[med-svn] [psortb] 02/04: Initial packaging attempt

[Andreas Tille]

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tille pushed a commit to branch master
in repository psortb.

commit 3d9ac48deabd05c372ae64423046e75eff7824e5
Author: Andreas Tille <tille at debian.org>
Date:   Fri Mar 17 10:51:33 2017 +0100

    Initial packaging attempt
---
 debian/changelog         |  5 +++++
 debian/clean             |  2 ++
 debian/compat            |  1 +
 debian/control           | 24 ++++++++++++++++++++++++
 debian/copyright         | 16 ++++++++++++++++
 debian/rules             | 17 +++++++++++++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 12 ++++++++++++
 debian/watch             |  3 +++
 9 files changed, 81 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..8e121d4
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+psortb (3.0.4-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Fri, 17 Mar 2017 10:23:15 +0100
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..2ee17ff
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1,2 @@
+psort/conf/analysis/sclblast/gramneg/sclblast.*
+psort/conf/analysis/sclblast/grampos/sclblast.*
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..60eef05
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: psortb
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 10),
+               bioperl,
+               ncbi-blast+-legacy
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/psortb.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/psortb.git
+Homepage: http://www.psort.org/
+
+Package: psortb
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${perl:Depends},
+         ${misc:Depends}
+Description: bacterial localization prediction tool
+ PSORTb enables prediction of bacterial protein subcellular localization
+ (SCL) and provides a quick and inexpensive means for gaining insight
+ into protein function, verifying experimental results, annotating newly
+ sequenced bacterial genomes, detecting potential cell surface/secreted
+ drug targets, as well as identifying biomarkers for microbes.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..58c8b54
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,16 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: PSORTb:
+Source: http://www.psort.org/downloads
+Comment: **** Before manually editing this file you should give ****
+           scan-copyrights
+         **** available in cme + lib-config-model-dpkg-perl     ****
+         **** package a try.  For existing copyright files try  ****
+           cme update dpkg-copyright
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2017 maintainername <maintainer at e.mail>
+License: <license>
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..7fe2395
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,17 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+%:
+	dh $@
+
+override_dh_auto_clean:
+	dh_auto_clean
+	if [ -x psort/bin/psort.debsave ] ; then
+	    mv psort/bin/psort.debsave psort/bin/psort
+	fi
+
+override_dh_auto_configure:
+	cp -a psort/bin/psort psort/bin/psort.debsave
+	dh_auto_configure
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..acf4a7a
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: Nancy Y. Yu and James R. Wagner and Matthew R. Laird and Gabor Melli and Sébastien Rey and Raymond Lo and Phuong Dao and S. Cenk Sahinalp and Martin Ester and Leonard J. Foster and F. S. Brinkman
+  Title: "PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes"
+  Journal: Bioinformatics
+  Year: 2010
+  Volume: 26
+  Number: 13
+  Pages: 1608-1615
+  DOI: 10.1093/bioinformatics/btq249
+  PMID: 20472543
+  URL: https://academic.oup.com/bioinformatics/article/26/13/1608/201357/PSORTb-3-0-improved-protein-subcellular
+  eprint: https://academic.oup.com/bioinformatics/article-pdf/26/13/1608/516044/btq249.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..f679bd6
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+http://www.psort.org/downloads .*/bio-tools-psort-all.(\d[.\d]+)\.tar\.gz

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