[med-svn] [Git][med-team/sibelia][master] 6 commits: Remove snpEff from package source, add README.Debian to explain the situation
Andreas Tille
gitlab at salsa.debian.org
Fri Feb 15 09:03:58 GMT 2019
Andreas Tille pushed to branch master at Debian Med / sibelia
Commits:
affbec17 by Andreas Tille at 2019-02-15T08:47:39Z
Remove snpEff from package source, add README.Debian to explain the situation
- - - - -
9a4240df by Andreas Tille at 2019-02-15T08:49:01Z
Without snpEff package is dfsg free
- - - - -
840b4925 by Andreas Tille at 2019-02-15T08:50:19Z
New upstream version 3.0.7+dfsg
- - - - -
2a160d9f by Andreas Tille at 2019-02-15T08:50:52Z
Update upstream source from tag 'upstream/3.0.7+dfsg'
Update to upstream version '3.0.7+dfsg'
with Debian dir 7edf86692e32569ea0607c6553d29749f7cab5d1
- - - - -
5aae61a2 by Andreas Tille at 2019-02-15T08:57:55Z
snpEff is removed
- - - - -
3a7985eb by Andreas Tille at 2019-02-15T09:03:30Z
Be verbose
- - - - -
13 changed files:
- + debian/README.Debian
- debian/changelog
- debian/control
- debian/copyright
- debian/createmanpages
- debian/patches/series
- + debian/patches/snpeff_is_removed.patch
- debian/rules
- debian/tests/run-unit-test
- debian/watch
- − src/annotation/snpEff/genomes.txt
- − src/annotation/snpEff/snpEff.config
- − src/annotation/snpEff/snpEff.jar
Changes:
=====================================
debian/README.Debian
=====================================
@@ -0,0 +1,16 @@
+sibelia for Debian
+==================
+
+Due to removal of the binary JAR of snpEff from the Debian package
+source the annotation feature is not available. The removal was needed
+to enable uploading sibelia to Debian main. If you really need the
+annotation feature via snpEff there are two options:
+
+ 1. Help packaging snpEff from source. The process had started in Git
+ https://salsa.debian.org/med-team/snpeff
+ 2. Ask for creating a separate package sibelia-annotation that needs
+ to got to non-free.
+
+
+ -- Andreas Tille <tille at debian.org> Thu, 14 Feb 2019 14:52:05 +0100
+
=====================================
debian/changelog
=====================================
@@ -1,7 +1,5 @@
-sibelia (3.0.7+ds-1) UNRELEASED; urgency=medium
+sibelia (3.0.7+dfsg-1) UNRELEASED; urgency=medium
* Initial release (Closes: #<bug>)
- As long as we have no official snpeff package I do not intend to
- package this.
-- Andreas Tille <tille at debian.org> Thu, 14 Feb 2019 14:52:05 +0100
=====================================
debian/control
=====================================
@@ -51,23 +51,23 @@ Description: comparative genomics tool (example data)
.
This package contains example data for sibelia.
-Package: sibelia-annotate
-Architecture: all
-Depends: ${misc:Depends},
- python,
- openjdk-11-jre | default-jre
-Description: comparative genomics tool (annotation tool using snpEFF)
- Sibelia (Synteny Block ExpLoration tool) is a comparative genomics tool:
- It assists biologists in analysing the genomic variations that correlate
- with pathogens, or the genomic changes that help microorganisms adapt in
- different environments. Sibelia will also be helpful for the
- evolutionary and genome rearrangement studies for multiple strains of
- microorganisms.
- .
- Sibelia is useful in finding:
- .
- 1) shared regions,
- 2) regions that present in one group of genomes but not in others,
- 3) rearrangements that transform one genome to other genomes.
- .
- This package contains an annotation tool using snpEFF.
+#Package: sibelia-annotate
+#Architecture: all
+#Depends: ${misc:Depends},
+# python,
+# openjdk-11-jre | default-jre
+#Description: comparative genomics tool (annotation tool using snpEFF)
+# Sibelia (Synteny Block ExpLoration tool) is a comparative genomics tool:
+# It assists biologists in analysing the genomic variations that correlate
+# with pathogens, or the genomic changes that help microorganisms adapt in
+# different environments. Sibelia will also be helpful for the
+# evolutionary and genome rearrangement studies for multiple strains of
+# microorganisms.
+# .
+# Sibelia is useful in finding:
+# .
+# 1) shared regions,
+# 2) regions that present in one group of genomes but not in others,
+# 3) rearrangements that transform one genome to other genomes.
+# .
+# This package contains an annotation tool using snpEFF.
=====================================
debian/copyright
=====================================
@@ -3,17 +3,14 @@ Upstream-Name: SiBELia
Source: https://sourceforge.net/projects/sibelia-bio/files/
Files-Excluded: */libdivsufsort*
*/lagan
+ */snpEff
+Comment: Due to removal of snpEff the annotation feature is not available.
