[med-svn] [Git][med-team/kent-core][master] Rudimentary packaging (not building yet)
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Apr 1 13:23:50 BST 2023
Andreas Tille pushed to branch master at Debian Med / kent-core
Commits:
49c2a894 by Andreas Tille at 2023-04-01T14:01:10+02:00
Rudimentary packaging (not building yet)
- - - - -
12 changed files:
- + debian/changelog
- + debian/control
- + debian/copyright
- + debian/patches/fix_makefile.patch
- + debian/patches/series
- + debian/rules
- + debian/salsa-ci.yml
- + debian/source/format
- + debian/tests/control
- + debian/tests/run-unit-test
- + debian/upstream/metadata
- + debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -0,0 +1,5 @@
+kent-core (446-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #???)
+
+ -- Andreas Tille <tille at debian.org> Fri, 31 Mar 2023 07:34:06 +0200
=====================================
debian/control
=====================================
@@ -0,0 +1,42 @@
+Source: kent-core
+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-compat (= 13),
+ libpng-dev,
+ uuid-dev,
+ libmariadb-dev
+Standards-Version: 4.6.2
+Vcs-Browser: https://salsa.debian.org/med-team/kent-core
+Vcs-Git: https://salsa.debian.org/med-team/kent-core.git
+Homepage: https://github.com/ucscGenomeBrowser/kent-core
+Rules-Requires-Root: no
+
+Package: kent-core
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: free parts of the UCSC Genome Browser
+ This is a partial copy of the UCSC Genome Browser source code repository
+ https://github.com/ucscGenomeBrowser/kent/. It includes all files that
+ are under an MIT license or in the public domain. All files can be
+ packaged, redistributed and modified as needed by other projects.
+ .
+ A few selected tools that are useful when building track and
+ assembly hubs:
+ .
+ bedToBigBed create a bigBed file for rectangle-shaped annotations
+ (genes, enhancers, promoters, etc)
+ .
+ bigBedToBed the inverse of bedToBigBed
+ .
+ bigBedInfo Show information about a bigBed file. Can extract .autoSql
+ field definitions
+ .
+ wigToBigWig create a bigWig file for signal (barchart) annotations from
+ a .wig file
+ .
+ bigWigToWig the inverse of wigToBigWig
+ .
+ bigWigInfo show information about bigWig files
=====================================
debian/copyright
=====================================
@@ -0,0 +1,16 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: kent-core
+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: 2023 Andreas Tille <tille at debian.org>
+License: <license>
=====================================
debian/patches/fix_makefile.patch
=====================================
@@ -0,0 +1,86 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 31 Mar 2023 07:34:06 +0200
+Description: The makefiles contain code that references directories
+ with code that is not MIT licensed and thus only in the
+ original project and not in kent-core.
+ This patch verifies whether the dirs exist or not.
+
+--- a/src/makefile
++++ b/src/makefile
+@@ -16,7 +16,9 @@ update:
+ topLibs:
+ @./checkUmask.sh
+ @MACHTYPE=${MACHTYPE} ./machTest.sh
++ifneq ($(wildcard lib/*),)
+ cd lib && ${MAKE}
++endif
+ ifneq ($(wildcard jkOwnLib/*),)
+ cd jkOwnLib && ${MAKE}
+ endif
+@@ -29,9 +31,13 @@ optLib:
+ hgLib:
+ ifneq ($(wildcard hg/makefile),)
+ @./hg/sqlEnvTest.sh
++ifneq ($(wildcard hg/lib/*),)
+ cd hg/lib && ${MAKE}
++endif
++ifneq ($(wildcard hg/cgilib/*),)
+ cd hg/cgilib && ${MAKE}
+ endif
++endif
+
+ libs: topLibs hgLib optLib
+
+@@ -108,7 +114,9 @@ clean:
+ fi ;\
+ done
+ cd parasol && ${MAKE} clean
++ifneq ($(wildcard lib/*),)
+ cd lib && ${MAKE} clean
++endif
