[jalview] 01/01: Use libbio4-java, add mkdir so building from git works

[Ximin Luo]

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infinity0 pushed a commit to branch master
in repository jalview.

commit f87e863f65a8903380e4405f253f3e3fc9c8cafc
Author: Ximin Luo <infinity0 at debian.org>
Date:   Sat Dec 10 16:28:19 2016 +0100

    Use libbio4-java, add mkdir so building from git works
---
 debian/TODO    | 6 ------
 debian/control | 1 +
 debian/rules   | 4 +++-
 3 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/debian/TODO b/debian/TODO
index 63c0c6d..ff43236 100644
--- a/debian/TODO
+++ b/debian/TODO
@@ -31,12 +31,6 @@ The following dependencies appear not to be in Debian:
     [javac] src/jalview/ext/htsjdk/HtsContigDb.java:27: error: package htsjdk.samtools.reference does not exist
     [javac] src/jalview/ext/htsjdk/HtsContigDb.java:28: error: package htsjdk.samtools.util does not exist
     [javac] src/jalview/ext/htsjdk/HtsContigDb.java:54: error: package htsjdk.samtools.reference does not exist
-    [javac] src/jalview/ext/so/SequenceOntology.java:40: error: package org.biojava.nbio.ontology does not exist
-    [javac] src/jalview/ext/so/SequenceOntology.java:41: error: package org.biojava.nbio.ontology does not exist
-    [javac] src/jalview/ext/so/SequenceOntology.java:42: error: package org.biojava.nbio.ontology.Term does not exist
-    [javac] src/jalview/ext/so/SequenceOntology.java:43: error: package org.biojava.nbio.ontology does not exist
-    [javac] src/jalview/ext/so/SequenceOntology.java:44: error: package org.biojava.nbio.ontology.io does not exist
-    [javac] src/jalview/ext/so/SequenceOntology.java:45: error: package org.biojava.nbio.ontology.utils does not exist
     [javac] src/jalview/ext/varna/RnaModel.java:26: error: package fr.orsay.lri.varna.models.rna does not exist
     [javac] src/jalview/gui/AppVarna.java:52: error: package fr.orsay.lri.varna does not exist
     [javac] src/jalview/gui/AppVarna.java:53: error: package fr.orsay.lri.varna.exceptions does not exist
diff --git a/debian/control b/debian/control
index 947b8d0..66fc233 100644
--- a/debian/control
+++ b/debian/control
@@ -15,6 +15,7 @@ Build-Depends: ant,
                jmol-applet (>= 12.1.42),
                libapache-mime4j-java (>= 0.7.2),
                libaxis-java,
+               libbiojava4-java,
                libcastor-xml-java,
                libcommons-discovery-java,
                libcommons-logging-java,
diff --git a/debian/rules b/debian/rules
index 2e4b48f..512ca9a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -23,7 +23,9 @@ DEB_JARS             := castor-xml commons-logging log4j-1.2 \
 	jswingreader miglayout /usr/share/icedtea-web/plugin.jar \
 	httpmime httpcore apache-mime4j-core httpclient jsearch-indexer \
 	json-simple servlet-api-3.1 jetty9-server javax.ws.rs-api \
-	jersey1-client slf4j-api groovy
+	jersey1-client slf4j-api groovy biojava4-ontology
+
+$(shell mkdir -p lib appletlib)
 
 
 ANT_OPTS             := -Dbuild.sysclasspath=last \

-- 
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