[med-svn] [trnascan-se] 02/02: Initial packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Fri Oct 30 08:20:22 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository trnascan-se.
commit ee156a5c9b40374b3ebd59eeddd791cfbe8100da
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Fri Oct 30 01:18:55 2015 -0700
Initial packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 27 +++++++++++++++++++++++++++
debian/copyright | 28 ++++++++++++++++++++++++++++
debian/patches/cflags.patch | 19 +++++++++++++++++++
debian/patches/install-location.patch | 19 +++++++++++++++++++
debian/patches/perl5dir.patch | 35 +++++++++++++++++++++++++++++++++++
debian/patches/series | 3 +++
debian/rules | 14 ++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
11 files changed, 164 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..516c790
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+trnascan-se (1.3.1-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #nnnn)
+
+ -- Afif Elghraoui <afif at ghraoui.name> Thu, 29 Oct 2015 23:36:46 -0700
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..993bd06
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,27 @@
+Source: trnascan-se
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Afif Elghraoui <afif at ghraoui.name>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Homepage: http://lowelab.ucsc.edu/tRNAscan-SE
+Vcs-Git: git://anonscm.debian.org/debian-med/trnascan-se.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/trnascan-se.git
+
+Package: trnascan-se
+Architecture: any
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ ${perl:Depends}
+Description: detection of transfer RNA genes in genomic sequence
+ tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while
+ giving less than one false positive per 15 gigabases. Two previously described
+ tRNA detection programs are used as fast, first-pass prefilters to identify
+ candidate tRNAs, which are then analyzed by a highly selective tRNA covariance
+ model. This work represents a practical application of RNA covariance models,
+ which are general, probabilistic secondary structure profiles based on
+ stochastic context-free grammars. tRNAscan-SE searches at ~ 30 000 bp/s.
+ Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as
+ selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..ba9881d
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,28 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: tRNAscan-SE
+Source: http://lowelab.ucsc.edu/software/
+
+Files: *
+Copyright: 1996 Todd M.J. Lowe & Sean R. Eddy
+License: GPL-2.0+
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui <afif at ghraoui.name>
+License: GPL-2.0+
+
+License: GPL-2.0+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
diff --git a/debian/patches/cflags.patch b/debian/patches/cflags.patch
new file mode 100644
index 0000000..215119f
--- /dev/null
+++ b/debian/patches/cflags.patch
@@ -0,0 +1,19 @@
+Description: Append to CFLAGS and don't forcibly set CC
+Author: Afif Elghraoui
+Forwarded: no
+Last-Update: 2015-10-30
+--- trnascan-se.orig/Makefile
++++ trnascan-se/Makefile
+@@ -33,11 +33,8 @@
+ ## where you want temporary files stored
+ TEMPDIR = /tmp
+
+-## your compiler
+-CC = gcc # GNU cc (if available) otherwise use vendor's cc
+-
+ ## any special compiler flags you want
+-CFLAGS = -O # ok for most machines (remove -O for DEC OSF/1 cc compiler)
++CFLAGS += -O # ok for most machines (remove -O for DEC OSF/1 cc compiler)
+
+ ## machine specific definitions
+ # You shouldn't need any. The specific #define's in squid are historical.
diff --git a/debian/patches/install-location.patch b/debian/patches/install-location.patch
new file mode 100644
index 0000000..af9c8ad
--- /dev/null
+++ b/debian/patches/install-location.patch
@@ -0,0 +1,19 @@
+Description: Set install destination directories
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: not-needed
+Last-Update: 2015-10-30
+--- trnascan-se.orig/Makefile
++++ trnascan-se/Makefile
+@@ -20,9 +20,9 @@
+ PERLBIN = perl
+
+ ## where you want things installed
+-BINDIR = $(HOME)/bin
+-LIBDIR = $(HOME)/lib/tRNAscan-SE
+-MANDIR = $(HOME)/man
++BINDIR = $(DESTDIR)/usr/bin
++LIBDIR = $(DESTDIR)/usr/lib/tRNAscan-SE
++MANDIR = $(DESTDIR)/usr/share/man
+
+ ## NOTE !! If you later manually move the location of
+ ## binaries or data files in the BINDIR or LIBDIR directories,
diff --git a/debian/patches/perl5dir.patch b/debian/patches/perl5dir.patch
new file mode 100644
index 0000000..b3eaf2b
--- /dev/null
+++ b/debian/patches/perl5dir.patch
@@ -0,0 +1,35 @@
+Description: install perl modules where they belong
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: no
+Last-Update: 2015-10-30
+--- trnascan-se.orig/Makefile
++++ trnascan-se/Makefile
+@@ -23,6 +23,7 @@
+ BINDIR = $(DESTDIR)/usr/bin
+ LIBDIR = $(DESTDIR)/usr/lib/tRNAscan-SE
+ MANDIR = $(DESTDIR)/usr/share/man
++PERL5DIR = $(DESTDIR)/usr/share/perl5
+
+ ## NOTE !! If you later manually move the location of
+ ## binaries or data files in the BINDIR or LIBDIR directories,
+@@ -158,17 +159,18 @@
+ @echo "be sure to make the following changes:"
+ @echo ""
+ @echo "1) Add $(BINDIR) to your PATH variable"
+- @echo "2) Add $(BINDIR) to your PERl5LIB variable"
++ @echo "2) Add $(PERL5DIR) to your PERl5LIB variable"
+ @echo "3) Add $(MANDIR) to your MANPATH variable"
+ @echo ""
+
+ install: $(PROGS) tRNAscanSE
+ @if test -d $(BINDIR); then echo .; else mkdir -p $(BINDIR); fi
+ @if test -d $(LIBDIR); then echo .; else mkdir -p $(LIBDIR); fi
++ @if test -d $(PERL5DIR); then echo .; else mkdir -p $(PERL5DIR); fi
+ @if test -d $(TEMPDIR); then echo .; else mkdir -p $(TEMPDIR); fi
+ @if test -d $(MANDIR)/man$(MANSUFFIX); then echo .; else mkdir -p $(MANDIR)/man$(MANSUFFIX); fi
+ cp $(PROGS) tRNAscan-SE $(BINDIR)/.
+- cp -R tRNAscanSE $(BINDIR)/
++ cp -R tRNAscanSE $(PERL5DIR)/
+ cp TPCsignal Dsignal *.cm gcode.* $(LIBDIR)/.
+ @if test -r trnascan-1.4-NA; then cp trnascan-1.4-NA $(BINDIR)/.; fi
+ @if test -r eufindtRNA-NA; then cp eufindtRNA-NA $(BINDIR)/.; fi
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..8ac56d0
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+install-location.patch
+perl5dir.patch
+cflags.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..e15fcea
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+CFLAGS := $(CPPFLAGS) $(CFLAGS)
+
+%:
+ dh $@
+
+override_dh_installchangelogs:
+ dh_installchangelogs Release.history
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..4bc3e99
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Todd M Lowe and Sean R Eddy
+ Title: "tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence"
+ Journal: Nucleic Acids Research
+ Year: 1997
+ Volume: 25
+ Number: 5
+ Pages: 955-964
+ DOI: 10.1093/nar/25.5.0955
+ PMID: 9023104
+ URL: http://nar.oxfordjournals.org/content/25/5/0955.abstract
+ eprint: http://nar.oxfordjournals.org/content/25/5/0955.full.pdf+html
--
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