvox_final_withPhylo.conf
docs/tutorial/conf_files/volvox_Phylo.conf
-docs/tutorial/data_files/directory.index
docs/tutorial/data_files/dog1_1700.wig
docs/tutorial/data_files/elegans.fa
docs/tutorial/data_files/elegans_acceptor.gff
@@ -236,7 +226,6 @@ docs/tutorial/data_files/volvox8.gff3
docs/tutorial/data_files/volvox9.gff
docs/tutorial/data_files/volvox9.gff3
docs/tutorial/data_files/volvox_all.fa
-docs/tutorial/data_files/volvox_all.fa.index
docs/tutorial/data_files/volvox_all.gff
docs/tutorial/data_files/volvox_all.gff3
docs/tutorial/data_files/volvox_geneproducts.gff3
@@ -254,7 +243,6 @@ docs/tutorial/dbgff/conf_files/volvox3.conf
docs/tutorial/dbgff/conf_files/volvox4.conf
docs/tutorial/dbgff/conf_files/volvox5.conf
docs/tutorial/dbgff/conf_files/volvox_final.conf
-docs/tutorial/dbgff/data_files/directory.index
docs/tutorial/dbgff/data_files/elegans.fa
docs/tutorial/dbgff/data_files/elegans_acceptor.gff
docs/tutorial/dbgff/data_files/elegans_core.gff
@@ -278,7 +266,6 @@ docs/tutorial/dbgff/data_files/volvox7.gff
docs/tutorial/dbgff/data_files/volvox8.gff
docs/tutorial/dbgff/data_files/volvox9.gff
docs/tutorial/dbgff/data_files/volvox_all.fa
-docs/tutorial/dbgff/data_files/volvox_all.fa.index
docs/tutorial/dbgff/data_files/volvox_all.gff
docs/tutorial/dbgff/data_files/volvox_trace.scf
docs/tutorial/dbgff/figures/adding_dna_to_alignments1.gif
@@ -437,15 +424,13 @@ htdocs/css/tracks.css
htdocs/databases/ideograms/human_cytobands.gff
htdocs/databases/ideograms/mouse_cytobands.gff
htdocs/databases/ideograms/rat_cytobands.gff
-htdocs/databases/volvox/directory.index
htdocs/databases/volvox/volvox.fa
htdocs/databases/volvox/volvox.gff
htdocs/databases/volvox2/volvox2.gff
htdocs/databases/volvox3/volvox3.gff
htdocs/databases/volvox4/volvox4.gff3
htdocs/databases/yeast_chr1+2/chr1.fa
htdocs/databases/yeast_chr1+2/chr2.fa
-htdocs/databases/yeast_chr1+2/directory.index
htdocs/databases/yeast_chr1+2/yeast_chr1+2.gff3
htdocs/databases/yeast_chr1/chromosome1.fa
htdocs/databases/yeast_chr1/chromosome1.gff
@@ -584,11 +569,9 @@ libalign/CAlign.xs
libalign/Changes
libalign/README
libalign/realign.h
-libalign/realign_test.pl
Makefile.PL
MANIFEST This list of files
META.yml
-pkg_config.in
README
README.fedora_and_selinux
README.GBrowse-2.00
View
@@ -36,3 +36,6 @@ libalign/.+\.c
History
prototype-.*\.pdf
lib/Bio/Graphics/Browser/CAlign
+\.index
+\.patch$
+\.notes$
View
@@ -3,9 +3,9 @@
# as the various constants formerly scattered amongst scripts and libraries
[GENERAL]
-config_base = /etc/apache2/gbrowse.conf # overriden by environment $GBROWSE_CONF
-htdocs_base = /var/www # overriden by environment $GBROWSE_HTDOCS
-url_base = /gbrowse # overriden by environment $GBROWSE_ROOT
+config_base = /etc/GBrowse2 # overriden by environment variable GBROWSE_CONF
+htdocs_base = /var/www # overriden by environment variable GBROWSE_HTDOCS
+url_base = /gbrowse # overriden by environment variable GBROWSE_ROOT
# These paths are relative to the url base
buttons = images/buttons
@@ -64,7 +64,7 @@ head =
header =
# At the footer
-footer = <hr /><pre>$Id: GBrowse.conf,v 1.24 2008-10-11 00:02:42 lstein Exp $</pre>
+footer = <hr /><pre>$Id: GBrowse.conf,v 1.25 2008-10-17 17:11:30 lstein Exp $</pre>
# Various places where you can insert your own HTML -- see configuration docs
html1 =
@@ -1,54 +0,0 @@
-# default configuration for gbrowse_karyotype
-
-[GENERAL]
-description = no source
-
-max segment = 1000000000000
-
-# Web site configuration info
-tmpimages = /gbrowse/tmp
-stylesheet = /gbrowse/gbrowse.css
-buttons = /gbrowse/images/buttons
-
-# how long to save cached images
-image cachetime = 2_592_000
-
-[karyotype]
-max_height = 500
-cwidth = 25
-cytoband_track = ideogram
-bands = chromosome_band cytoband centromere
-
-# Default glyph settings
-[TRACK DEFAULTS]
-glyph = triangle
-height = 8
-bgcolor = black
-fgcolor = black
-label density = 25
-bump density = 50
-description = 0
-label = 0
-orient = E
-point = 1
-
-[ideogram]
-glyph = ideogram
-fgcolor = black
-bgcolor = gneg:white gpos25:silver gpos50:gray gpos:gray gpos75:darkgray gpos100:black gvar:var stalk:#666666
-arcradius = 7
-height = 20
-bump = 0
-
-
-
-
-
-
-
-
-
-
-
-
-
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