Author: tille
Date: 2008-09-11 13:01:12 +0000 (Thu, 11 Sep 2008)
New Revision: 2483
Added:
trunk/packages/agdbnet/trunk/debian/agdbnet.xml
trunk/packages/agdbnet/trunk/debian/links
trunk/packages/agdbnet/trunk/debian/patches/10_bioperl.patch
trunk/packages/agdbnet/trunk/debian/patches/10_moreinfo.patch
trunk/packages/agdbnet/trunk/debian/patches/10_preconf.patch
Modified:
trunk/packages/agdbnet/trunk/debian/control
trunk/packages/agdbnet/trunk/debian/install
trunk/packages/agdbnet/trunk/debian/patches/series
trunk/packages/agdbnet/trunk/debian/rules
Log:
More adaptations to Debian locations
Added: trunk/packages/agdbnet/trunk/debian/agdbnet.xml
===================================================================
--- trunk/packages/agdbnet/trunk/debian/agdbnet.xml
(rev 0)
+++ trunk/packages/agdbnet/trunk/debian/agdbnet.xml 2008-09-11 13:01:12 UTC
(rev 2483)
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="ISO-8859-1" ?>
+<agdb>
+
+<!-- ______________________________________________________ -->
+<!-- Before you start -->
+<!-- ________________ -->
+<!-- As long as there are values marked like ##this## the -->
+<!-- XML file is not usable -->
+<!-- Make sure you read /usr/share/doc/agdbnet/README.Debian -->
+<!-- to learn what has to be done! -->
+<!-- ______________________________________________________ -->
+
+<system
+ longcode="##codename##" webroot="/##codename##" indexpage=""
+ description="##Description##"
+ downloadFASTAonly="yes"
+>
+##Name##</system>
+
+<!-- LOCI -->
+<locus fullname="##Shortname##">##codename##
+<nucleotide>
+<field type="int" length="##?##" userupdate="no" comments="primary
key">id</field>
+<field type="text" length="##?##" width="30" maindisplay="no">sequence</field>
+<field type="int" length="##?##" comments="foreign key to peptide
table">peptide_id</field>
+<field type="text" length="##?##" required="no"
maindisplay="no">genbank</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed
number if published">reference1</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed
number if published">reference2</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed
number if published">reference3</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed
number if published">reference4</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed
number if published">reference5</field>
+<field type="int" maindisplay="no" length="4" comments="sender unique name,
link to users">sender</field>
+<field type="DATE" maindisplay="no" userupdate="no" length="10" comments="date
last modified">datestamp</field>
+<field type="int" maindisplay="no" userupdate="no" length="4"
comments="curator who entered data,link to users">curator</field>
+</nucleotide>
+
+<peptide>
+<field type="int" length="##?##" userupdate="no" comments="primary
key">id</field>
+<field type="text" length="##?##" userupdate="no" width="30">sequence</field>
+<field type="text" length="##?##" required="no"
maindisplay="no">genbank</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed
number if published">reference1</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed
number if published">reference2</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed
number if published">reference3</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed
number if published">reference4</field>
+<field type="int" required="no" maindisplay="no" length="10" comments="PubMed
number if published">reference5</field>
+<field type="int" maindisplay="no" length="4" comments="sender unique name,
link to users">sender</field>
+<field type="DATE" maindisplay="no" userupdate="no" length="10" comments="date
last modified">datestamp</field>
+<field type="int" maindisplay="no" userupdate="no" length="4"
comments="curator who entered data,link to users">curator</field>
+</peptide>
+</locus>
+
+</agdb>
Modified: trunk/packages/agdbnet/trunk/debian/control
===================================================================
--- trunk/packages/agdbnet/trunk/debian/control 2008-09-11 12:17:16 UTC (rev
2482)
+++ trunk/packages/agdbnet/trunk/debian/control 2008-09-11 13:01:12 UTC (rev
2483)
@@ -12,7 +12,7 @@
Package: agdbnet
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, emboss-lib, blast2,
postgresql-8.3,
+Depends: ${shlibs:Depends}, ${misc:Depends}, emboss, blast2, postgresql-8.3,
libcgi-pm-perl, libdbd-pg-perl, libxml-perl
Description: antigen sequence database software for web-based bacterial typing
AgdbNet facilitates simultaneous BLAST querying of multiple loci using
Modified: trunk/packages/agdbnet/trunk/debian/install
===================================================================
--- trunk/packages/agdbnet/trunk/debian/install 2008-09-11 12:17:16 UTC (rev
2482)
+++ trunk/packages/agdbnet/trunk/debian/install 2008-09-11 13:01:12 UTC (rev
2483)
@@ -1 +1,2 @@
-cgi-bin usr/lib
+cgi-bin usr/lib
+debian/agdbnet.xml etc/agdbnet
Added: trunk/packages/agdbnet/trunk/debian/links
===================================================================
--- trunk/packages/agdbnet/trunk/debian/links (rev 0)
+++ trunk/packages/agdbnet/trunk/debian/links 2008-09-11 13:01:12 UTC (rev
2483)
@@ -0,0 +1,2 @@
+etc/agdbnet/agdbnet.xml usr/lib/cgi-bin/agdbnet.xml
+
Added: trunk/packages/agdbnet/trunk/debian/patches/10_bioperl.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/10_bioperl.patch
(rev 0)
+++ trunk/packages/agdbnet/trunk/debian/patches/10_bioperl.patch
2008-09-11 13:01:12 UTC (rev 2483)
@@ -0,0 +1,10 @@
+--- agdbnet_v1.0.0.orig/cgi-bin/agdbnet.pl
++++ agdbnet_v1.0.0/cgi-bin/agdbnet.pl
+@@ -31,6 +31,7 @@
+ ###########Optional modules###########################
+ #Bio::AlignIO used for generating sequences in different formats.