Files: *
Copyright: 2011-2018 Saint-Petersburg Academic University
Ilya Minkin, Nikolay Vyahhi, Mikhail Kolmogorov, Son Pham
License: GPL-2
-Files: src/annotation/snpEff/*
-Copyright: © 2008-2016, Pablo Cingolani <pcingola at users.sourceforge.net>
-License: Apache-2.0 or BSD or LGPL-2 or LGPL-2.1
-Comment: Unfortunately that's a binary JAR which is not packaged from source
-
Files: debian/*
Copyright: 2019 Andreas Tille <tille at debian.org>
License: GPL-2
=====================================
debian/createmanpages
=====================================
@@ -24,11 +24,11 @@ help2man --no-info --no-discard-stderr \
--version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
echo $AUTHOR >> $MANDIR/${progname}.1
-progname=snpEffAnnotate.py
-help2man --no-info --no-discard-stderr \
- --name="Script for variants annotation" \
- --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
-echo $AUTHOR >> $MANDIR/${progname}.1
+#progname=snpEffAnnotate.py
+#help2man --no-info --no-discard-stderr \
+# --name="Script for variants annotation" \
+# --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+#echo $AUTHOR >> $MANDIR/${progname}.1
cat > debian/sibelia.manpages <<EOT
debian/C*.1
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
use_debian_packaged_libdivsufsort.patch
use_debian_packaged_lagan.patch
+snpeff_is_removed.patch
=====================================
debian/patches/snpeff_is_removed.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 14 Feb 2019 14:52:05 +0100
+Description: snpEff is removed - see README.Debian
+
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -28,8 +28,6 @@ else()
+ if(NOT ONLY_SIBELIA)
+ include(ExternalProject)
+ install(PROGRAMS csibelia/C-Sibelia.py DESTINATION bin)
+- install(PROGRAMS annotation/snpEffAnnotate.py DESTINATION bin)
+- install(DIRECTORY annotation/snpEff DESTINATION ${LIB_DIR})
+ install(DIRECTORY utils DESTINATION ${SHARE_DIR})
+ install(DIRECTORY ${SOURCE_DIR} DESTINATION ${LIB_DIR} FILE_PERMISSIONS USE_SOURCE_PERMISSIONS DIRECTORY_PERMISSIONS USE_SOURCE_PERMISSIONS REGEX "${SOURCE_DIR}/Readmes|Makefile|${SOURCE_DIR}/src" EXCLUDE)
+ endif()
=====================================
debian/rules
=====================================
@@ -17,8 +17,8 @@ override_dh_install:
override_dh_installman:
dh_installman
- mkdir -p debian/$(DEB_SOURCE)-annotate//usr/share/man/man1
- mv debian/$(DEB_SOURCE)-annotate/usr/share/man/py/man1/snpEffAnnotate.1 debian/$(DEB_SOURCE)-annotate/usr/share/man/man1/snpEffAnnotate.py.1
- rm -rf debian/$(DEB_SOURCE)-annotate/usr/share/man/py/
+# mkdir -p debian/$(DEB_SOURCE)-annotate//usr/share/man/man1
+# mv debian/$(DEB_SOURCE)-annotate/usr/share/man/py/man1/snpEffAnnotate.1 debian/$(DEB_SOURCE)-annotate/usr/share/man/man1/snpEffAnnotate.py.1
+# rm -rf debian/$(DEB_SOURCE)-annotate/usr/share/man/py/
mv debian/$(DEB_SOURCE)/usr/share/man/py/man1/C-Sibelia.1 debian/$(DEB_SOURCE)/usr/share/man/man1/C-Sibelia.py.1
rm -rf debian/$(DEB_SOURCE)/usr/share/man/py
=====================================
debian/tests/run-unit-test
=====================================
@@ -13,6 +13,7 @@ cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
cd $AUTOPKGTEST_TMP
gunzip -r *
+set -x
cd C-Sibelia/Staphylococcus_aureus
C-Sibelia.py NCTC8325.fasta RN4220.fasta
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
-opts="repacksuffix=+ds,dversionmangle=auto,repack,compression=xz" \
+opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
http://sf.net/sibelia-bio/Sibelia@ANY_VERSION@-Source@ARCHIVE_EXT@
=====================================
src/annotation/snpEff/genomes.txt deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
src/annotation/snpEff/snpEff.config deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
src/annotation/snpEff/snpEff.jar deleted
=====================================
Binary files a/src/annotation/snpEff/snpEff.jar and /dev/null differ
View it on GitLab: https://salsa.debian.org/med-team/sibelia/compare/e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453...3a7985ebf97ca9ad8de91bcbae55faec4f4ea4f1
--
View it on GitLab: https://salsa.debian.org/med-team/sibelia/compare/e81d4a8bf4f2d9445babebe1fb0a4f17cc2bb453...3a7985ebf97ca9ad8de91bcbae55faec4f4ea4f1
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