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 <[email protected]> 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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
