[med-svn] [sprai] 04/12: Install all but the user-facing executables to /usr/lib/sprai

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository sprai.

commit 4b8caac6be967452fde0029df294454410059c17
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Thu Apr 14 23:18:26 2016 -0700

    Install all but the user-facing executables to /usr/lib/sprai
---
 debian/patches/libexec.patch | 53 ++++++++++++++++++++++++++++++++++++++++++++
 debian/rules                 |  7 ++++++
 2 files changed, 60 insertions(+)

diff --git a/debian/patches/libexec.patch b/debian/patches/libexec.patch
new file mode 100644
index 0000000..e2b3b6c
--- /dev/null
+++ b/debian/patches/libexec.patch
@@ -0,0 +1,53 @@
+Description: Set sprai libexec path and blast path for system-wide installation
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: not-needed
+Last-Update: 2016-04-14
+--- sprai.orig/ezez4qsub_vx1.pl
++++ sprai/ezez4qsub_vx1.pl
+@@ -109,8 +109,8 @@
+ my $trim="";
+ my $estimated_genome_size="";
+ my $ca_path="";
+-my $blast_path="";
+-my $sprai_path="";
++my $blast_path="/usr/bin";
++my $sprai_path="/usr/lib/sprai";
+ my $queue_req="";
+ my $longestXx_queue_req="";
+ my $blast_rreq="";
+--- sprai.orig/ezez_vx1.pl
++++ sprai/ezez_vx1.pl
+@@ -9,7 +9,7 @@
+ my $opt_dryrun;
+ my $opt_ec_only;
+ my $opt_foobar;
+-my $sprai_path="";
++my $sprai_path="/usr/lib/sprai";
+ 
+ my $now = `date +%Y%m%d_%H%M%S`;
+ chomp $now;
+--- sprai.orig/ec.spec
++++ sprai/ec.spec
+@@ -11,6 +11,8 @@
+ estimated_depth 100
+ 
+ # ca_path: where Celera Assembler exist in
++# If you don't have it and only want to run error-correction,
++# use /dev/null for this variable.
+ ca_path /home/imai/wgs/Linux-amd64/bin/
+ 
+ # the number of processes used by all vs. all alignment
+@@ -19,13 +21,6 @@
+ pre_partition 2
+ partition 12
+ 
+-# sprai prefer full paths
+-# if you use ezez4qsub*.pl. you MUST specify blast_path & sprai_path
+-# blast_path: where blastn and makeblastdb exist in
+-blast_path /home/imai/bin/
+-# sprai_path: where binaries of sprai (bfmt72s, nss2v_v3 and so on) exist in
+-sprai_path /home/imai/sprai/bin/
+-
+ #### many node mode (advanced) ####
+ 
+ #sge: options for all the SGE jobs
diff --git a/debian/rules b/debian/rules
index 2efdd45..2120a21 100755
--- a/debian/rules
+++ b/debian/rules
@@ -17,6 +17,13 @@ override_dh_auto_build:
 override_dh_auto_install:
 	$(WAF) install --destdir=$(CURDIR)/debian/sprai
 
+override_dh_install:
+	mkdir -p $(CURDIR)/debian/sprai/usr/lib/sprai
+	cd $(CURDIR)/debian/sprai/usr/bin \
+	&& mv * ../lib/sprai/ \
+	&& mv ../lib/sprai/ezez* .
+	dh_install
+
 override_dh_auto_clean:
 	$(WAF) distclean
 	find waflib -name "*.pyc" -delete

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