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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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: [email protected] + [email protected] (via request tracker) + [email protected], [email protected], [email protected] +Source: ftp://ftp.lausanne.sib.swiss/pub/software/unix/pftools/pft2.3/ + +Files: * +Copyright: 2002-2011 Alan Bridge, Christian Sigrist, Gregoire Rossier +License: GPL + [email protected] 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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
