[med-svn] [rapmap] 06/06: Package with example data

[Andreas Tille]

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

tille pushed a commit to branch master
in repository rapmap.

commit dff235ae29ea2a0fc6e514a8bed7f31ce8e53d85
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jan 12 19:34:29 2018 +0100

    Package with example data
---
 debian/changelog                     |  2 +-
 debian/control                       | 18 ++++++++++++++++++
 debian/rapmap-example-data.install   |  1 +
 debian/{docs => rapmap.docs}         |  0
 debian/{install => rapmap.install}   |  1 +
 debian/{manpages => rapmap.manpages} |  0
 debian/tests/control                 |  3 +--
 debian/tests/run-unit-test           | 13 ++++---------
 8 files changed, 26 insertions(+), 12 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 7c4bad9..c9898e7 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,6 @@
 rapmap (0.5.0+dfsg-3) UNRELEASED; urgency=medium
 
-  * 
+  * Add binary package containing example data
 
  -- Andreas Tille <tille at debian.org>  Fri, 12 Jan 2018 18:55:20 +0100
 
diff --git a/debian/control b/debian/control
index 0d25286..5f640ea 100644
--- a/debian/control
+++ b/debian/control
@@ -48,3 +48,21 @@ Description: rapid sensitive and accurate DNA read mapping via quasi-mapping
  mapping and pseudo-alignment (originally introduced in Bray et al.
  2016), these two are not the same thing. They are distinct concepts, and
  RapMap simply happens to implement algorithms for computing both.
+
+Package: rapmap-example-data
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: rapmap
+Description: example data for rapmap - rapid sensitive and accurate DNA read mapping
+ RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
+ pseudo) transcriptome alignment. That means that, at this point, it is
+ somewhat experimental. The develop branch will have the latest
+ improvements and additions, but is not guaranteed to be stable between
+ commits. Breaking changes to the master branch will be accompanied by a
+ tag to the version before the breaking change. Currently, RapMap is a
+ stand-alone quasi-mapper that can be used with other tools. It is also
+ being used as part of Sailfish and Salmon. Eventually, the hope is to
+ create and stabilize an API so that it can be used as a library from
+ other tools.
+ .
+ This package contains example data to test this program.
diff --git a/debian/rapmap-example-data.install b/debian/rapmap-example-data.install
new file mode 100644
index 0000000..369a088
--- /dev/null
+++ b/debian/rapmap-example-data.install
@@ -0,0 +1 @@
+sample_data/*	usr/share/doc/rapmap/examples
diff --git a/debian/docs b/debian/rapmap.docs
similarity index 100%
rename from debian/docs
rename to debian/rapmap.docs
diff --git a/debian/install b/debian/rapmap.install
similarity index 53%
rename from debian/install
rename to debian/rapmap.install
index 8e71dae..47490fa 100644
--- a/debian/install
+++ b/debian/rapmap.install
@@ -1 +1,2 @@
 debian/bin	usr
+usr/bin		usr
diff --git a/debian/manpages b/debian/rapmap.manpages
similarity index 100%
rename from debian/manpages
rename to debian/rapmap.manpages
diff --git a/debian/tests/control b/debian/tests/control
index 0bd1ddc..2b5a0bd 100644
--- a/debian/tests/control
+++ b/debian/tests/control
@@ -1,6 +1,5 @@
 Tests: run-unit-test
-Depends: @
+Depends: @, rapmap-example-data
 Restrictions: allow-stderr
 
 
-
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
index 5ab759e..9fa45c0 100644
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -1,23 +1,18 @@
 #!/bin/bash
-#set -e
+set -e
+set -x
 
 pkg="rapmap"
 
-#If i do not include the symbolic link manually before runing 'autopkgtest -- null' the
-#package fails to build. If i do include the link then it builds succesfully. It 
-#throws an error when it tests the function 'quasiindex' -  i'm still working ot it!
-
-ln -s ~/spdlog/include/spdlog/ ~/${pkg}/include
-
 
 if [ "$AUTOPKGTEST_TMP" = "" ] ; then
   AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
   trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cp -a ${pkg}/* $AUTOPKGTEST_TMP
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
 
 cd $AUTOPKGTEST_TMP
+gunzip -r *
 
 rapmap quasiindex -t transcripts.fasta -i sample_quasi_index
-

-- 
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