[med-svn] [easel] 02/02: initial debianization
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed Apr 19 19:42:44 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository easel.
commit d77e5c11eead0f81c290ec1cf520edc1d6bdf00e
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Apr 19 05:51:04 2017 -0700
initial debianization
---
debian/TODO | 3 +
debian/changelog | 5 +
debian/clean | 1 +
debian/compat | 1 +
debian/control | 61 ++++++++
debian/copyright | 383 +++++++++++++++++++++++++++++++++++++++++++++
debian/docker/Dockerfile | 17 ++
debian/easel-apps.install | 1 +
debian/easel-apps.manpages | 1 +
debian/easel-dev.install | 2 +
debian/easel-doc.doc-base | 15 ++
debian/easel-doc.docs | 2 +
debian/patches/docs | 25 +++
debian/patches/hardening | 19 +++
debian/patches/mans | 33 ++++
debian/patches/series | 4 +
debian/patches/spelling | 46 ++++++
debian/rules | 44 ++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++
debian/watch | 3 +
21 files changed, 679 insertions(+)
diff --git a/debian/TODO b/debian/TODO
new file mode 100644
index 0000000..6d8b775
--- /dev/null
+++ b/debian/TODO
@@ -0,0 +1,3 @@
+libeasel with a shared library
+build the apps linking against the shared library
+migrate hmmer, infernal packages to use this package
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..407efa5
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+easel (0.43-1) UNRELEASED; urgency=medium
+
+ * Initial release. (Closes: #860746)
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 19 Apr 2017 04:30:05 -0700
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..a702eef
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+miniapps/*.1
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..66573df
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,61 @@
+Source: easel
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>
+Build-Depends: debhelper (>= 10),
+ autotools-dev,
+ libgsl-dev,
+ mpi-default-dev,
+ help2man,
+ texlive-latex-base,
+ texlive-latex-extra,
+ texlive-fonts-recommended
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/easel.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/easel.git
+Homepage: https://github.com/EddyRivasLab/easel
+
+Package: easel-dev
+Architecture: any
+Depends: ${misc:Depends}
+Description: library of C functions for biological sequence analysis
+ Easel is an ANSI C code library for computational analysis of
+ biological sequences using probabilistic models. Easel is used by
+ HMMER, the profile hidden Markov model software that underlies the
+ Pfam protein families database, and by Infernal, the profile
+ stochastic context-free grammar software that underlies the Rfam RNA
+ family database. Easel aims to make similar applications more robust
+ and easier to develop, by providing a set of reusable, documented, and
+ well-tested functions.
+
+Package: easel-apps
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: miniapps from easel
+ Easel is an ANSI C code library for computational analysis of
+ biological sequences using probabilistic models. Easel is used by
+ HMMER, the profile hidden Markov model software that underlies the
+ Pfam protein families database, and by Infernal, the profile
+ stochastic context-free grammar software that underlies the Rfam RNA
+ family database. Easel aims to make similar applications more robust
+ and easier to develop, by providing a set of reusable, documented, and
+ well-tested functions.
+ .
+ This package contains the "miniapps"
+
+Package: easel-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Description: docs for a library of C functions for biological sequence analysis
+ Easel is an ANSI C code library for computational analysis of
+ biological sequences using probabilistic models. Easel is used by
+ HMMER, the profile hidden Markov model software that underlies the
+ Pfam protein families database, and by Infernal, the profile
+ stochastic context-free grammar software that underlies the Rfam RNA
+ family database. Easel aims to make similar applications more robust
+ and easier to develop, by providing a set of reusable, documented, and
+ well-tested functions.
+ .
+ This package contains the PDF documentation
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..b8eebdf
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,383 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: easel
+Source: https://github.com/EddyRivasLab/easel
+Files-Excluded: demotic/*
+
+Files: *
+Copyright: © 2004-2016 Sean R. Eddy
+ © 2004-2016 Howard Hughes Medical Institute
+ © 2015-2016 President and Fellows of Harvard College
+ © 2004-2006 Washington University School of Medicine
+License: BSD-3-clause
+
+Files: debian/*
+Copyright: © 2017 Michael R. Crusoe <michael.crusoe at gmail.com>
+License: BSD-3-clause
+
+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:
+ .
