[med-svn] [bbmap] 01/01: Use openmpi instead of mpj; install scripts to /usr/lib/debian-med/bin

[Andreas Tille]

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tille pushed a commit to branch master
in repository bbmap.

commit f028a034beaf1d2b90f7a8c7fdd2584e3a8c2319
Author: Andreas Tille <tille at debian.org>
Date:   Wed Mar 23 21:53:54 2016 +0100

    Use openmpi instead of mpj; install scripts to /usr/lib/debian-med/bin
---
 debian/README.Debian | 14 ++++++++++++++
 debian/clean         |  1 +
 debian/control       |  2 +-
 debian/rules         | 16 +++++++++++++++-
 4 files changed, 31 insertions(+), 2 deletions(-)

diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..460bd47
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,14 @@
+BBMap for Debian
+----------------
+
+BBMap ships with several tools featuring perfectly generic names.
+This would cause a lot of naming conflicts.  The solution is to
+install these tools into
+
+    /usr/lib/debian-med/bin
+
+and let users add this dir to their PATH via
+
+    export PATH=/usr/lib/debian-med/bin:$PATH
+
+ -- Andreas Tille <tille at debian.org>  Fri, 18 Mar 2016 13:50:56 +0100
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..5463785
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+bbmap.jar
diff --git a/debian/control b/debian/control
index 99847d0..9151e0a 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,7 @@ Priority: optional
 Build-Depends: debhelper (>= 9),
                javahelper,
                default-jdk,
-               libmpj-java
+               libopenmpi-java
 Standards-Version: 3.9.7
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bbmap.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/bbmap.git
diff --git a/debian/rules b/debian/rules
index 8c2bad5..ffe4c2e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,10 +3,12 @@
 # DH_VERBOSE := 1
 
 DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+PKGBINDIR    := debian/$(DEBPKGNAME)/usr/lib/debian-med/bin
+PKGSHAREDIR    := debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)
 
 export JAVA_HOME  := /usr/lib/jvm/default-java
 DEBJAR    := /usr/share/java
-export CLASSPATH := $(DEBJAR)/mpj.jar
+export CLASSPATH := $(DEBJAR)/mpi.jar
 
 %:
 	dh $@ --with javahelper
@@ -21,3 +23,15 @@ override_dh_clean:
 override_dh_auto_build:
 	jh_build $(DEBPKGNAME).jar current
 
+override_dh_install:
+	dh_install
+	mkdir -p $(PKGSHAREDIR)
+	mkdir -p $(PKGBINDIR)
+	cp -a calcmem.sh $(PKGSHAREDIR)/calcmem
+	for scr in *.sh ; do \
+	    if [ "$${scr}" != "calcmem.sh" ] ; then \
+		sed -e 's:^CP=".DIR""current/":CP=/usr/share/java/bbmap.jar:' \
+		    -e 's:source ".DIR""/calcmem.sh":source "/usr/share/$(DEBPKGNAME)/calcmem":' \
+		    $${scr} > $(PKGBINDIR)/`basename $${scr} .sh` ; \
+	    fi ; \
+	done

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