+ # if not installed ensure that 'bioperl=0' is set in agdbnet.conf
++use Bio::AlignIO;
+ #
+ ######################################################
+
Added: trunk/packages/agdbnet/trunk/debian/patches/10_moreinfo.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/10_moreinfo.patch
(rev 0)
+++ trunk/packages/agdbnet/trunk/debian/patches/10_moreinfo.patch
2008-09-11 13:01:12 UTC (rev 2483)
@@ -0,0 +1,23 @@
+--- agdbnet_v1.0.0.orig/cgi-bin/agcurate.pl
++++ agdbnet_v1.0.0/cgi-bin/agcurate.pl
+@@ -129,7 +129,7 @@
+ print $q->header;
+ if ($invalidXML) {
+ print $q->start_html( -title => "Invalid XML file" );
+- print "<p>Invalid (or no) database description file
specified!</p>";
++ print "<p>Invalid (or no) database description file
specified!<br />Please follow the instructions at
/usr/share/doc/agdbnet/README.Debian to get a running system.</p>";
+ print $q->end_html;
+ return;
+ }
+--- agdbnet_v1.0.0.orig/cgi-bin/agdbnet.pl
++++ agdbnet_v1.0.0/cgi-bin/agdbnet.pl
+@@ -198,7 +198,8 @@
+ }
+ if ($invalidXML) {
+ print $q->start_html( -title => "Invalid XML file" );
+- print "<p>Invalid (or no) database description file
specified!</p>";
++ print "<p>Invalid (or no) database description file specified!
(agdbnet.pl) Please follow the instructions at
/usr/share/doc/agdbnet/README.Debian to get a running system.
($system{'webroot'}/$system{'longcode'})</p>";
++ print $system{'webroot'} . "//" . $system{'longcode'};
+ print $q->end_html;
+ return;
+ }
Added: trunk/packages/agdbnet/trunk/debian/patches/10_preconf.patch
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/10_preconf.patch
(rev 0)
+++ trunk/packages/agdbnet/trunk/debian/patches/10_preconf.patch
2008-09-11 13:01:12 UTC (rev 2483)
@@ -0,0 +1,23 @@
+--- agdbnet_v1.0.0.orig/conf/agdbnet.conf
++++ agdbnet_v1.0.0/conf/agdbnet.conf
+@@ -1,17 +1,17 @@
+ ###GENERAL####
+-tmp_dir=/var/www/html/tmp
++tmp_dir=/var/www/agdbnet/tmp
+
+ ####EMBOSS####
+ #used for sequence alignment in allele query
+ #set 'emboss=0' to remove functionality
+ emboss=1
+-emboss_path=/usr/local/bin
++emboss_path=/usr/lib/emboss
+
+ ####BLAST######
+ #Used for databases where sequences are of unequal
+ #length.
+ blast=1
+-blast_path=/usr/local/blast/bin
++blast_path=/usr/bin
+
+ ####BIOPERL####
+ #Used for creating sequences in multiple formats.
Modified: trunk/packages/agdbnet/trunk/debian/patches/series
===================================================================
--- trunk/packages/agdbnet/trunk/debian/patches/series 2008-09-11 12:17:16 UTC
(rev 2482)
+++ trunk/packages/agdbnet/trunk/debian/patches/series 2008-09-11 13:01:12 UTC
(rev 2483)
@@ -1,3 +1,4 @@
10_conf_location.patch
10_bioperl.patch
10_preconf.patch
+10_moreinfo.patch
Modified: trunk/packages/agdbnet/trunk/debian/rules
===================================================================
--- trunk/packages/agdbnet/trunk/debian/rules 2008-09-11 12:17:16 UTC (rev
2482)
+++ trunk/packages/agdbnet/trunk/debian/rules 2008-09-11 13:01:12 UTC (rev
2483)
@@ -7,6 +7,8 @@
pkg=agdbnet
+DEB_COMPRESS_EXCLUDE := .xml
+
common-binary-post-install-arch::
# Directory conf has to be copied to /etc/agdbnet
- cp -a conf debian/$(pkg)/etc/$(pkg)
+ cp -a conf/* debian/$(pkg)/etc/$(pkg)
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