Help doesn't work with EMBOSS v6.1.0
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#18 Help doesn't work with EMBOSS v6.1.0
The EMBOSS Explorer (EE) v2.2.0 help pages don't work with the current release of EMBOSS (v6.1.0). When you click on "read the manual" link at the top of an EMBOSS application web page, only a blank page is opened. A quick look in the install script indicates support for v3 and v4 EMBOSS help file paths. Although the v3 help file path seems to match the v6 HTML help directory, the script only copies non-html files (i.e. image files such as .gif) over to EE's manual directory - presumably due to the presence of the ! unary operator. However, even when the EMBOSS help HTML files are copied over manually, they are not opened in EE.
I think it wound make EE more robust to change if instead of copying the local EMBOSS help files, EE pointed to the online documentation, which is always kept up-to-date and is the default setting for the Jemboss GUI e.g. http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/\*.html
This approach might need a question in the EE install script to make EE use this URL. Please take a look at the way Jemboss achieves this programmatically. I think it probes the version of EMBOSS via the "embossversion" binary (/usr/local/emboss/bin) and then appends the returned version number to the base URL (http://emboss.sourceforge.net/) that is set at the time of installation via the Jemboss install script.
I agree this is a problem, but as a quick fix I copied the contents of EMBOSS-6.1.0/doc/programs/html to /usr/share/EMBOSS/doc/html on my Fedora 12 installation, and EMBOSS Explorer 2.2.0 now displays the help files when clicking on the "read the manual" link.
I'd already tried this, but it didn't work for me. However I moved the HTML help file directory to the /usr/share/EMBOSS/doc/ retrospectively, after I'd installed EMBOSS Explorer. Perhaps if I placed it in the expected location before installing EE, it would work? The other possible reason that it didn't work is that I was using a pre-release version of EMBOSS-6.2.0. The final version was officially released today, so I'll try that and let you know how I get on.
I can confirm that the work around described by mcoyne does work, when used with the official final release of EMBOSS-6.2.0. As far as I can see, it doesn't matter whether the EMBOSS help files are moved into the directory expected by EMBOSS Explorer 2.2.0 either before or after EE is installed. Many thanks for your help.
On reflection, please ignore my suggestion to have EMBOSS Explorer pointing to the online documentation. It would be much better if the EE installer script was modified to include an option to point to the path of the locally stored EMBOSS html documentation, as the EMBOSS team appears to change its location from time to time within their directory structure. With this modification, the user just has to check where the EMBOSS documentation is located prior to installing EE.