[med-svn] [pftools] 02/02: Initial packaging
Andreas Tille
tille at debian.org
Wed Mar 22 11:55:47 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository pftools.
commit 12f45cb271133b42054ce7ba3131aa9bedb22111
Author: Andreas Tille <tille at debian.org>
Date: Wed Mar 22 12:55:18 2017 +0100
Initial packaging
---
debian/changelog | 5 +++
debian/clean | 1 +
debian/compat | 1 +
debian/control | 62 ++++++++++++++++++++++++++++++
debian/copyright | 19 ++++++++++
debian/manpages | 1 +
debian/patches/fix_clean_target.patch | 15 ++++++++
debian/patches/fix_install.patch | 71 +++++++++++++++++++++++++++++++++++
debian/patches/series | 2 +
debian/rules | 22 +++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++
debian/watch | 3 ++
13 files changed, 215 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..25116bb
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+pftools (2.3.5.d-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 21 Mar 2017 22:14:51 +0100
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..9daeafb
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+test
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..ffd60a4
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,62 @@
+Source: pftools
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 10),
+ gfortran
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pftools.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/pftools.git
+Homepage: http://web.expasy.org/pftools/
+
+Package: pftools
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: build and search protein and DNA generalized profiles
+ The pftools package contains all the software necessary to build protein
+ and DNA generalized profiles and use them to scan and align sequences,
+ and search databases.
+ .
+ File formats used by the pftools
+ * Generalized profiles format and syntax.
+ * The multiple sequence alignment format (PSA).
+ * The extended header multiple sequence alignment format (XPSA).
+ .
+ Programs to build generalized profiles
+ pfmake
+ Build a profile from a multiple sequence alignment.
+ pfscale
+ Fit parameters of an extreme-value distribution to a profile score list.
+ pfw
+ Weight sequences of a multiple sequence alignment to correct for
+ sampling bias.
+ .
+ Programs to search with generalized profiles
+ pfsearch
+ Search a protein or DNA sequence library for sequence segments matching
+ a profile.
+ pfscan
+ Scan a protein or DNA sequence with a profile library
+ .
+ Conversion programs
+ psa2msa
+ Reformat PSA file to Pearson/Fasta multiple sequence alignment file.
+ ptof
+ Convert a protein profile into a frame-search profile to search DNA
+ sequences. To be used with 2ft.
+ 2ft
+ Converts both strands of DNA into so-called interleaved
+ frame-translated DNA sequences to search with protein profiles. To be
+ used with ptof.
+ 6ft
+ Translates all six reading frames of a double-stranded DNA sequence
+ into individual protein sequences.
+ pfgtop
+ Convert a profile in GCG format into PROSITE format.
+ pfhtop
+ Convert a HMMER1 ASCII-formatted HMM into an equivalent PROSITE profile.
+ ptoh
+ Converts a generalized profile into an approximately equivalent HMM
+ profile in HMMER1 format (can be read by the hmmconvert program from
+ the HMMER2 package).
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..5927eeb
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,19 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: pftools at isb-sib.ch
+ prosite at expasy.org (via request tracker)
+ Alan.Bridge at sib.swiss, Christian.Sigrist at sib.swiss, Gregoire.Rossier at sib.swiss
+Source: ftp://ftp.lausanne.sib.swiss/pub/software/unix/pftools/pft2.3/
+
+Files: *
+Copyright: 2002-2011 Alan Bridge, Christian Sigrist, Gregoire Rossier
+License: GPL
+ Christian.Sigrist at sib.swiss confirmed GPL in private mail:
+ .
+ The pftools are under a GNU general license. You can find information in
+ the COPYING file distributed with the pftools.
+ .
+ Since there is no such file in the archive I asked back ...
