[med-svn] r12009 - in trunk/packages/hmmer2/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Tue Aug 7 16:51:57 UTC 2012
Author: lkajan-guest
Date: 2012-08-07 16:51:57 +0000 (Tue, 07 Aug 2012)
New Revision: 12009
Added:
trunk/packages/hmmer2/trunk/debian/README.source
trunk/packages/hmmer2/trunk/debian/patches/userguidepdf
Removed:
trunk/packages/hmmer2/trunk/debian/hmmer2-doc.doc-base
Modified:
trunk/packages/hmmer2/trunk/debian/hmmer2-doc.docs
trunk/packages/hmmer2/trunk/debian/hmmer2-pvm.1
trunk/packages/hmmer2/trunk/debian/hmmer2-pvm.README.Debian
trunk/packages/hmmer2/trunk/debian/patches/series
trunk/packages/hmmer2/trunk/debian/rules
Log:
added code to repackage upstream in order to remove source-less Userguide.pdf; added explanation of this; patched man pages with the URL of the Userguide.pdf document
Added: trunk/packages/hmmer2/trunk/debian/README.source
===================================================================
--- trunk/packages/hmmer2/trunk/debian/README.source (rev 0)
+++ trunk/packages/hmmer2/trunk/debian/README.source 2012-08-07 16:51:57 UTC (rev 12009)
@@ -0,0 +1,8 @@
+hmmer2 for Debian
+=================
+
+Repackaged Upstream Source
+--------------------------
+The non-policy-compliant 'get-orig-source' target is provided to build the upstream tarball.
+The problem with the upstream tarball is that upstream packs a pdf (Userguide.pdf) without sources. In 'get-orig-source' this file is deleted from the archive.
+I have decided to keep d/watch and use uscan in 'get-orig-source' in order to keep the process simpler, sacrificing the "get-orig-source [...] may be invoked in any directory" requirement of the policy (point 4.9).
Deleted: trunk/packages/hmmer2/trunk/debian/hmmer2-doc.doc-base
===================================================================
--- trunk/packages/hmmer2/trunk/debian/hmmer2-doc.doc-base 2012-08-07 13:22:35 UTC (rev 12008)
+++ trunk/packages/hmmer2/trunk/debian/hmmer2-doc.doc-base 2012-08-07 16:51:57 UTC (rev 12009)
@@ -1,15 +0,0 @@
-Document: hmmer2
-Title: Hmmer 2.3.2 Userguide
-Author: Sean Eddy
-Abstract: HMMER is an implementation of profile hidden Markov model methods for
- sensitive searches of biological sequence databases using multiple sequence
- alignments as queries.
- .
- Given a multiple sequence alignment as input, HMMER builds a statistical
- model called a "hidden Markov model" which can then be used as a query into
- a sequence database to find (and/or align) additional homologues of the
- sequence family.
-Section: Science/Biology
-
-Format: PDF
-Files: /usr/share/doc/hmmer2-doc/Userguide.pdf.gz
Modified: trunk/packages/hmmer2/trunk/debian/hmmer2-doc.docs
===================================================================
--- trunk/packages/hmmer2/trunk/debian/hmmer2-doc.docs 2012-08-07 13:22:35 UTC (rev 12008)
+++ trunk/packages/hmmer2/trunk/debian/hmmer2-doc.docs 2012-08-07 16:51:57 UTC (rev 12009)
@@ -1,2 +1 @@
-Userguide.pdf
tutorial/
Modified: trunk/packages/hmmer2/trunk/debian/hmmer2-pvm.1
===================================================================
--- trunk/packages/hmmer2/trunk/debian/hmmer2-pvm.1 2012-08-07 13:22:35 UTC (rev 12008)
+++ trunk/packages/hmmer2/trunk/debian/hmmer2-pvm.1 2012-08-07 16:51:57 UTC (rev 12009)
@@ -8,7 +8,7 @@
.B hmmpfam-pvm
and
.B hmmsearch-pvm
-is available on the section "Configuring a PVM cluster for HMMER" (page 15) at the User's Guide (/usr/share/doc/hmmer2-doc/Userguide.pdf.gz), installed with the package "hmmer2-doc".
+is available on the section "Configuring a PVM cluster for HMMER" (page 15) at the User's Guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf).
