<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<br>
<br>
Le 12/29/11 7:08 PM, Justin B Rye a écrit :
<blockquote cite="mid:20111229180835.GA2614@xibalba.demon.co.uk"
type="cite">
<pre wrap="">Christian PERRIER wrote:
</pre>
<blockquote type="cite">
<pre wrap=""> Template: biomaj/jdk_home
Type: string
+_Description: JDK home directory:
+ Please enter the directory where the Java Development Kit,
+ which is used by BioMAJ, is installed.
</pre>
</blockquote>
<pre wrap="">
That's European-style relative clause punctuation. You want:
Please specify the directory where the Java Development Kit
which is used by BioMAJ is installed.
Or, since the place where it's installed is the place where it is,
simplify to:
Please specify the path to the Java Development Kit for BioMAJ.
</pre>
<blockquote type="cite">
<pre wrap="">Give more details. I however wonder why this has to be
configured. Shouldn't the package depends on a JDK and therefore
"know" where it is installed?
</pre>
</blockquote>
<pre wrap="">
It does have a "Depends: openjdk-6-jdk|default-jdk|sun-java6-jdk", so
yes, this sounds like a job for policy and/or $JAVA_HOME.</pre>
</blockquote>
In fact, JDK path is required somewhere in configuration files,
that's why question is asked, even if jdk dependency is set.<br>
<blockquote cite="mid:20111229180835.GA2614@xibalba.demon.co.uk"
type="cite">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap=""> Template: biomaj/mysql
Type: boolean
+_Description: Configure MySQL connection now?
+ Please choose whether you want to configure connection
+ parameters for the BioMAJ MySQL database.
+ .
+ Please note that the database has to be created and configured
+ before it can be used.
Use "BioMAJ" as this seems to be the "official" way to write the
software name?
</pre>
</blockquote>
<pre wrap="">
Upstream seem to think so. I notice there's a bit more information in
the revised version, but it's still rather unclear to me exactly what
it is that needs to happen first or what this allows to happen second.
Candidates for both include:
a) the package mysql-server-x.y being fully installed
b) a "biomaj_log" database and dbadmin being created
c) the connection parameters being set up via debconf
d) BioMAJ being configured to populate the database automatically
I'm guessing that (a) is a prerequisite for (c) which gives you (d),
but is doing (b) also a prerequisite or is it automated?
</pre>
</blockquote>
<br>
(a) is a prerequisite<br>
For automation, (b) and (c) are required for (d).<br>
If (b) or (c) is not satistifed, then database population has to be
done manually after package installation.<br>
<br>
<blockquote cite="mid:20111229180835.GA2614@xibalba.demon.co.uk"
type="cite">
<pre wrap="">
Maybe:
Once the MySQL database for BioMAJ has been created and configured, it
can populate itself automatically instead of needing to be updated
manually.
.
Please specify whether the database connection should be configured now.
</pre>
<blockquote type="cite">
<pre wrap=""> Template: biomaj/mysql_host
</pre>
</blockquote>
<pre wrap="">[...]
</pre>
<blockquote type="cite">
<pre wrap=""> Template: biomaj/mysql_login
</pre>
</blockquote>
<pre wrap="">[...]
</pre>
<blockquote type="cite">
<pre wrap=""> Template: biomaj/mysql_passwd
</pre>
</blockquote>
<pre wrap="">
These look good.
</pre>
<blockquote type="cite">
<pre wrap=""> Package: biomaj
</pre>
</blockquote>
<pre wrap="">[...]
</pre>
<blockquote type="cite">
<pre wrap="">+Description: biological banks updater
</pre>
</blockquote>
<pre wrap="">
The top hits for "biological banks" are all talking about tissue
sample repositories. What you mean is
Description: biological data-bank updater</pre>
</blockquote>
Correct<br>
<blockquote cite="mid:20111229180835.GA2614@xibalba.demon.co.uk"
type="cite">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">+ BioMAJ downloads remote data banks, checks their status and applies transformation
+ workflows, with consistent state, to provide ready-to-use data to biologists and
bioinformaticians. For example, it can transform original fasta files to blast
indexes. It is very flexible and post-processes can be extended very easily.
No leading uppercase in synopsis.
Some grammar corrections.
</pre>
</blockquote>
<pre wrap="">
Better, but: s/fasta/FASTA/, s/blast/BLAST/ (not to be confused with
the Debian package "blast"), and I'm not sure about "post-processes" -
maybe "its post-processing facilities"?</pre>
</blockquote>
Post-processing sounds better indeed.<br>
The software execute some programs, defined in a property file,
after the download of the data. Those programs are referred here as
the "post-processes".<br>
<blockquote cite="mid:20111229180835.GA2614@xibalba.demon.co.uk"
type="cite">
<pre wrap="">
BioMAJ downloads remote data banks, checks their status and applies
transformation workflows, with consistent state, to provide ready-to-use
data for biologists and bioinformaticians. For example, it can transform
original FASTA files into BLAST indexes. It is very flexible and its
post-processing facilities can be extended very easily.
</pre>
<blockquote type="cite">
<pre wrap=""> Package: biomaj-properties
</pre>
</blockquote>
<pre wrap="">[...]
</pre>
<blockquote type="cite">
<pre wrap=""> Description: bank properties file examples
</pre>
</blockquote>
<pre wrap="">
Even worse - "bank properties" means land owned by financial
institutions...
Description: biological data-bank updater - example properties files
</pre>
<blockquote type="cite">
<pre wrap=""> This package contains a set of bank properties that can be used as
+ examples for BioMAJ. It contains many existing banks descriptions
+ with or without workflows to transform data. Some files may require
+ additional programs for post-processes such as blast.
</pre>
</blockquote>
<pre wrap="">
A couple of extra tweaks (for instance, they're existing data banks,
not existing descriptions):
This package contains a set of data bank properties files that can be
used as examples for BioMAJ. It contains descriptions for many existing
data banks with or without workflows to transform data. Some files may
require additional programs (such as BLAST) for post-processing.
</pre>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Debian-med-packaging mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Debian-med-packaging@lists.alioth.debian.org">Debian-med-packaging@lists.alioth.debian.org</a>
<a class="moz-txt-link-freetext" href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging</a></pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (pgp.mit.edu)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
</pre>
</body>
</html>