+
+Files: debian/*
+Copyright: 2017 Andreas Tille <tille at debian.org>
+License: GPL
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..85c5e00
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+man/*
diff --git a/debian/patches/fix_clean_target.patch b/debian/patches/fix_clean_target.patch
new file mode 100644
index 0000000..84ee3ff
--- /dev/null
+++ b/debian/patches/fix_clean_target.patch
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 21 Mar 2017 22:14:51 +0100
+Description: Do not fail by trying to remove non-existing files
+
+--- a/Makefile
++++ b/Makefile
+@@ -55,7 +55,7 @@ install: $(PROGS)
+ ./install_pftools.sh $(PKGDIR)
+
+ clean:
+- rm $(PROGS) io.o
++ rm -f $(PROGS) io.o
+
+ io.o : io.c
+ $(CC) -c io.c -o io.o $(CFLAGS) $(PRFLAG)
diff --git a/debian/patches/fix_install.patch b/debian/patches/fix_install.patch
new file mode 100644
index 0000000..7a5dd29
--- /dev/null
+++ b/debian/patches/fix_install.patch
@@ -0,0 +1,71 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 21 Mar 2017 22:14:51 +0100
+Description: Do not request user input
+
+--- a/install_pftools.sh
++++ b/install_pftools.sh
+@@ -67,19 +67,13 @@ echo "Make sure you have write permissio
+ echo
+
+ # Get package directory
+-echo -n "Where should the pftools package be installed ? [ $pkgDir ] "
+-read userInput
+-pkgDir=${userInput:-$pkgDir}
++pkgDir=$DESTDIR/usr/lib/pftools
+
+ # Get binary directory
+-echo -n "Where should the pftools executables be installed ? [ $binDir ] "
+-read userInput
+-binDir=${userInput:-$binDir}
++binDir=$DESTDIR/usr/bin
+
+ # Get man page directory
+-echo -n "Where should the pftools man pages be installed ? [ $manDir ] "
+-read userInput
+-manDir=${userInput:-$manDir}
++manDir=$DESTDIR/usr/share/man
+
+ # Test and remove package directory
+ if [ -d $pkgDir ]; then
+@@ -113,41 +107,17 @@ done
+
+ # Test and create binary directory
+ if [ ! -d $binDir ]; then
+- echo
+- echo "Binary directory $binDir does not exist."
+- echo "Create directory $binDir ? [ y/n ] "
+- read -s -n 1 userInput
+- if [ "$userInput" == 'y' ]; then
+- echo -n " Creating directory $binDir ... "
+ mkdir -p $binDir 2>/dev/null || Fatal "Failed to create $binDir";
+- echo "OK"
+- else
+- Fatal "... aborting."
+- fi
+ fi
+
+ # Test and create man directory
+ if [ ! -d $manDir ]; then
+- echo
+- echo "Man page directory $manDir does not exist."
+- echo "Create directory $manDir ? [ y/n ] "
+- read -s -n 1 userInput
+- if [ "$userInput" == 'y' ]; then
+- echo -n " Creating directory $manDir ... "
+ mkdir -p $manDir 2>/dev/null || Fatal "Failed to create $manDir";
+- echo "OK"
+- else
+- Fatal "... aborting."
+- fi
+ fi
+
+ # Test and create man1 and man5 directories
+ for subDir in ${manDir}/man1 ${manDir}/man5; do
+- if [ ! -d $subDir ]; then
+- echo -n " Creating directory $subDir ... "
+ mkdir -p $subDir 2>/dev/null || Fatal "Failed to create $subDir";
+- echo "OK"
+- fi
+ done
+
+ # Copy package files to package directory
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..0e31a45
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+fix_clean_target.patch
+fix_install.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..26ebbdf
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+%:
+ dh $@ --no-parallel
+
+override_dh_link:
+ dh_link
+ for lnk in debian/$(DEBPKGNAME)/usr/bin/* ; do \
+ ln -sf ../lib/$(DEBPKGNAME)/bin/`basename $${lnk}` $${lnk} ; \
+ done
+ # Avoid name spacing conflict with htop and consequently also rename gtop
+ mv debian/$(DEBPKGNAME)/usr/bin/gtop debian/$(DEBPKGNAME)/usr/bin/pfgtop
+ mv debian/$(DEBPKGNAME)/usr/bin/htop debian/$(DEBPKGNAME)/usr/bin/pfhtop
+
+override_dh_installman:
+ rm -rf debian/$(DEBPKGNAME)/usr/share/man
+ rm -rf debian/$(DEBPKGNAME)/usr/*/$(DEBPKGNAME)/man
+ dh_installman
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..93c74da
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Christian J. A. Sigrist and Lorenzo Cerutti and Nicolas Hulo and Alexandre Gattiker and Laurent Falquet and Marco Pagni and Amos Bairoch and Philipp Bucher
+ Title: "PROSITE: a documented database using patterns and profiles as motif descriptors"
+ Journal: Briefings in Bioinformatics
+ Year: 2002
+ Volume: 3
+ Number: 3
+ Pages: 265-74
+ DOI: 10.1093/bib/3.3.265
+ PMID: 12230035
+ URL: https://academic.oup.com/bib/article-lookup/doi/10.1093/bib/3.3.265
+ eprint: https://academic.oup.com/bib/article-pdf/3/3/265/659046/265.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..6029c4a
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+ftp://ftp.lausanne.sib.swiss/pub/software/unix/pftools/pft2.3/pft(\d.*)\.tar\.gz
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pftools.git
More information about the debian-med-commit
mailing list