[med-svn] [giira] 01/01: Make sure Python helper scripts will be found

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository giira.

commit 70d74213976fcc501a54650dbb692626f556e078
Author: Andreas Tille <tille at debian.org>
Date:   Mon Feb 10 15:59:58 2014 +0100

    Make sure Python helper scripts will be found
---
 debian/install                        |  1 +
 debian/patches/fix_scripts-path.patch | 36 +++++++++++++++++++++++++++++++++++
 debian/patches/series                 |  1 +
 3 files changed, 38 insertions(+)

diff --git a/debian/install b/debian/install
index 8e71dae..d079ef8 100644
--- a/debian/install
+++ b/debian/install
@@ -1 +1,2 @@
 debian/bin	usr
+scripts		usr/share/giira
diff --git a/debian/patches/fix_scripts-path.patch b/debian/patches/fix_scripts-path.patch
new file mode 100644
index 0000000..c0ea1ca
--- /dev/null
+++ b/debian/patches/fix_scripts-path.patch
@@ -0,0 +1,36 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Updated: Mon, 10 Feb 2014 14:38:38 +0100
+Description: Hardcode path to Python helper scripts
+ The documentation says that you can set the path to the Python
+ helper scripts via
+    -script /usr/share/giira/scipts
+ but this is wrong as the output looks like
+ .
+ Call: 
+ java -Xmx894m -cp /usr/share/java/giira.jar:/usr/share/java/giira-0.0.20140210.jar geneFinder.GeneFinder -opti glpk -scripts /usr/share/giira/scripts -iG example/Scer_chr4.fasta -iR example/scer_example_reads.fastq -out GIIRA_example/ -iter 1 -scripts /usr/share/java/giira-0.0.201scripts/
+ .
+ which seems to magically force some wrong scriptPath.  This patch
+ forces the correct installation path of the Debian package.
+
+--- a/src/geneFinder/ReadInParameters_GeneFinder.java
++++ b/src/geneFinder/ReadInParameters_GeneFinder.java
+@@ -357,7 +357,7 @@ public class ReadInParameters_GeneFinder
+ 			try {
+ 				String decodedPath = URLDecoder.decode(path, "UTF-8");
+ 				String scriptPath = decodedPath.substring(0,decodedPath.length()-9);
+-				GeneFinder.pathToHelpFiles = scriptPath + "scripts/";
++				GeneFinder.pathToHelpFiles = "/usr/share/giira/scripts/";
+ 			} catch (UnsupportedEncodingException e) {
+ 				e.printStackTrace();
+ 			}
+--- a/src/geneFinder/Giira.java
++++ b/src/geneFinder/Giira.java
+@@ -43,7 +43,7 @@ public class Giira {
+ 		
+ 		try {
+ 			String decodedPath = URLDecoder.decode(path, "UTF-8");
+-			String scriptPath = decodedPath.substring(0,decodedPath.length()-9);
++			String scriptPath = "/usr/share/giira/";
+ 			//System.out.println("Path of Giira: " + decodedPath);
+ 			
+ 			classPath = "";
diff --git a/debian/patches/series b/debian/patches/series
index 0b13371..2eb66d5 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 remove_cplex_code.patch
 fix_non-ascii_characters.patch
+fix_scripts-path.patch

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/giira.git