[med-svn] [transdecoder] 05/05: add ITP#, ignore removed directory, install libs

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository transdecoder.

commit 4f3c0c5ae1b2772d0c902a329265380f538be191
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date:   Fri Feb 13 06:43:12 2015 -0500

    add ITP#, ignore removed directory, install libs
---
 debian/changelog                 |  2 +-
 debian/control                   |  5 +++--
 debian/patches/cd-hit-est-rename | 11 +++++++++++
 debian/patches/series            |  1 +
 debian/rules                     | 10 ++++++++++
 5 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index c8a3e83..94d6c19 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
 transdecoder (2.0.1+dfsg-1) UNRELEASED; urgency=low
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #778300)
 
  -- Michael R. Crusoe <mcrusoe at msu.edu>  Fri, 13 Feb 2015 06:26:24 -0500 
diff --git a/debian/control b/debian/control
index cf5c0cb..8c19f39 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Michael R. Crusoe <mcrusoe at msu.edu>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9)
+Build-Depends: debhelper (>= 9), cd-hit
 Standards-Version: 3.9.6
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
@@ -13,7 +13,8 @@ Package: transdecoder
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         ${perl:Depends}
+         ${perl:Depends},
+         cd-hit
 Description: find coding regions within transcripts
  TransDecoder identifies candidate coding regions within transcript sequences,
  such as those generated by de novo RNA-Seq transcript assembly using Trinity,
diff --git a/debian/patches/cd-hit-est-rename b/debian/patches/cd-hit-est-rename
new file mode 100644
index 0000000..3bf3805
--- /dev/null
+++ b/debian/patches/cd-hit-est-rename
@@ -0,0 +1,11 @@
+--- transdecoder.orig/TransDecoder.Predict
++++ transdecoder/TransDecoder.Predict
+@@ -56,7 +56,7 @@
+ $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
+ 
+ 
+-my ($cd_hit_est_exec) = &check_program('cd-hit-est');
++my ($cd_hit_est_exec) = &check_program('/usr/lib/cd-hit/cd-hit-est');
+ 
+ my ($transcripts_file,$train_file);
+ 
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..93b3752
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+cd-hit-est-rename
diff --git a/debian/rules b/debian/rules
index 850d07a..e72cecb 100755
--- a/debian/rules
+++ b/debian/rules
@@ -19,5 +19,15 @@ DH_VERBOSE := 1
 %:
 	dh $@
 
+override_dh_auto_clean:
+	cd ./sample_data && ./cleanme.pl
+
+override_dh_auto_build:
+
+override_dh_install:
+	dh_install TransDecoder* /usr/bin/
+	dh_install PerlLib/* /usr/share/perl5/
+	find debian/transdecoder -name '*.p?' | xargs sed -i \
+                's=^#!/usr/local/bin/perl=#!/usr/bin/perl='
 get-orig-source:
 	uscan --verbose --force-download --repack --compression xz

-- 
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