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commit ee156a5c9b40374b3ebd59eeddd791cfbe8100da Author: Afif Elghraoui <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Afif Elghraoui <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trnascan-se.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