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+Files: esl_stopwatch.c
+Copyright: 2012, David Robert Nadeau, http:NadeauSoftware.com
+License: CC-BY-3.0
+ Creative Commons Attribution 3.0 Unported
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diff --git a/debian/docker/Dockerfile b/debian/docker/Dockerfile
new file mode 100644
index 0000000..4e0e0da
--- /dev/null
+++ b/debian/docker/Dockerfile
@@ -0,0 +1,17 @@
+# for communicating with upstream
+
+FROM debian:sid
+
+RUN apt-get clean all &&\
+ apt-get update &&\
+ apt-get install -y wget make autoconf gcc texlive-latex-base \
+ texlive-latex-extra texlive-fonts-recommended
+
+RUN wget https://github.com/EddyRivasLab/easel/archive/0.43.tar.gz &&\
+ tar xzf *.tar.gz &&\
+ cd easel* && chmod a+x devkit/cexcerpt &&\
+ autoconf && ./configure && make check
+
+RUN cd easel*/documentation && make pdf || /bin/true
+
+CMD /bin/bash
diff --git a/debian/easel-apps.install b/debian/easel-apps.install
new file mode 100644
index 0000000..1df36c6
--- /dev/null
+++ b/debian/easel-apps.install
@@ -0,0 +1 @@
+usr/bin/*
diff --git a/debian/easel-apps.manpages b/debian/easel-apps.manpages
new file mode 100644
index 0000000..a702eef
--- /dev/null
+++ b/debian/easel-apps.manpages
@@ -0,0 +1 @@
+miniapps/*.1
diff --git a/debian/easel-dev.install b/debian/easel-dev.install
new file mode 100644
index 0000000..d275658
--- /dev/null
+++ b/debian/easel-dev.install
@@ -0,0 +1,2 @@
+usr/lib/*
+usr/include/*
diff --git a/debian/easel-doc.doc-base b/debian/easel-doc.doc-base
new file mode 100644
index 0000000..abf93f8
--- /dev/null
+++ b/debian/easel-doc.doc-base
@@ -0,0 +1,15 @@
+Document: easel
+Title: Easel Userguide
+Author: Sean Eddy
+Abstract: Easel is an ANSI C code library for computational analysis of
+ biological sequences using probabilistic models. Easel is used by
+ HMMER, the profile hidden Markov model software that underlies the
+ Pfam protein families database, and by Infernal, the profile
+ stochastic context-free grammar software that underlies the Rfam RNA
+ family database. Easel aims to make similar applications more robust
+ and easier to develop, by providing a set of reusable, documented, and
+ well-tested functions.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/easel-doc/current.pdf.gz
diff --git a/debian/easel-doc.docs b/debian/easel-doc.docs
new file mode 100644
index 0000000..d3214db
--- /dev/null
+++ b/debian/easel-doc.docs
@@ -0,0 +1,2 @@
+documentation/current.pdf
+00README
diff --git a/debian/patches/docs b/debian/patches/docs
new file mode 100644
index 0000000..5fb373f
--- /dev/null
+++ b/debian/patches/docs
@@ -0,0 +1,25 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: try to build the docs as best as we can
+Forwarded: https://github.com/EddyRivasLab/easel/issues/21
+--- easel.orig/documentation/Makefile.in
++++ easel/documentation/Makefile.in
+@@ -112,7 +112,7 @@
+ done
+ @echo " LATEX current.pdf (see latex.log for output)"
+ @pdflatex -interaction=nonstopmode main > latex.log 2>&1
+- @bibtex main >> latex.log 2>&1
++ #@bibtex main >> latex.log 2>&1
+ @pdflatex main >> latex.log 2>&1
+ @pdflatex main >> latex.log 2>&1
+ @mv main.pdf current.pdf
+--- easel.orig/documentation/codestyle.tex
++++ easel/documentation/codestyle.tex
+@@ -1077,7 +1077,7 @@
+ \ccode{obj}. Shadow creation arises in multithreading, when threads
+ can share some but not all internal object data. A shadow keeps
+ constant data as pointers to the original object. The object needs to
+-know whether it is a shadow or not, so that <_Destroy()> works
++know whether it is a shadow or not, so that <\_Destroy()> works
+ properly on both the original and its shadows.
