Changeset 7982 for trunk/doc/src/docbook/overview

Timestamp:

Jun 14, 2021, 10:01:21 AM (2 years ago)

Author:

Nicklas Nordborg

Message:

Merge BASE 3.18.2 to the trunk

Location:

trunk

Files:

• . (modified) (1 prop)
• doc/src/docbook/overview/features.xml (modified) (4 diffs)
• doc/src/docbook/overview/resources.xml (modified) (7 diffs)
• doc/src/docbook/overview/why_base.xml (modified) (1 diff)

trunk/doc/src/docbook/overview/features.xml

@@ -158 +158 @@
       of tools are pre-installed with BASE, and optional plug-ins can
       be downloaded from the <ulink
-      url="http://baseplugins.thep.lu.se">BASE plug-in site
+      url="https://baseplugins.thep.lu.se">BASE plug-in site
       </ulink>. BASE capitalise from other software tools, such as
       MEV, by integrating them into the user interface. Such
@@ -257 +257 @@
       BASE comes with a specific Affymetrix platform and Illumina can
       be supported by customising BASE (go to the <ulink
-      url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
+      url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
       Illumina package</ulink> web site for more information on adding
       Illumina support to BASE).
@@ -335 +335 @@
               platform support is not included in a standard BASE
               installation but there is a <ulink
-              url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
+              url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
               Illumina package</ulink> available for seamless
               integration of the Illumina array platform to BASE.
@@ -472 +472 @@
               Not available in BASE directly but it is added with the
               <ulink
-              url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
+              url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
               Illumina plug-in</ulink> that adds Illumina array
               platform support to BASE.

trunk/doc/src/docbook/overview/resources.xml

@@ -38 +38 @@
     <para>
       The BASE project site is located at
-      <ulink url='http://base.thep.lu.se'>http://base.thep.lu.se</ulink>.
+      <ulink url='https://base.thep.lu.se'>https://base.thep.lu.se</ulink>.
       Here is a lot of useful information about the project and the program, e.g.
       documentation/manuals, download-pages, contact information and much more. The most
@@ -48 +48 @@
         The download page is accessed from the download section, on the home page, by
         following the link to
-        <guilabel><ulink url='http://base.thep.lu.se/wiki/DownloadPage'
+        <guilabel><ulink url='https://base.thep.lu.se/wiki/DownloadPage'
           >Download Page</ulink></guilabel>. 
         From this page you can download BASE releases as packaged tar.gz
@@ -110 +110 @@
         A ticket is a note about a bug or a new feature that has not yet been
         implemented. To show the list of outstanding tickets use the
-        <guibutton><ulink url="http://base.thep.lu.se/query"
+        <guibutton><ulink url="https://base.thep.lu.se/query"
           >View Tickets</ulink></guibutton> button on BASE web site. 
         It is a good idea to have a look at this list before reporting a bug
@@ -131 +131 @@
       <para>
         The roadmap of BASE is accessed from the 
-        <guibutton><ulink url="http://base.thep.lu.se/roadmap"
+        <guibutton><ulink url="https://base.thep.lu.se/roadmap"
           >Roadmap</ulink></guibutton> button on the home page. This page 
         contains information about the plans for future development, including
@@ -197 +197 @@
       Plug-ins which are not included in the installation of BASE, have their own site,
       called
-      <ulink url="http://baseplugins.thep.lu.se/">BASE plug-ins web site</ulink>
+      <ulink url="https://baseplugins.thep.lu.se/">BASE plug-ins web site</ulink>
       which includes a download page for submitted none-core plug-ins.      
       Here is also information how to become a plug-in developer, with 
@@ -211 +211 @@
       explore BASE without having to install it. Follow the link on
       BASE web site to the demo server or go directly to
-      <ulink url="http://base.onk.lu.se/demo/">
-        http://base.onk.lu.se/demo/
+      <ulink url="https://base.onk.lu.se/demo/">
+        https://base.onk.lu.se/demo/
       </ulink>. NOTE! The demo server is currently down!
     </para>
@@ -229 +229 @@
     <para>
       BASE project has three different mailing lists available for subscription. Visit the
-      <ulink url="http://base.thep.lu.se/wiki/MailingLists">mailing list page</ulink>
+      <ulink url="https://base.thep.lu.se/wiki/MailingLists">mailing list page</ulink>
       to get more information about each one of the mailing lists. All posted mails are saved
       in an archive for each list, it can therefore be a good idea to have a look here before

trunk/doc/src/docbook/overview/why_base.xml

@@ -104 +104 @@
       BASE. This implies interplay with adopting the BASE software
       (the <ulink
-      url='http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie'>Reggie
+      url='https://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie'>Reggie
       extension</ulink> is an example of adaptation on BASE to
       specific needs in SCAN-B) and the laboratory work to achieve