[med-svn] [Git][med-team/bismark][master] Initial packaging

[Liubov Chuprikova]

Liubov Chuprikova pushed to branch master at Debian Med / bismark


Commits:
016b49af by Liubov Chuprikova at 2019-03-10T14:27:45Z
Initial packaging

- - - - -


14 changed files:

- + debian/README.test
- + debian/changelog
- + debian/compat
- + debian/control
- + debian/copyright
- + debian/docs
- + debian/install
- + debian/lintian-overrides
- + debian/rules
- + debian/source/format
- + debian/tests/control
- + debian/tests/run-unit-test
- + debian/upstream/metadata
- + debian/watch


Changes:

=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+    sh run-unit-test
+
+in order to confirm its integrity.


=====================================
debian/changelog
=====================================
@@ -0,0 +1,5 @@
+bismark (0.20.1-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #<bug>)
+
+ -- Liubov Chuprikova <chuprikovalv at gmail.com>  Sun, 10 Mar 2019 10:38:35 +0200


=====================================
debian/compat
=====================================
@@ -0,0 +1 @@
+12


=====================================
debian/control
=====================================
@@ -0,0 +1,20 @@
+Source: bismark
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Liubov Chuprikova <chuprikovalv at gmail.com>
+Build-Depends: debhelper (>= 12~)
+Standards-Version: 4.3.0
+Vcs-Browser: https://salsa.debian.org/med-team/bismark
+Vcs-Git: https://salsa.debian.org/med-team/bismark.git
+Homepage: https://www.bioinformatics.babraham.ac.uk/projects/bismark/
+
+Package: bismark
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends},
+	 perl,
+         samtools,
+         bowtie2,
+	 hisat2
+Description: A bisulfite read mapper and methylation caller
+ <long_description>


=====================================
debian/copyright
=====================================
@@ -0,0 +1,16 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: <pkg>
+Source: <path_to_download>
+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: 2019 maintainername <maintainer at e.mail>
+License: <license>


=====================================
debian/docs
=====================================
@@ -0,0 +1,5 @@
+README.md
+CHANGELOG.md
+Bismark_alignment_modes.pdf
+license.txt
+Docs/Bismark_User_Guide.html


=====================================
debian/install
=====================================
@@ -0,0 +1,4 @@
+./bam2nuc /usr/bin
+./bismark* /usr/bin
+./deduplicate_bismark /usr/bin
+./filter_non_conversion /usr/bin


=====================================
debian/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+#PKGNAME#: script-with-language-extension usr/bin/*.*


=====================================
debian/rules
=====================================
@@ -0,0 +1,34 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+include /usr/share/dpkg/default.mk
+# this provides:
+# DEB_SOURCE: the source package name
+# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
+# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
+# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
+# DEB_VERSION_UPSTREAM: the package's upstream version
+# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
+# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
+#                    specified by <https://reproducible-builds.org/specs/source-date-epoch/>
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+	dh $@
+
+override_dh_auto_build:
+	# PASS
+
+### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
+#override_dh_auto_test:
+#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+#	do_stuff_for_testing
+#endif
+
+### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script
+#get-orig-source:
+#	. debian/get-orig-source


=====================================
debian/source/format
=====================================
@@ -0,0 +1 @@
+3.0 (quilt)


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,18 @@
+#!/bin/bash
+set -e
+
+pkg=#PACKAGENAME#
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  # Double quote below to expand the temporary directory variable now versus
+  # later is on purpose.
+  # shellcheck disable=SC2064
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+#do_stuff_to_test_package#


=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,12 @@
+Reference:
+  Author: 
+  Title: 
+  Journal: 
+  Year: 
+  Volume: 
+  Number: 
+  Pages: 
+  DOI: 
+  PMID:
+  URL: 
+  eprint: 


=====================================
debian/watch
=====================================
@@ -0,0 +1,3 @@
+version=4
+
+https://github.com/FelixKrueger/Bismark/releases/latest .*/archive/@ANY_VERSION@@ARCHIVE_EXT@



View it on GitLab: https://salsa.debian.org/med-team/bismark/commit/016b49af0bf3f4575b7a7e3edd957af21bf01389

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