+
+ \end{sreapi}
diff --git a/debian/patches/hardening b/debian/patches/hardening
new file mode 100644
index 0000000..f048d42
--- /dev/null
+++ b/debian/patches/hardening
@@ -0,0 +1,19 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: Pass CPPFLAGS to enable hardening
+--- easel.orig/miniapps/Makefile.in
++++ easel/miniapps/Makefile.in
+@@ -115,12 +115,12 @@
+ check: ${PROGS}
+
+ ${PROGS}: @EXEC_DEPENDENCY@ ../libeasel.a
+- ${QUIET_GEN}${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -L.. -o $@ $@.o ${LIBS}
++ ${QUIET_GEN}${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} ${CPPFLAGS} -L.. -o $@ $@.o ${LIBS}
+
+ ${PROGOBJS}: ../libeasel.a
+
+ .c.o: ../libeasel.a
+- ${QUIET_CC}${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ -c $<
++ ${QUIET_CC}${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${CPPFLAGS} -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ -c $<
+
+ install:
+ for file in ${PROGS}; do \
diff --git a/debian/patches/mans b/debian/patches/mans
new file mode 100644
index 0000000..6ccbc59
--- /dev/null
+++ b/debian/patches/mans
@@ -0,0 +1,33 @@
+Description: fill out substitution macros in manpages
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+--- easel.orig/configure.ac
++++ easel/configure.ac
+@@ -540,6 +540,28 @@
+ fi
+ AC_CONFIG_FILES([documentation/Makefile])
+
++AC_CONFIG_FILES([miniapps/esl-selectn.1:miniapps/esl-selectn.man])
++AC_CONFIG_FILES([miniapps/esl-seqrange.1:miniapps/esl-seqrange.man])
++AC_CONFIG_FILES([miniapps/esl-ssdraw.1:miniapps/esl-ssdraw.man])
++AC_CONFIG_FILES([miniapps/esl-weight.1:miniapps/esl-weight.man])
++AC_CONFIG_FILES([miniapps/esl-alirev.1:miniapps/esl-alirev.man])
++AC_CONFIG_FILES([miniapps/esl-compstruct.1:miniapps/esl-compstruct.man])
++AC_CONFIG_FILES([miniapps/esl-alimerge.1:miniapps/esl-alimerge.man])
++AC_CONFIG_FILES([miniapps/esl-seqstat.1:miniapps/esl-seqstat.man])
++AC_CONFIG_FILES([miniapps/esl-translate.1:miniapps/esl-translate.man])
++AC_CONFIG_FILES([miniapps/esl-alipid.1:miniapps/esl-alipid.man])
++AC_CONFIG_FILES([miniapps/esl-mask.1:miniapps/esl-mask.man])
++AC_CONFIG_FILES([miniapps/esl-alimask.1:miniapps/esl-alimask.man])
++AC_CONFIG_FILES([miniapps/esl-shuffle.1:miniapps/esl-shuffle.man])
++AC_CONFIG_FILES([miniapps/esl-histplot.1:miniapps/esl-histplot.man])
++AC_CONFIG_FILES([miniapps/esl-construct.1:miniapps/esl-construct.man])
++AC_CONFIG_FILES([miniapps/esl-reformat.1:miniapps/esl-reformat.man])
++AC_CONFIG_FILES([miniapps/esl-alimanip.1:miniapps/esl-alimanip.man])
++AC_CONFIG_FILES([miniapps/esl-alistat.1:miniapps/esl-alistat.man])
++AC_CONFIG_FILES([miniapps/esl-sfetch.1:miniapps/esl-sfetch.man])
++AC_CONFIG_FILES([miniapps/esl-compalign.1:miniapps/esl-compalign.man])
++AC_CONFIG_FILES([miniapps/esl-alimap.1:miniapps/esl-alimap.man])
++AC_CONFIG_FILES([miniapps/esl-afetch.1:miniapps/esl-afetch.man])
+
+ #################################################################
+ # 14. et voila!
