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

Merge BASE 3.18.2 to the trunk

4 edited


  • trunk

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

    r6465 r7982  
    158158      of tools are pre-installed with BASE, and optional plug-ins can
    159159      be downloaded from the <ulink
    160       url="http://baseplugins.thep.lu.se">BASE plug-in site
     160      url="https://baseplugins.thep.lu.se">BASE plug-in site
    161161      </ulink>. BASE capitalise from other software tools, such as
    162162      MEV, by integrating them into the user interface. Such
    257257      BASE comes with a specific Affymetrix platform and Illumina can
    258258      be supported by customising BASE (go to the <ulink
    259       url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
     259      url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
    260260      Illumina package</ulink> web site for more information on adding
    261261      Illumina support to BASE).
    335335              platform support is not included in a standard BASE
    336336              installation but there is a <ulink
    337               url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
     337              url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
    338338              Illumina package</ulink> available for seamless
    339339              integration of the Illumina array platform to BASE.
    472472              Not available in BASE directly but it is added with the
    473473              <ulink
    474               url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
     474              url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">
    475475              Illumina plug-in</ulink> that adds Illumina array
    476476              platform support to BASE.
  • trunk/doc/src/docbook/overview/resources.xml

    r6576 r7982  
    3838    <para>
    3939      The BASE project site is located at
    40       <ulink url='http://base.thep.lu.se'>http://base.thep.lu.se</ulink>.
     40      <ulink url='https://base.thep.lu.se'>https://base.thep.lu.se</ulink>.
    4141      Here is a lot of useful information about the project and the program, e.g.
    4242      documentation/manuals, download-pages, contact information and much more. The most
    4848        The download page is accessed from the download section, on the home page, by
    4949        following the link to
    50         <guilabel><ulink url='http://base.thep.lu.se/wiki/DownloadPage'
     50        <guilabel><ulink url='https://base.thep.lu.se/wiki/DownloadPage'
    5151          >Download Page</ulink></guilabel>.
    5252        From this page you can download BASE releases as packaged tar.gz
    110110        A ticket is a note about a bug or a new feature that has not yet been
    111111        implemented. To show the list of outstanding tickets use the
    112         <guibutton><ulink url="http://base.thep.lu.se/query"
     112        <guibutton><ulink url="https://base.thep.lu.se/query"
    113113          >View Tickets</ulink></guibutton> button on BASE web site.
    114114        It is a good idea to have a look at this list before reporting a bug
    131131      <para>
    132132        The roadmap of BASE is accessed from the
    133         <guibutton><ulink url="http://base.thep.lu.se/roadmap"
     133        <guibutton><ulink url="https://base.thep.lu.se/roadmap"
    134134          >Roadmap</ulink></guibutton> button on the home page. This page
    135135        contains information about the plans for future development, including
    197197      Plug-ins which are not included in the installation of BASE, have their own site,
    198198      called
    199       <ulink url="http://baseplugins.thep.lu.se/">BASE plug-ins web site</ulink>
     199      <ulink url="https://baseplugins.thep.lu.se/">BASE plug-ins web site</ulink>
    200200      which includes a download page for submitted none-core plug-ins.     
    201201      Here is also information how to become a plug-in developer, with
    211211      explore BASE without having to install it. Follow the link on
    212212      BASE web site to the demo server or go directly to
    213       <ulink url="http://base.onk.lu.se/demo/">
    214         http://base.onk.lu.se/demo/
     213      <ulink url="https://base.onk.lu.se/demo/">
     214        https://base.onk.lu.se/demo/
    215215      </ulink>. NOTE! The demo server is currently down!
    216216    </para>
    229229    <para>
    230230      BASE project has three different mailing lists available for subscription. Visit the
    231       <ulink url="http://base.thep.lu.se/wiki/MailingLists">mailing list page</ulink>
     231      <ulink url="https://base.thep.lu.se/wiki/MailingLists">mailing list page</ulink>
    232232      to get more information about each one of the mailing lists. All posted mails are saved
    233233      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

    r5844 r7982  
    104104      BASE. This implies interplay with adopting the BASE software
    105105      (the <ulink
    106       url='http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie'>Reggie
     106      url='https://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie'>Reggie
    107107      extension</ulink> is an example of adaptation on BASE to
    108108      specific needs in SCAN-B) and the laboratory work to achieve
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