[med-svn] [Git][med-team/pilon][master] 2 commits: Fix build (thanks to Markus Koschany)

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / pilon


Commits:
44b4e37e by Andreas Tille at 2018-08-02T07:34:30Z
Fix build (thanks to Markus Koschany)

- - - - -
ee45a7e7 by Andreas Tille at 2018-08-02T07:41:05Z
Install JAR and wrapper script, conflict with pilon-non-free

- - - - -


4 changed files:

- + debian/bin/pilon
- debian/control
- + debian/install
- debian/rules


Changes:

=====================================
debian/bin/pilon
=====================================
--- /dev/null
+++ b/debian/bin/pilon
@@ -0,0 +1,10 @@
+#! /bin/sh
+set -e
+
+# export JAVA_HOME=/usr/lib/jvm/default-java
+export JAVA_CMD=java
+
+# Include the wrappers utility script
+. /usr/lib/java-wrappers/java-wrappers.sh
+
+run_java -Xms128M -Xmx1G -jar /usr/share/java/pilon.jar "$@"


=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),
                scala,
-               libscala-pickling-java
+               libhtsjdk-java
 Standards-Version: 4.1.4
 Vcs-Browser: https://salsa.debian.org/med-team/pilon
 Vcs-Git: https://salsa.debian.org/med-team/pilon.git
@@ -15,6 +15,8 @@ Package: pilon
 Architecture: all
 Depends: ${misc:Depends},
          libhtsjdk-java
+Conflicts: pilon-non-free
+Replaces: pilon-non-free
 Description: automated genome assembly improvement and variant detection tool
  Pilon is a software tool which can be used to:
   * Automatically improve draft assemblies


=====================================
debian/install
=====================================
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,2 @@
+pilon*.jar	usr/share/java
+debian/bin	usr


=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -5,3 +5,6 @@ export LC_ALL=C.UTF-8
 
 %:
 	dh $@
+
+override_dh_auto_build:
+	scalac -classpath /usr/share/java/htsjdk.jar -d pilon.jar src/main/scala/org/broadinstitute/pilon/*



View it on GitLab: https://salsa.debian.org/med-team/pilon/compare/7159319ad3831c33d12c4f59558ad6583017022a...ee45a7e70eeaa0048188eded5e8915c4c00e99b8

-- 
View it on GitLab: https://salsa.debian.org/med-team/pilon/compare/7159319ad3831c33d12c4f59558ad6583017022a...ee45a7e70eeaa0048188eded5e8915c4c00e99b8
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