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..46c198f
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,4 @@
+hardening
+mans
+docs
+spelling
diff --git a/debian/patches/spelling b/debian/patches/spelling
new file mode 100644
index 0000000..8cf3af9
--- /dev/null
+++ b/debian/patches/spelling
@@ -0,0 +1,46 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: some spelling fixes
+--- easel.orig/miniapps/esl-alimerge.c
++++ easel/miniapps/esl-alimerge.c
+@@ -43,7 +43,7 @@
+ static char usage2[] = "[options] --list <file listing n > 1 ali files to merge>\n\
+ \n\
+ Input alignments must be in Stockholm or Pfam format.\n\
+- Ouput format choices\n\
++ Output format choices\n\
+ --------------------\n\
+ stockholm [default]\n\
+ pfam\n\
+--- easel.orig/miniapps/esl-alimask.c
++++ easel/miniapps/esl-alimask.c
+@@ -168,7 +168,7 @@
+ puts("\n Only one usage listed above can be used per execution with the exception of");
+ puts(" -p and -g, which can be used in combination with each other.\n");
+ puts(" With -t, <coords> is a string that specifies positive integer start and end");
+- puts(" coordinates seperated by any nonnumeric, nonspace character(s).");
++ puts(" coordinates separated by any nonnumeric, nonspace character(s).");
+ puts(" For example, \"23..100\" or \"23/100\" or \"23-100\" all specify that columns");
+ puts(" 23 to 100 be kept and all other columns be removed. Additionally, to retrieve");
+ puts(" all columns from a position to the end, omit the end coord; \"23:\" will work.");
+--- easel.orig/miniapps/esl-ssdraw.c
++++ easel/miniapps/esl-ssdraw.c
+@@ -549,7 +549,7 @@
+ { "--no-ntpp", eslARG_NONE, FALSE, NULL, NULL, NULL,"--indi", "--no-pp", "w/--indi, do not draw nts on individual post prob diagrams", 9 },
+
+ { "--no-cnt", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, NULL, "do not draw consensus nts on alignment summary diagrams", 7 },
+- { "--cthresh",eslARG_REAL, "0.75", NULL,"0<x<=1.0", NULL,NULL, "--no-cnt", "capitalize cons nts occuring in >= <x> fraction of seqs", 7 },
++ { "--cthresh",eslARG_REAL, "0.75", NULL,"0<x<=1.0", NULL,NULL, "--no-cnt", "capitalize cons nts occurring in >= <x> fraction of seqs", 7 },
+ { "--cambig", eslARG_NONE, FALSE, NULL, NULL, NULL,NULL, "--no-cnt", "allow ambiguous nts in consensus sequence", 7 },
+ { "--athresh",eslARG_REAL, "0.9", NULL,"0<x<=1.0", NULL,"--cambig",NULL, "w/--cambig, cons nt must represent >= <x> fraction of seqs", 7 },
+
+--- easel.orig/miniapps/esl-ssdraw.man
++++ easel/miniapps/esl-ssdraw.man
+@@ -288,7 +288,7 @@
+ legend and <f3> specifies how many extra points should be between the
+ right hand edge of the legend and the end of the page. the offset of
+ the right hand end of the legend . For example, the line '% 34
+--40. -30. 12 0.' specfies that the legend be placed 40 points to the left
++-40. -30. 12 0.' specifies that the legend be placed 40 points to the left
+ and 30 points below the 34th consensus position, that cells
+ appearing in the legend be squares of size 12 points by 12 points, and
+ that the right hand side of the legend flush against the right hand
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..9f68b3f
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,44 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+export AUTOHEADER=true # confusingly, this skips autoheader
+
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/buildflags.mk
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+%:
+ dh $@
+
+override_dh_auto_configure:
+ ls miniapps/*.man | xargs sed -i 's=\.pp=\.PP=g'
+ ls miniapps/*.man | xargs sed -i 's=@RELEASEDATE@=@EASEL_DATE@=g'
+ ls miniapps/*.man | xargs sed -i 's=@PACKAGE@=@PACKAGE_NAME@=g'
+ ls miniapps/*.man | xargs sed -i 's=@RELEASE@=@EASEL_VERSION@=g'
+ dh_auto_configure -- --enable-mpi # --with-gsl
+ ls miniapps/*.man | xargs sed -i 's=\.PP=\.pp=g'
+
+override_dh_auto_build:
+ chmod a+x devkit/cexcerpt
+ dh_auto_build
+ PATH=$${PATH}:miniapps help2man --help-option="-h" \
+ --version-string "$(VERSION)" --no-info \
+ --name "Clusters tabular data." esl-cluster \
+ > miniapps/esl-cluster.1
+ cd documentation
+ make pdf
+ chmod a-x devkit/cexcerpt
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..d8b5812
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author:
+ Title:
+ Journal:
+ Year:
+ Volume:
+ Number:
+ Pages:
+ DOI:
+ PMID:
+ URL:
+ eprint:
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..753a3f6
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+https://github.com/EddyRivasLab/easel/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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