[med-svn] [sra-sdk] 01/02: Deal with name space conflict of kget

[Andreas Tille]

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

tille pushed a commit to branch master
in repository sra-sdk.

commit e08bfaa5708f0d3ee0c311ad65ee6c0d17d1b624
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jan 13 09:21:13 2017 +0100

    Deal with name space conflict of kget
---
 debian/README.Debian     | 34 ++++++++++++++++++++++++++++++++++
 debian/changelog         |  7 +++++++
 debian/control           |  1 +
 debian/rules             |  4 ++++
 debian/sra-toolkit.links |  1 +
 5 files changed, 47 insertions(+)

diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..83b97e2
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,34 @@
+sra-toolkit for Debian
+----------------------
+
+There is a name conflict of the executable kget with the kget download
+manager.  So in Debian the executable is renamed to sra-kget.  Upstream
+was recommended to change the name in
+   https://github.com/ncbi/sra-tools/issues/55
+
+The Debian Med team deals with situation usually the following way:
+
+  1. The kget executable belonging to sra-toolkit is renamed to
+        /usr/bin/sra-kget
+     and can be used as this or users can use
+  2. symlink with the original name in
+        /usr/lib/debian-med/bin/kget
+
+If you want to use sra-toolkit's kget right from the command line just set
+the PATH variable like
+
+  export PATH=/usr/lib/debian-med/bin:$PATH
+
+If a user creates a file
+
+    ${HOME}/.blends
+
+with the content
+
+# Add Blend names here which should prepend its bin dir to PATH
+debian-med
+
+the med-config package automatically adds this PATH to the users
+environment (when using bash).
+
+ -- Andreas Tille <tille at debian.org>  Thu, 05 Jan 2017 10:33:38 +0100
diff --git a/debian/changelog b/debian/changelog
index e2eff5e..2b158c6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+sra-sdk (2.8.1+dfsg-2) UNRELEASED; urgency=medium
+
+  * Deal with name space conflict with kget
+    Closes: #851219
+
+ -- Andreas Tille <tille at debian.org>  Fri, 13 Jan 2017 09:22:01 +0100
+
 sra-sdk (2.8.1+dfsg-1) unstable; urgency=medium
 
   * New upstream version
diff --git a/debian/control b/debian/control
index 93fed0f..231ca36 100644
--- a/debian/control
+++ b/debian/control
@@ -20,6 +20,7 @@ Package: sra-toolkit
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends}
+Recommends: med-config (>= 2.1)
 Description: utilities for the NCBI Sequence Read Archive
  Tools for reading the SRA archive, generally by converting individual runs
  into some commonly used format such as fastq.
diff --git a/debian/rules b/debian/rules
index 1434672..ed90ff0 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,6 +3,8 @@
 # +pie breaks the build
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
+pkg := sra-toolkit
+
 %:
 	dh $@
 
@@ -42,6 +44,8 @@ override_dh_install:
 	dh_install
 	# remove susipcious file which is not executable and conflicts with package magic
 	rm -f debian/*/usr/bin/magic
+	# rename kget which conflicts with kget download manager (see #851219)
+	mv debian/$(pkg)/usr/bin/kget debian/$(pkg)/usr/bin/sra-kget
 
 #override_dh_auto_test:
 #	echo "FIXME: try activating tests!!!!!!!!!!!!!!!!!!!!!!!!"
diff --git a/debian/sra-toolkit.links b/debian/sra-toolkit.links
new file mode 100644
index 0000000..f8a8660
--- /dev/null
+++ b/debian/sra-toolkit.links
@@ -0,0 +1 @@
+usr/bin/sra-kget	/usr/lib/debian-med/bin/kget

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