[med-svn] [baitfisher] 03/07: include examples

[Olivier Sallou]

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

osallou pushed a commit to branch master
in repository baitfisher.

commit ce6d9b7066f303311c8e45db322981dc306ed350
Author: Olivier Sallou <osallou at debian.org>
Date:   Sat Jan 14 08:03:11 2017 +0000

    include examples
---
 debian/dirs                         |  1 +
 debian/patches/adapt_examples.patch | 25 +++++++++++++++++++++++++
 debian/patches/series               |  1 +
 debian/rules                        |  6 ++++--
 4 files changed, 31 insertions(+), 2 deletions(-)

diff --git a/debian/dirs b/debian/dirs
index e772481..b4c3671 100644
--- a/debian/dirs
+++ b/debian/dirs
@@ -1 +1,2 @@
 usr/bin
+usr/share/doc/baitfisher/example/BaitFisher-results
diff --git a/debian/patches/adapt_examples.patch b/debian/patches/adapt_examples.patch
new file mode 100644
index 0000000..38806cd
--- /dev/null
+++ b/debian/patches/adapt_examples.patch
@@ -0,0 +1,25 @@
+Subject: update example command to match debian binary
+Description: in Debian, binary does not contain version name,
+ use base name and exec in PATH
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2017-01-14
+Forwarded: no
+--- a/Example/Example-without-alignment-cutting/run-command
++++ b/Example/Example-without-alignment-cutting/run-command
+@@ -1 +1 @@
+-../../BaitFisher-v1.2.7 parameter.txt 1> console_output 2> console_error_output 
++BaitFisher parameter.txt 1> console_output 2> console_error_output 
+--- a/Example/Example-without-alignment-cutting/BaitFilter-analysis/run-BaitFilter
++++ b/Example/Example-without-alignment-cutting/BaitFilter-analysis/run-BaitFilter
+@@ -1,6 +1,6 @@
+-../../../BaitFilter-v1.0.5  -m ab -i ../BaitFisher-results/loci_baits.txt  -o baits_filtered_best-in-alignment_minNumBaits.txt  1> console_o_filter_bestBaits 2> console_e_filter_bestBaits
+-../../../BaitFilter-v1.0.5  -m as -i ../BaitFisher-results/loci_baits.txt  -o baits_filtered_best-in-alignment_maxNumSeq.txt    1> console_o_filter_bestSeqs  2> console_e_filter_bestSeqs
++BaitFilter  -m ab -i ../BaitFisher-results/loci_baits.txt  -o baits_filtered_best-in-alignment_minNumBaits.txt  1> console_o_filter_bestBaits 2> console_e_filter_bestBaits
++BaitFilter  -m as -i ../BaitFisher-results/loci_baits.txt  -o baits_filtered_best-in-alignment_maxNumSeq.txt    1> console_o_filter_bestSeqs  2> console_e_filter_bestSeqs
+ 
+ ## Produce bait file that can be uploaded at a bait producing company. So war all companies accepted the file produced with the following command.
+-../../../BaitFilter-v1.0.5 -c Agilent-Germany -i baits_filtered_best-in-alignment_maxNumSeq.txt   -o Final_baits_filtered_best-in-alignment_maxNumSeq.txt   --ID-prefix My-project-name- 1> conversion_maxNumSeq.o   2> conversion_maxNumSeq.e
+-../../../BaitFilter-v1.0.5 -c Agilent-Germany -i baits_filtered_best-in-alignment_minNumBaits.txt -o Final_baits_filtered_best-in-alignment_minNumBaits.txt --ID-prefix My-project-name- 1> conversion_minNumBaits.o 2> conversion_minNumBaits.e
+\ No newline at end of file
++BaitFilter -c Agilent-Germany -i baits_filtered_best-in-alignment_maxNumSeq.txt   -o Final_baits_filtered_best-in-alignment_maxNumSeq.txt   --ID-prefix My-project-name- 1> conversion_maxNumSeq.o   2> conversion_maxNumSeq.e
++BaitFilter -c Agilent-Germany -i baits_filtered_best-in-alignment_minNumBaits.txt -o Final_baits_filtered_best-in-alignment_minNumBaits.txt --ID-prefix My-project-name- 1> conversion_minNumBaits.o 2> conversion_minNumBaits.e
diff --git a/debian/patches/series b/debian/patches/series
index ac462d5..1390f96 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
+adapt_examples.patch
 fix_gcc6.patch
diff --git a/debian/rules b/debian/rules
index 5def6d3..25dbe1b 100755
--- a/debian/rules
+++ b/debian/rules
@@ -13,7 +13,7 @@ include /usr/share/dpkg/pkg-info.mk
 	dh $@
 
 override_dh_install:
-	cp BaitFilter-v* debian/baitfisher/usr/bin/BaitFiler
+	cp BaitFilter-v* debian/baitfisher/usr/bin/BaitFilter
 	cp BaitFisher-v* debian/baitfisher/usr/bin/BaitFisher
 	dh_install
 
@@ -22,5 +22,7 @@ override_dh_installman:
 	help2man --no-discard-stderr -o BaitFisher.1 ./BaitFisher-v*
 	dh_installman
 
-
+override_dh_installdocs:
+	cp -r Example/* usr/share/doc/baitfisher/example/
+	dh_installdocs
 

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