.PP
.SH SEE ALSO
.BR hmmer2 (1),
Modified: trunk/packages/hmmer2/trunk/debian/hmmer2-pvm.README.Debian
===================================================================
--- trunk/packages/hmmer2/trunk/debian/hmmer2-pvm.README.Debian 2012-08-07 13:22:35 UTC (rev 12008)
+++ trunk/packages/hmmer2/trunk/debian/hmmer2-pvm.README.Debian 2012-08-07 16:51:57 UTC (rev 12009)
@@ -2,7 +2,7 @@
--------------------
Please, read the section "Configuring a PVM cluster for HMMER" (page 15)
- at the User's Guide (/usr/share/doc/hmmer2-doc/Userguide.pdf.gz), installed with the package "hmmer2-doc", to see how to configure properly Hmmer on a PVM
+ at the User's Guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf), to see how to configure properly Hmmer on a PVM
cluster.
-- Nelson A. de Oliveira <naoliv at gmail.com> Tue, 08 Aug 2006 23:07:12 -0300
Modified: trunk/packages/hmmer2/trunk/debian/patches/series
===================================================================
--- trunk/packages/hmmer2/trunk/debian/patches/series 2012-08-07 13:22:35 UTC (rev 12008)
+++ trunk/packages/hmmer2/trunk/debian/patches/series 2012-08-07 16:51:57 UTC (rev 12009)
@@ -1 +1,2 @@
version2-manpage
+userguidepdf
Added: trunk/packages/hmmer2/trunk/debian/patches/userguidepdf
===================================================================
--- trunk/packages/hmmer2/trunk/debian/patches/userguidepdf (rev 0)
+++ trunk/packages/hmmer2/trunk/debian/patches/userguidepdf 2012-08-07 16:51:57 UTC (rev 12009)
@@ -0,0 +1,180 @@
+Description: corrections to man pages
+ The WWW home of hmmer (URL) is updated. Also, as we now do not include
+ Userguide.pdf in this package, references to that are changed to
+ ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf .
+ .
+ No need to forward this patch as it tackles issues with the way this hmmer version
+ is packaged for Debian.
+Author: Laszlo Kajan <lkajan at rostlab.org>
+Forwarded: no
+
+--- a/00README
++++ b/00README
+@@ -14,8 +14,9 @@
+
+
+ o Getting HMMER
+- WWW home: http://hmmer.wustl.edu/
++ WWW home: http://hmmer.janelia.org/
+ Distribution: ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/
++ User's Guide: ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf
+
+
+ o Installing HMMER
+--- a/documentation/man/hmmalign.man
++++ b/documentation/man/hmmalign.man
+@@ -129,9 +129,8 @@
+ pages: see
+ .B hmmer2(1).
+ .PP
+-For complete documentation, see the user guide that came with the
+-distribution (Userguide.pdf); or see the HMMER web page,
+-http://hmmer.wustl.edu/.
++For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page,
++http://hmmer.janelia.org/.
+
+ .SH COPYRIGHT
+
+--- a/documentation/man/hmmbuild.man
++++ b/documentation/man/hmmbuild.man
+@@ -438,9 +438,8 @@
+ pages: see
+ .B hmmer2(1).
+ .PP
+-For complete documentation, see the user guide that came with the
+-distribution (Userguide.pdf); or see the HMMER web page,
+-http://hmmer.wustl.edu/.
++For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page,
++http://hmmer.janelia.org/.
+
+ .SH COPYRIGHT
+
+--- a/documentation/man/hmmcalibrate.man
++++ b/documentation/man/hmmcalibrate.man
+@@ -135,9 +135,8 @@
+ pages: see
+ .B hmmer2(1).
+ .PP
+-For complete documentation, see the user guide that came with the
+-distribution (Userguide.pdf); or see the HMMER web page,
+-http://hmmer.wustl.edu/.
++For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page,
++http://hmmer.janelia.org/.
+
+ .SH COPYRIGHT
+
+--- a/documentation/man/hmmconvert.man
++++ b/documentation/man/hmmconvert.man
+@@ -86,9 +86,8 @@
+ pages: see
+ .B hmmer2(1).
+ .PP
+-For complete documentation, see the user guide that came with the
+-distribution (Userguide.pdf); or see the HMMER web page,
+-http://hmmer.wustl.edu/.
++For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page,
++http://hmmer.janelia.org/.
+
+ .SH COPYRIGHT
+
+--- a/documentation/man/hmmemit.man
++++ b/documentation/man/hmmemit.man
+@@ -91,9 +91,8 @@
+ pages: see
+ .B hmmer2(1).
+ .PP
+-For complete documentation, see the user guide that came with the
+-distribution (Userguide.pdf); or see the HMMER web page,
+-http://hmmer.wustl.edu/.
