Re: Java question: How to query picard-tools for --version
----- Mail original -----
> De: "Andreas Tille" <andreas@an3as.eu>
> À: "Debian Med Project List" <debian-med@lists.debian.org>
> Envoyé: Jeudi 28 Juillet 2016 14:43:27
> Objet: Java question: How to query picard-tools for --version
>
> Hi,
>
> I'm struggling to package metaBIT[1] and I'm currently stumbling upon
> the fact that it is querying picard-tools for its version number. While
> I could proably simply skip this test and make sure via dependencies
> that this is fullfilled I'd like to understand the issue myself.
>
> When grepping picard-tools source there is a definition of --version
> option:
>
> /picard-tools(master) $ grep -R -- "-version" | grep ^src
> src/main/resources/release_picard.sh:# java_version=`java -version 2>&1 |
> fgrep -i version`
> src/main/java/picard/cmdline/CommandLineParser.java: {"--version",
> null, "Displays program version."}
> src/main/java/picard/cmdline/CommandLineParser.java: if
> (arg.equals("--version")) {
>
>
> When trying
>
> /usr/bin/PicardCommandLine --version
>
> I get
>
> ...
> '--version' is not a valid command. See PicardCommandLine --help for more
> information.
>
>
> Funny enough also
>
> /usr/bin/PicardCommandLine --help
>
> ends up in
>
> ...
> '--help' is not a valid command. See PicardCommandLine --help for more
> information.
>
>
> When calling the command inside PicardCommandLine manually and add the
> specific
> class that contains the --version option
>
>
> java -XX:MaxPermSize=256m -jar /usr/share/java/picard.jar
> picard.cmdline.CommandLineParser --version
>
> I get
>
> ...
> 'picard.cmdline.CommandLineParser' is not a valid command. See
> PicardCommandLine --help for more information.
>
>
> I also tried
>
> ava -classpath /usr/share/java/picard.jar
> main=picard.cmdline.CommandLineParser --version
> Error: Could not find or load main class
> main=picard.cmdline.CommandLineParser
>
>
> So how can I successfully query for the picard-tools version.
--version is not used directly. PicardCommandLine accepts -h or a program name.
Then you can query --version for a specific program, example:
PicardCommandLine SortVcf --version
Olivier
>
> Kind regards
>
> Andreas.
>
>
> [1] https://anonscm.debian.org/git/debian-med/metabit.git
>
> --
> http://fam-tille.de
>
>
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