+ cd hg && ${MAKE} clean
+ cd hg && ${MAKE} clean_utils
+ ifneq ($(wildcard jkOwnLib/*),)
+--- a/src/hg/makefile
++++ b/src/hg/makefile
+@@ -228,8 +228,12 @@ APPS = $(UTIL_DIRS) $(UTILS_APPLIST)
+ all:: cgi utils
+
+ hgLib:
++ifneq ($(wildcard lib/*),)
+ cd lib && ${MAKE}
++endif
++ifneq ($(wildcard lib/*),)
+ cd cgilib && ${MAKE}
++endif
+
+ userApps: $(UTILS_APPLIST:%=%.userApp)
+ cd altSplice/lib && $(MAKE)
+@@ -279,22 +283,24 @@ install: ${BROWSER_BINS:%=%.install} ${B
+ cd $* && echo $* && $(MAKE) install
+
+ clean::
++ifneq ($(wildcard lib/*),)
+ cd lib && ${MAKE} clean
++endif
+ @for D in ${BROWSER_BINS} ${BROWSER_LOADERS}; do \
+- (cd $${D} && ${MAKE} clean;) \
++ (if [ -d $${D} ] ; then cd $${D} && ${MAKE} clean; fi) \
+ done
+ touch non-empty-rm.o
+ - find . -name \*.o -print | xargs rm
+
+ clean_utils::
+ @for D in ${UTIL_DIRS}; do \
+- (cd $${D} && ${MAKE} clean;) \
++ (if [ -d $${D} ] ; then cd $${D} && ${MAKE} clean; fi) \
+ done
+
+ clean:: ${TEST_DIRS:%=%.clean}
+
+ %.clean:
+- cd $* && ${MAKE} clean
++ if [ -d $* ] ; then cd $* && ${MAKE} clean ; fi
+
+ testAll: $(APPS:%=%.testAll)
+
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+fix_makefile.patch
=====================================
debian/rules
=====================================
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# for hardening you might like to uncomment this:
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+ dh $@ --sourcedirectory=src --no-parallel # FIXME: no-parallel is just set for debugging - remove it before uploading
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,17 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+
+# To exclude single tests you can use
+#variables:
+# SALSA_CI_DISABLE_APTLY: 1
+# SALSA_CI_DISABLE_AUTOPKGTEST: 1
+# SALSA_CI_DISABLE_BLHC: 1
+# SALSA_CI_DISABLE_LINTIAN: 1
+# SALSA_CI_DISABLE_PIUPARTS: 1
+# SALSA_CI_DISABLE_REPROTEST: 1
+# SALSA_CI_DISABLE_BUILD_PACKAGE_ALL: 1
+# SALSA_CI_DISABLE_BUILD_PACKAGE_ANY: 1
+# In case for instance i386 is explicitly excluded by Build-Depends
+# SALSA_CI_DISABLE_BUILD_PACKAGE_I386: 1
=====================================
debian/source/format
=====================================
@@ -0,0 +1 @@
+3.0 (quilt)
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,16 @@
+#!/bin/bash
+set -e
+
+pkg=#PACKAGENAME#
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+#do_stuff_to_test_package#
=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,19 @@
+Reference:
+ Author: W. Jim Kent
+ Title: "BLAT--the BLAST-like alignment tool"
+ Journal: Genome Research
+ Year: 2002
+ Volume: 12
+ Number: 4
+ Pages: 656-64
+ DOI: 10.1101/gr.229202
+ PMID: 11932250
+ URL: http://genome.cshlp.org/content/12/4/656
+ eprint: http://genome.cshlp.org/content/12/4/656.full.pdf+html
+Registry:
+ - Name: OMICtools
+ Entry: OMICS_01434
+ - Name: SciCrunch
+ Entry: SCR_011919
+ - Name: bio.tools
+ Entry: blat
=====================================
debian/watch
=====================================
@@ -0,0 +1,7 @@
+version=4
+
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
+ https://github.com/ucscGenomeBrowser/kent-core/tags (?:.*?/)?v?@ANY_VERSION@\.tar\.gz
+
+#opts="mode=git,pretty=0.0+git%cd.%h" \
+# https://github.com/ucscGenomeBrowser/kent-core.git HEAD
View it on GitLab: https://salsa.debian.org/med-team/kent-core/-/commit/49c2a89408bbf3ec7e85e14fdc835e3e7fede7db
--
View it on GitLab: https://salsa.debian.org/med-team/kent-core/-/commit/49c2a89408bbf3ec7e85e14fdc835e3e7fede7db
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230401/b501f940/attachment-0001.htm>
More information about the debian-med-commit
mailing list