[med-svn] [bcl2fastq2] 02/02: initial Debian packaging - no intend to release this officially for the moment, thought
Andreas Tille
tille at debian.org
Tue Jun 20 14:08:15 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bcl2fastq2.
commit f3e0971ba30100086b49e0b77cd9cb81f3bc0f90
Author: Andreas Tille <tille at debian.org>
Date: Tue Jun 20 16:06:45 2017 +0200
initial Debian packaging - no intend to release this officially for the moment, thought
---
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 34 +++++++++
debian/copyright | 140 ++++++++++++++++++++++++++++++++++
debian/patches/fix_lib_versions.patch | 23 ++++++
debian/patches/series | 1 +
debian/rules | 20 +++++
debian/source/format | 1 +
debian/watch | 4 +
9 files changed, 229 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..f1c0e97
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+bcl2fastq2 (2.19.1.403-1) UNRELEASED; urgency=low
+
+ * local package
+
+ -- Andreas Tille <tille at debian.org> Tue, 20 Jun 2017 14:40:44 +0200
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..ffb8e7f
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,34 @@
+Source: bcl2fastq2
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tillea at rki.de>
+Section: non-free/science
+Priority: optional
+Build-Depends: debhelper (>= 10),
+ cmake,
+ libboost-chrono-dev,
+ libboost-date-time-dev,
+ libboost-filesystem-dev,
+ libboost-iostreams-dev,
+ libboost-program-options-dev,
+ libboost-regex-dev,
+ libboost-serialization-dev,
+ libboost-system-dev,
+ libboost-timer-dev,
+ libboost-thread-dev,
+ zlib1g-dev,
+ libxml2-dev,
+ libxslt1-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bcl2fastq2.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/bcl2fastq2.git
+Homepage: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
+
+Package: bcl2fastq2
+Architecture: amd64
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: demultiplex data and convert BCL files to FASTQ
+ The bcl2fastq2 Conversion Software can be used to convert BCL files from
+ MiniSeq, MiSeq, NextSeq, HiSeq, and NovaSeq sequening systems. For conversion
+ of data generated on Illumina sequencing systems using versions of RTA
+ earlier than RTA 1.18.54, use bcl2fastq v1.8.4.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..32914ca
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,140 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/downloads.html
+Files-Excluded: boost_1_54_0.tar.bz2
+ cmake-2.8.9.tar.gz
+ libxml2-2.7.8.tar.gz
+ libxslt-1.1.26.tar.gz
+
+Files: *
+Copyright: 2015-2017 Illumina, Inc. All rights reserved
+License: ILLUMINA
+ ILLUMINA SOFTWARE LICENSE AGREEMENT
+ .
+ PLEASE READ THESE TERMS CAREFULLY BEFORE OPENING, INSTALLING, USING, ACCESSING OR MANIPULATING
+ THE SOFTWARE (AS DEFINED BELOW), AS BY SUCH ACTIONS YOU ACKNOWLEDGE THAT YOU HAVE READ THIS
+ AGREEMENT, UNDERSTAND IT AND AGREE TO BE BOUND BY ITS TERMS.
+ .
+ ILLUMINA, INC. (“LICENSOR”) IS WILLING TO LICENSE THE ENCLOSED SOFTWARE (THE “SOFTWARE”) TO YOU ONLY ON
+ THE CONDITION THAT YOU ACCEPT ALL OF THE TERMS IN THIS AGREEMENT. IF YOU DO NOT AGREE TO THESE TERMS,
+ LICENSOR IS UNWILLING TO LICENSE THE SOFTWARE TO YOU, AND YOU SHOULD NOT USE OR INSTALL THE SOFTWARE.
+ .
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+ solely in executable code form and solely in conjunction with this hardware (the “Product”). In the case of Software
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+ 13. THIRD PARTY SOFTWARE. To the extent third party code is included in Program and any term or condition of a
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+ THE SOFTWARE IS PROTECTED BY UNITED STATES COPYRIGHT LAW AND INTERNATIONAL TREATY.
+ UNAUTHORIZED REPRODUCTION OR DISTRIBUTION IS SUBJECT TO CIVIL AND CRIMINAL PENALTIES.
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+
+Files: debian/*
+Copyright: 2017 Andreas Tille <tillea at rki.de>
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ 3. Neither the name of the University nor the names of its contributors
+ may be used to endorse or promote products derived from this software
+ without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
diff --git a/debian/patches/fix_lib_versions.patch b/debian/patches/fix_lib_versions.patch
new file mode 100644
index 0000000..343321e
--- /dev/null
+++ b/debian/patches/fix_lib_versions.patch
@@ -0,0 +1,23 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 20 Jun 2017 14:40:44 +0200
+Description: Redist untaring attempt even after correct version was found
+ just force cmake to ignore the redistributed code copies.
+
+--- a/src/cmake/cxxConfigure.cmake
++++ b/src/cmake/cxxConfigure.cmake
+@@ -103,15 +103,6 @@ if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXS
+ find_package_version(LibXslt ${BCL2FASTQ_LIBXSLT_VERSION})
+ endif((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT))
+
+-if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT))
+- redist_package(LIBXML2 ${BCL2FASTQ_LIBXML2_VERSION}
+- "--prefix=${REINSTDIR};--without-modules;--without-http;--without-ftp;--without-python;--without-threads;--without-schematron;--without-debug;--without-iconv")
+- find_library_redist(LIBXML2 ${REINSTDIR} libxml/xpath.h xml2)
+- redist_package(LIBXSLT ${BCL2FASTQ_LIBXSLT_VERSION} "--prefix=${REINSTDIR};--with-libxml-prefix=${REINSTDIR};--without-plugins;--without-crypto")
+- find_library_redist(LIBEXSLT ${REINSTDIR} libexslt/exslt.h exslt)
+- find_library_redist(LIBXSLT ${REINSTDIR} libxslt/xsltconfig.h xslt)
+-endif((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT))
+-
+ include_directories(BEFORE SYSTEM ${LIBXML2_INCLUDE_DIR})
+ include_directories(BEFORE SYSTEM ${LIBXSLT_INCLUDE_DIR})
+ include_directories(BEFORE SYSTEM ${LIBEXSLT_INCLUDE_DIR})
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..66b09b1
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+fix_lib_versions.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..409d259
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,20 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+ dh $@
+
+override_dh_clean:
+ dh_clean
+ rm -rf bcl2fastq-build
+
+override_dh_auto_configure:
+ mkdir bcl2fastq-build
+ cd bcl2fastq-build && ../src/configure --verbose --with-cmake=/usr/bin/cmake --prefix=$(CURDIR)/debian/tmp/usr
+
+override_dh_auto_build:
+ cd bcl2fastq-build && make
+
+override_dh_auto_install:
+ cd bcl2fastq-build && make install
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/watch b/debian/watch
new file mode 100644
index 0000000..9c49716
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+
+# https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/downloads.html
+https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-19.html .*/bcl2fastq/bcl2fastq2-v(\d[.\d]+)-tar\.zip
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