++For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page,
++http://hmmer.janelia.org/.
+
+ .SH COPYRIGHT
+
+--- a/documentation/man/hmmfetch.man
++++ b/documentation/man/hmmfetch.man
+@@ -56,9 +56,8 @@
+ pages: see
+ .B hmmer2(1).
+ .PP
+-For complete documentation, see the user guide that came with the
+-distribution (Userguide.pdf); or see the HMMER web page,
+-http://hmmer.wustl.edu/.
++For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page,
++http://hmmer.janelia.org/.
+
+ .SH COPYRIGHT
+
+--- a/documentation/man/hmmindex.man
++++ b/documentation/man/hmmindex.man
+@@ -37,9 +37,8 @@
+ pages: see
+ .B hmmer2(1).
+ .PP
+-For complete documentation, see the user guide that came with the
+-distribution (Userguide.pdf); or see the HMMER web page,
+-http://hmmer.wustl.edu/.
++For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page,
++http://hmmer.janelia.org/.
+
+ .SH COPYRIGHT
+
+--- a/documentation/man/hmmpfam.man
++++ b/documentation/man/hmmpfam.man
+@@ -282,9 +282,8 @@
+ pages: see
+ .B hmmer2(1).
+ .PP
+-For complete documentation, see the user guide that came with the
+-distribution (Userguide.pdf); or see the HMMER web page,
+-http://hmmer.wustl.edu/.
++For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page,
++http://hmmer.janelia.org/.
+
+ .SH COPYRIGHT
+
+--- a/documentation/man/hmmsearch.man
++++ b/documentation/man/hmmsearch.man
+@@ -249,9 +249,8 @@
+ pages: see
+ .B hmmer2(1).
+ .PP
+-For complete documentation, see the user guide that came with the
+-distribution (Userguide.pdf); or see the HMMER web page,
+-http://hmmer.wustl.edu/.
++For complete documentation, see the user guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf); or see the HMMER web page,
++http://hmmer.janelia.org/.
+
+ .SH COPYRIGHT
+
+--- a/INSTALL
++++ b/INSTALL
+@@ -3,7 +3,7 @@
+ ------------------------------------------
+
+ These are quick installation instructions. For complete documentation,
+-see the Installation chapter in the HMMER User's Guide (Userguide.pdf).
++see the Installation chapter in the HMMER User's Guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf).
+
+ For a source distribution (hmmer-2.3.2.tar.gz):
+
+--- a/documentation/man/hmmer.man
++++ b/documentation/man/hmmer.man
+@@ -73,7 +73,7 @@
+ with the software distribution, which includes a tutorial introduction
+ and more detailed descriptions of the programs.
+
+-See http://hmmer.wustl.edu/ for on-line documentation and
++See http://hmmer.janelia.org/ for on-line documentation and
+ the current HMMER release.
+
+ .PP
+--- a/NOTES
++++ b/NOTES
+@@ -1,5 +1,5 @@
+ HMMER 2.3.2 release notes
+-http://hmmer.wustl.edu/
++http://hmmer.janelia.org/
+ SRE, Fri Oct 3 14:04:44 2003
+ ________________________________________________________________
+
Modified: trunk/packages/hmmer2/trunk/debian/rules
===================================================================
--- trunk/packages/hmmer2/trunk/debian/rules 2012-08-07 13:22:35 UTC (rev 12008)
+++ trunk/packages/hmmer2/trunk/debian/rules 2012-08-07 16:51:57 UTC (rev 12009)
@@ -6,6 +6,21 @@
export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS)
export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
+# lkajan: The following violates point 4.9 of the Debian policy: "get-orig-source [...] may be invoked in any directory [...]" as uscan needs to find the watch file.
+.PHONY: get-orig-source
+get-orig-source:
+ set -e; \
+ t=$$(mktemp -d) || exit 1; \
+ trap "rm -rf -- '$$t'" EXIT; \
+ pwd; \
+ uscan --no-conf --force-download --rename --destdir "$$t"; \
+ ( cd "$$t"; \
+ gunzip *.tar.gz; \
+ tar --delete -f *.tar --wildcards 'hmmer-*/Userguide.pdf'; \
+ gzip --best --no-name *.tar; \
+ ); \
+ mv $$t/*.tar.gz ./
+
.PHONY: override_dh_auto_configure
override_dh_auto_configure:
dh_auto_configure -- --enable-threads --enable-lfs --enable-pvm
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