For VarDict-Java, install utility scripts. (#12488)

* For VarDict-Java, install utility scripts.

Utility script that were previously only shipped with VarDict are not
part of VarDict-Java as well, making installation of both packages
unnecessary.

* Bump build.

* Improve variable name.

* Make vardict depend on vardict-java for utility scripts.

recipes/vardict-java/build.sh

@@ -7,5 +7,8 @@ mkdir -p $PREFIX/bin
 
 cp lib/*.jar $outdir/lib
 cp bin/VarDict $outdir/bin/vardict-java
-chmod +x $outdir/bin/vardict-java
-ln -s $outdir/bin/vardict-java $PREFIX/bin
+cp bin/*.{R,pl} $outdir/bin
+for executable in vardict-java testsomatic.R teststrandbias.R var2vcf_paired.pl var2vcf_valid.pl; do
+  chmod +x $outdir/bin/$executable
+  ln -s $outdir/bin/$executable $PREFIX/bin
+done

recipes/vardict-java/meta.yaml

@@ -9,16 +9,19 @@ source:
   sha256: 36a177b06114ea939d24f7037b6e339b58e572763736a589232f0ced3731735b
 
 build:
-  number: 0
+  number: 1
   noarch: generic
 
 requirements:
   run:
     - openjdk
+    - perl
+    - r-base
 
 test:
   commands:
     - vardict-java -h
+    - var2vcf_paired.pl -h
 
 about:
   home: https://github.com/AstraZeneca-NGS/VarDictJava

recipes/vardict/build.sh

@@ -12,8 +12,4 @@ chmod a+x $outdir/*.pl
 chmod a+x $outdir/*.R
 ln -s $outdir/vardict.pl $PREFIX/bin/vardict
 ln -s $outdir/vardict.pl $PREFIX/bin
-ln -s $outdir/testsomatic.R $PREFIX/bin
-ln -s $outdir/teststrandbias.R $PREFIX/bin
-ln -s $outdir/var2vcf_valid.pl $PREFIX/bin
-ln -s $outdir/var2vcf_paired.pl $PREFIX/bin
 ln -s $outdir/vardict2mut.pl $PREFIX/bin

recipes/vardict/meta.yaml

@@ -12,15 +12,15 @@ source:
   sha256: '{{sha256}}'
 
 build:
-  number: 0
+  number: 1
 
 requirements:
   host:
     - perl
-    - r-base
+    - vardict-java
   run:
     - perl
-    - r-base
+    - vardict-java
 
 test:
   commands: