[med-svn] [art-nextgen-simulation-tools] 01/02: Move internal scripts out of /usr/bin

[Andreas Tille]

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tille pushed a commit to branch master
in repository art-nextgen-simulation-tools.

commit 894dddb2862d0ef99124e0b7f2eaeddfdcca83b3
Author: Andreas Tille <tille at debian.org>
Date:   Wed Feb 17 11:51:37 2016 +0100

    Move internal scripts out of /usr/bin
---
 debian/patches/adapt_path_to_perl_scripts.patch | 16 ++++++++++++++++
 debian/patches/series                           |  1 +
 debian/rules                                    |  9 ++++++++-
 3 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/debian/patches/adapt_path_to_perl_scripts.patch b/debian/patches/adapt_path_to_perl_scripts.patch
new file mode 100644
index 0000000..b98d7ed
--- /dev/null
+++ b/debian/patches/adapt_path_to_perl_scripts.patch
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 16 Feb 2016 15:19:22 +0100
+Description: Main executable and private scripts will not be installed
+ in the same place so the PATH needs to be adapted
+
+--- a/ART_profiler_illumina/art_profiler_illumina
++++ b/ART_profiler_illumina/art_profiler_illumina
+@@ -3,7 +3,7 @@
+ # fastq files
+ #Weichun Huang at whduke at gmail.com
+ 
+-pDIR=`dirname $0`
++pDIR=/usr/lib/art-nextgen-simulation-tools
+ ext=fq
+ if [[ $# -eq 2 ]]; then
+        	outFile=$1
diff --git a/debian/patches/series b/debian/patches/series
index 477d052..e4f7276 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 fix-test-comparison.patch
+adapt_path_to_perl_scripts.patch
diff --git a/debian/rules b/debian/rules
index e498de1..c303a49 100755
--- a/debian/rules
+++ b/debian/rules
@@ -19,8 +19,15 @@ endif
 
 override_dh_install-arch:
 	dh_install -a
+	# aln2bed.pl seems to be of general use - the other perl scripts are called by art_profiler_illumina
+	# see patch for the latter regarding PATH to *.pl files
+	mkdir -p debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)
 	for pl in debian/$(DEBPKGNAME)/usr/bin/*.pl ; do \
-	    mv $${pl} debian/$(DEBPKGNAME)/usr/bin/`basename $${pl} .pl` ; \
+	    if [ `basename $${pl}` = aln2bed.pl ] ; then \
+		mv $${pl} debian/$(DEBPKGNAME)/usr/bin/`basename $${pl} .pl` ; \
+	    else \
+		mv $${pl} debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME) ; \
+	    fi ; \
 	done
 
 override_dh_installexamples-arch:

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